U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
Marine Fisheries

Habitat Assessment Improvement Plan

Report of the National Marine Fisheries Service

Habitat Assessment Improvement Plan Team

Mary Yoklavich (Chair), Kristan Blackhart, Stephen K. Brown,

Correigh Greene, Th omas Minello, Th omas Noji, Michael Parke,

Frank Parrish, Katherine Smith, Robert Stone, and W. Waldo Wakefi eld

May 2010

NOAA Technical Memorandum NMFS-F/SPO-108

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

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

Offi ce 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/

Th e mention of trade names or commercial fi rms does not imply endorsement by the National Marine Fisheries Service, 

NOAA.

Th is publication may be cited as:

NMFS. 2010. Marine fi sheries habitat assessment improvement plan. Report of the National Marine Fisheries Service Habitat 

Assessment Improvement Plan Team. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-F/SPO-108, 115 p.

Page layout and cover design by Kristan Blackhart, National Marine Fisheries Service.

Cover images: Background - Palmer Seamount bathymetric map (NOAA, NOS). Photos (top to bottom) - swordspine rockfi sh 

resting in a sponge (SWFSC Fisheries Resources Division); juvenile fi sh in mangrove nursery habitat (Tom Minello, SEFSC); 

gray snappers on a Florida reef (Florida Keys National Marine Sanctuary); CTD and water sampling equipment (NOAA Climate Program Offi ce); California salmon stream survey (SWFSC); NOAA Ship John N. Cobb working in Glacier Bay, Alaska 

(Commander John Bortniak, NOAA Corps); Phantom S2 ROV working underwater in the Gulf of the Farallons National 

Marine Sanctuary (OAR, National Undersea Research Program).
iii

List of Figures

List of Tables

Preface

Executive Summary

Section 1: Introduction

Defi ning NMFS’ Habitat Assessment Mandates

Recommendations from Independent Reviews

Scope of the Habitat Assessment Improvement Plan

Gathering Information for the Plan

Section 2: Th e Nature of Habitats

What Is Habitat?

What Is Habitat Science?

What Is a Habitat Assessment?

Habitat Assessments and Climate Change

Section 3: How NMFS Can Use Habitat Assessments

Habitat Management

EFH Identifi cation and Conservation

Other Habitat Management Applications

Habitats and Stock Assessments

Habitats, Survey Design, and Estimates of Stock Size

Habitats and Catchability

Habitats and Population Dynamics

Habitats and Vital Rates

Habitats and Stock-recruit Functions

Habitats, Movement, and Spatial Variation

Capability of Stock Assessment Models to Include Habitat Data

Habitats, Integrated Ecosystem Assessments, and Coastal and Marine Spatial Planning

Section 4: Data for Habitat Assessments

Characterization and Delineation of Habitats

Ecological Value of Habitats

Status or Condition of Habitats

Management of Habitat Data

Adequacy of Habitat Data

Adequacy of the Synthesis of Habitat Data

Adequacy of Staffi ng

Contents

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Section 5: Resource Requirements

Programmatic Needs

Th ree Tiers of Assessment Excellence

Timeframes and Relationships Among Tiers

National Staffi ng Requirements to Meet Tier Goals

Program Operation Needs: Tools, Technology, and Infrastructure

Section 6: Measuring Performance

Section 7: Connecting HAIP to Other Habitat Science Programs

Section 8: Th e Benefi ts of Implementing the HAIP

Section 9: Recommendations

References

Acknowledgements

List of Acronyms

Appendix 1: Summary of Major U.S. Habitat Conservation Legislation

Appendix 2: Summary of Essential Fish Habitat Regulations and Programs

Appendix 3: Executive Summary of the “Marine Fisheries Stock Assessment Improvement Plan”

Appendix 4: Summary of Fish Stock Sustainability Index (FSSI) and List of FSSI Stocks

Appendix 5: Executive Summary of “A Research Plan - Assessing Ecosystem Impacts of Liquefi ed Natural 

Gas Processing Facilities on Marine Resources in the Gulf of Mexico”

Appendix 6: Habitat-Related Programs and Activities

Appendix 7: Region-Specifi c Habitat Science Programs and Staffi ng Needs 

Pacifi c Islands Fisheries Science Center (PIFSC)

Alaska Fisheries Science Center (AFSC)

Northwest Fisheries Science Center (NWFSC)

Southwest Fisheries Science Center (SWFSC)

Southeast Fisheries Science Center (SEFSC)

Northeast Fisheries Science Center (NEFSC)

Appendix 8: National Priorities for Habitat Science Identifi ed in the Our Living Oceans - Habitat Report 

and in “NOAA’s Habitat Program: NMFS Strategic Plan 2009-2013”

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Figure 1: Status of FMP stocks in quarter 3 of 2009

Figure 2: Number of FSSI stocks in four life history categories

Figure 3: Linkages among habitat science and assessments and other components of ecosystem-based fi shery 

management within NOAA

Figure 4: Flow diagram of a habitat assessment

Figure 5: Coast-wide seafl oor habitat map of the Pacifi c Coast region

Figure 6: Decision-making framework for the West Coast Groundfi sh EFH habitat assessment

Figure 7: Diagram outlining the fi sheries stock assessment process

Figure 8: Information types and uncertainty in stock assessments

Figure 9: Capability of stock assessment models to accommodate diff erent types of habitat data

Figure 10: Capability of stock assessment models to accommodate habitat data, sorted by fi sh stock life style 

(pelagic vs. demersal)

Figure 11: Capability of stock assessment models to accommodate habitat data, sorted by NMFS Fisheries 

Science Center

Figure 12: Schematic of the Atlantis ecosystem model, including habitat eff ects

Figure 13: Flow diagram of information used in a habitat assessment

Figure 14: Example of a habitat map based on an environmental proxy

Figure 15: Adequacy of information in three habitat data categories (type and area; ecological value; and 

status) by life stage of FSSI stocks

Figure 16: Adequacy of data integration and frequency of habitat assessments by life stage of FSSI stocks

Figure 17: Percent of time currently and ideally spent on all habitat-related activities by NMFS staff in three 

disciplines

Figure 18: Percent of time currently and ideally spent on specifi c habitat-related tasks for all regions combined

Figure 19: Obstacles to producing and/or using quality habitat assessments

List of Figures

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Figure 20: Fishery-independent data needs, sorted by fi sh stock life style (pelagic vs. demersal)

Figure 21: Resources most needed to produce and/or use quality habitat assessments, as identifi ed by NMFS 

Fisheries Science Center program managers

Figure 22: Relationships between the three Tiers of Excellence for habitat assessments

Figure 23: Current number of staff and additional staff required to meet the three Tiers of Excellence, by habitat-related activity at each NMFS Fisheries Science Center

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Table 1: Th e relation of habitat data to observations and biological processes tracked in stock assessment 

models

Table 2: Th e role of habitat assessments in an integrated ecosystem assessment

Table 3: Th e contributions of NMFS habitat science and assessments to the various functions of coastal and 

 marine spatial planning 

Table 4: Number of additional staff required to meet the three Tiers of Excellence by type of activity for all 

NMFS Fisheries Science Centers combined

Table 5: Number of additional staff required to meet the three Tiers of Excellence at each NMFS Fisheries 

Science Center and for all Centers combined

Table 6: Potential performance measures of the Habitat Assessment Improvement Plan

Table A7-1: Number of additional staff required to meet the three Tiers of Excellence by type of activity for 

the NMFS Pacifi c Islands Fisheries Science Center

Table A7-2: Number of additional staff required to meet the three Tiers of Excellence by type of activity for 

the NMFS Alaska Fisheries Science Center

Table A7-3: Number of additional staff required to meet the three Tiers of Excellence by type of activity for 

the NMFS Northwest Fisheries Science Center

Table A7-4: Number of additional staff required to meet the three Tiers of Excellence by type of activity for 

the NMFS Southwest Fisheries Science Center

Table A7-5: Number of additional staff required to meet the three Tiers of Excellence by type of activity for 

the NMFS Southeast Fisheries Science Center

Table A7-6: Number of additional staff required to meet the three Tiers of Excellence by type of activity for 

the NMFS Northeast Fisheries Science Center

List of Tables

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ix

A little more than a century ago, the ocean was considered by many to be capable of providing a 

boundless supply of seafood. Today, our views have changed radically. We have learned that it is 

very easy to overfi sh and that we must be cognizant of what we discharge into coastal waters. We 

also have learned that atmospheric emissions can have a profound impact on the chemistry of the 

oceans and aff ect climate regimes worldwide. We are now beginning to understand the connectedness of living things and their environment, and know that what happens to their habitats can aff ect 

their ability to survive and reproduce. 

Th e science of understanding the relationship of living marine resources to their habitats is still in 

its infancy. Virtually any piece of research into this relationship opens up new and intriguing vistas, 

generating more questions than answers. As American society places more demands on coastal 

and off shore regions for food, energy, transportation, waste disposal, community development, 

and recreation, the burden on the Federal government to provide scientifi c information to support 

informed management decisions becomes more onerous. 

Because of its mandated responsibility for promoting sustainability of marine fi sheries resources, 

the National Marine Fisheries Service has a unique role in habitat science and assessment. Th is 

document, for the fi rst time, defi nes that role and lays out a plan to integrate habitat science into 

everyday decision-making that aff ects the contribution of marine fi sheries to the U.S. and world 

economies, as well as the state of marine ecosystems. Recognizing that we cannot aff ord to delay decisions until we have a perfect understanding of the relationship between fi sheries and the habitats 

that support them, this document provides an incremental approach that allows factoring of scientifi c information into habitat assessments as more knowledge is gained. An incremental approach 

ensures that the best scientifi c information to support management decisions aff ecting habitats is 

available and continually improving. 

Now that we fi nally have the ball in play, let’s not drop it.

John Boreman

Director (retired)

NMFS, Offi ce of Science and Technology 

June 2009

Preface

1

NOAA’s National Marine Fisheries Service (NMFS) has a mandated responsibility to sustain marine fi sheries and associated 

habitats. Th e Marine Fisheries Habitat Assessment Improvement Plan (HAIP) defi nes NMFS’ unique role in pursuing habitat 

science and in developing habitat assessments to meet this mandate. Th rough this Plan, NMFS establishes the framework to 

coordinate its diverse habitat research, monitoring, and assessments and to guide the development of budget alternatives and 

increased support for habitat science. 

Th e HAIP has been developed by a team of scientists from NMFS Headquarters Offi ces and Science Centers. Th is Plan represents input from a variety of NMFS staff engaged in habitat science, stock assessments, and resource management at the six 

Science Centers and Regional Offi ces, the Offi ce of Science and Technology, the Offi ce of Habitat Conservation, and science 

program managers at each Science Center. Th e scope of the HAIP is restricted to the 519 managed stocks and stock complexes 

within Fishery Management Plans, with particular focus on the 230 stocks in the Fish Stock Sustainability Index (FSSI). Th e 

conclusions and recommendations of the HAIP, however, can be applied more broadly to other managed and protected species.

Th e goals of the HAIP are to:

• Assist the National Oceanic and Atmospheric Administration (NOAA) in developing the habitat science necessary to 

meet the mandates of the Magnuson-Stevens Fishery Conservation and Management Reauthorization Act (MSRA) and 

the economic, social, and environmental needs of the nation;

• Improve our ability to identify essential fi sh habitat (EFH) and habitat areas of particular concern (HAPC);

• Provide information needed to assess impacts to EFH;

• Reduce habitat-related uncertainty in stock assessments;

• Facilitate a greater number of “Marine Fisheries Stock Assessment Improvement Plan” (SAIP)1

 Tier 3 stock assessments, 

including those that explicitly incorporate ecosystem considerations and spatial analyses;

• Contribute to assessments of ecosystem services (i.e. the things people need and care about that are provided by marine 

systems); and

• Contribute to ecosystem-based fi shery management (EBFM), integrated ecosystem assessments (IEA’s), and coastal and 

marine spatial planning (CMSP).

Habitat, or the place where species live, can be characterized and described by the physical, chemical, biological, and geological components of the ocean environment. Habitat science is the study of relationships among species and their environment. 

Habitat science has received relatively little programmatic support compared to that received for other major disciplines (e.g.

stock assessment science), and yet habitat information is needed in almost every NOAA program. Habitat science is not synonymous with ecosystem science, but habitats form the structural matrix of ecosystems, and an understanding of geospatial 

associations of species and their habitats can be one of the fi rst steps in producing IEA’s. A habitat assessment is the process and 

the products associated with consolidating, analyzing, and reporting the best available information on habitat characteristics 

relative to the population dynamics of fi shery species and other living marine resources. Indicators of the value and condition 

(or status) of habitat can be developed through a habitat assessment by understanding the relationships between habitat characteristics, the productivity of fi shery species, and the type and magnitude of various impacts.

Th ere is an incontrovertible need for NMFS to move forward in implementing the HAIP. Th e role of marine habitats in 

supporting fi shery production and in providing other critical ecosystem services is poorly understood. Th ere are increasing 

Executive Summary

1

NMFS. 2001. Marine fi sheries stock assessment improvement plan: Report of the National Marine Fisheries Service National Task Force for Improving Fish Stock Assessments. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-F/SPO-56, 69 p.
2

demands and impacts on marine habitats across many sectors of the U.S. economy. Climate change, for example, can have 

potentially large and far-reaching impacts on marine habitats. Lack of knowledge about the association of marine species and 

their habitats impedes eff ective fi sheries and habitat management, protection, and restoration, and yet this information forms 

the basis for assessing impacts of human activities on ecosystem services in the context of CMSP. NMFS currently lacks a comprehensive habitat science program that is suffi ciently funded to address these issues.

Recommendations:

• NMFS should develop criteria to prioritize stocks and geographic locations that 

would benefi t from habitat assessments.

• NMFS habitat and stock assessment scientists should work together to initiate 

demonstration projects that incorporate 

habitat data into stock assessment models, perhaps focusing on well-studied 

species.

Recommendation:

• NMFS and NOAA should develop new 

budget and staffi ng initiatives to fund 

habitat science that is directly linked to 

NMFS mandates.

A number of uses for habitat assessments are highlighted in Section 3. 

EFH provisions in the MSRA form the cornerstone of NMFS’ mandated 

habitat responsibilities, yet designation of EFH for many Federally managed stocks has been based on inadequate information and has been too 

broadly defi ned to provide for meaningful management measures. NMFS 

mandates also require adequate assessments for Federally managed stocks. 

Accurate assessments of the distribution and abundance of many of these 

stocks would benefi t from improved information on their habitats. Th is report discusses these and other factors that defi ne 

NMFS’ habitat-related mandates as well as many independent reviews that recommend improved habitat science to support 

more eff ective marine resource management.

Habitat assessments can and should be used for habitat management, conservation, and restoration. Understanding the distribution, abundance, and functions of marine habitats also will assist in CMSP, particularly with eff ective siting, design, and 

monitoring of marine protected areas (MPA’s). Further, understanding and predicting the eff ects of climate change and other 

anthropogenic impacts on ocean resources will require an increased emphasis on habitat science.

Habitat science also can inform stock assessments. Most stock assessments currently lack integration of habitat data, aside from 

depth and geographic stratifi cation of fi sheries-independent surveys. Uncertainty in species abundance may be reduced by 

considering how habitats aff ect:

• Th e design of fi sheries-independent surveys and resultant estimates 

of stock size;

• Catchability coeffi cients;

• Vital rates, such as natural mortality, growth, and reproduction;

• Stock-recruit functions; 

• Nursery functions; and

• Th e spatial and temporal scales of animal movements.

Most NMFS stock assessment biologists surveyed by the HAIP Team 

thought that habitat-specifi c stock assessments would require at least some 

modifi cation of existing models, if not entirely new models. Th is conclusion varied based on the type of habitat data, the life history of the species 

studied, and the geographic region in which the scientist worked.

Habitat assessments require both collection and synthesis of multiple data types at a variety of temporal and spatial resolutions. 

In Section 4 we describe how research eff orts to collect habitat data have been fragmented and limited, with our greatest success demonstrated by the physical characterization of habitats. A survey of NMFS scientists indicated that most habitat data 

presently are inadequate and occur at low spatial and temporal resolutions.

From the HAIP questionnaires, NMFS scientists, resource managers, and Science Center program managers identifi ed the following as major obstacles to producing and using credible habitat assessments:
3

• Lack of habitat-specifi c abundances; 

• Insuffi cient staff to collect, process, analyze, and model habitat 

data; 

• Insuffi cient research on environmental eff ects; 

• Insuffi cient research on multispecies eff ects; and

• Lack of habitat-specifi c biological information.

Resource managers also identifi ed an inadequate number of staff to communicate habitat information to NMFS constituents as a major obstacle 

to producing and using habitat assessments.

Primary challenges to the eff ective management of habitat data are: 

• Th e multiplicity of data types and the large volume of habitat imagery data; 

Recommendations:

• NMFS should identify and prioritize 

data inadequacies for stocks and their 

respective habitats, as relevant to information gaps identifi ed in the HAIP.

• NMFS should increase collection of 

habitat data on fi shery-independent surveys and develop a plan for better utilizing new technologies (e.g. multibeam 

sonars) aboard the expanding NOAA 

fl eet of Fishery Survey Vessels (FSV’s).

• Th e lack of appropriate metadata and accessibility to research data; and

• Th e means to effi ciently collect and process data and produce the required products. 

In Section 5, the HAIP Team defi nes three Tiers of Excellence for Habitat Assessments, which can be summarized as:

Tier 1 – Assess habitat associations for all life stages of FSSI stocks using existing data.

Tier 2 – Upgrade habitat assessments to a minimally acceptable level for all FSSI stocks and life stages, which 

Recommendations:

• NMFS habitat scientists should engage 

partners within and outside of NOAA 

to exchange information about programs and capabilities. Habitat data collection and management eff orts should 

be coordinated, and data integration 

applications should be upgraded to improve accessibility and synthesis.

• NMFS should convene regional and national workshops to develop strategies 

to integrate habitat science and assessments, stock assessments, and IEA’s.

• NMFS should establish a habitat assessment fellowship program and provide 

funds to graduate students and post-doctoral associates of specifi c subdisciplines 

that would advance habitat modeling, 

evaluation, and assessment eff orts.

will require new or expanded data collection and research 

initiatives. Th is eff ort includes the production of habitat 

maps; determination of habitat-specifi c biomass or abundance; consideration of temporal and spatial variability in 

habitat use; and development of habitat theory and proxies 

to apply to data-poor stocks.

Tier 3 – Determine habitat-specifi c vital rates by life stage 

for all FSSI stocks to quantify relationships between habitats and fi shery production. Th is eff ort explicitly incorporates habitat and ecosystem considerations into stock assessments; develops habitat sensitivity and recovery indices 

to improve risk assessments and plans for protection and 

restoration; and develops baselines for IEA’s.

Th e tiers require increasing levels of resolution in assessment data and an 

increased understanding of the functioning of habitats for fi shery species. 

Progress through the tiers is not necessarily sequential and will depend 

on the research needs, staff expertise, and infrastructure available at each 

Science Center.

Inadequate numbers of technical and scientifi c staff have been identifi ed 

as a major obstacle to credible habitat assessments. Section 5 includes the 

national summary of staffi ng requirements, as identifi ed by program man-
4

agers at the Science Centers, that are needed to meet the three Tiers of Excellence for Habitat Assessments (see Appendix 7 

for region-by-region requirements). About 5% of total NMFS staff are currently working on habitat-related activities at the 

Science Centers, and an average of 33% of those staff are contractors and students supported with transient, non NMFS funds. 

Th is is a major concern given the ever-increasing demands on NMFS to eff ectively conserve, protect, and manage living marine 

resources. Full implementation of the HAIP will require a 250% increase in staff over the current habitat-related staff , and a 

substantial increase in funds for program operations, tools, technology, and infrastructure.

To demonstrate eff ectiveness of investments, NMFS must monitor program accomplishments through performance measures. 

In Section 6, the HAIP outlines characteristics of potential performance measures that will refl ect progress toward meeting 

the three Tiers of Excellence for Habitat Assessments. Topic areas for evaluating performance include biological and geospatial

information, habitat condition indices, and habitat assessments.

Th e HAIP is unique because it is the fi rst nationally coordinated plan to 

focus on the marine fi sheries aspects of habitat science. However, in order 

to make substantial progress toward collecting, managing, and synthesizing the data needed to improve our habitat assessments, it is essential that 

NMFS continue to foster partnerships and cooperative research programs 

with other groups. Section 7 and Appendix 6 of the HAIP highlight a number of important NMFS partners, including other NOAA line offi ces, non 

NOAA Federal agencies, state agencies, private foundations, universities, 

environmental groups, fi shing organizations, and others with an interest in 

collecting and using similar types of habitat data, albeit oft en for diff erent 

Recommendation:

• NMFS should unite with other NOAA 

line offi ces to develop a NOAA-wide 

strategic plan for habitat science and 

assessments in support of the nation’s 

ocean policy priorities for EBFM, 

CMSP, and the use of IEA’s.

purposes. Partners can contribute research and development, fi eld sites and equipment, raw data and synthesized products, 

scientifi c and technical expertise and training, and data management and archiving. All partners will benefi t from, as well as 

contribute to, the success of the HAIP.
5

Th e Marine Fisheries Habitat Assessment Improvement Plan 

(HAIP) defi nes the National Marine Fisheries Service’s (NMFS) 

unique role in pursuing habitat science and in developing habitat 

assessments to meet its mandated responsibility to sustain marine 

fi sheries and associated habitats. Th e HAIP presents an evaluation 

of NMFS’ current habitat science capabilities and unmet needs. In 

this Plan, defi ciencies in NMFS’ ability to provide accurate and defensible assessments of marine fi sheries habitats are identifi ed, and 

recommendations are provided for addressing these defi ciencies. 

Th rough this Plan, NMFS also establishes the framework to coordinate its diverse habitat research, monitoring, and assessments and to 

guide the development of budget alternatives and increased support 

for habitat science.

Th e goals of the HAIP are to:

• Assist the National Oceanic and Atmospheric Administration 

(NOAA) in developing the habitat science necessary to meet 

the mandates of the Magnuson-Stevens Fishery Conservation 

and Management Reauthorization Act (MSRA) and the economic, social, and environmental needs of the nation;

• Improve our ability to identify essential fi sh habitat (EFH) 

and habitat areas of particular concern (HAPC);

• Provide information needed to assess impacts to EFH;

• Reduce habitat-related uncertainty in stock assessments;

• Facilitate a greater number of “Marine Fisheries Stock Assessment Improvement Plan” (SAIP) Tier 3 stock assessments 

Section 1: Introduction

Comparison of healthy and impacted habitats. Top photo shows 

commercial groupers on healthy Oculina deep-sea coral habitat 

off the east coast of Florida. Bottom photo shows a similar Oculina

habitat that has been impacted by trawling. 

Grant Gilmore, Dynamac Corp. Lance Horn, NURC/UNCW

(NMFS, 2001), including those that explicitly incorporate ecosystem considerations and spatial analyses; 

• Contribute to assessments of ecosystem services (i.e. the things people need and care about that are provided by marine 

systems); and

At a Glance

• The Marine Fisheries Habitat Assessment Improvement Plan (HAIP) defines the National Marine Fisheries 

Service’s (NMFS’) unique role in pursuing habitat science and in developing habitat assessments to meet its 

mandated responsibility to sustain marine fisheries and associated habitats.

• Through the HAIP, NMFS establishes the framework to coordinate its diverse habitat research, monitoring, 

and assessments and to guide the development of budget alternatives and increased support for habitat science. 

• The scope of the HAIP is restricted to managed stocks and stock complexes within fishery management plans, 

with particular focus on the stocks in the Fish Stock Sustainability Index. 

• The conclusions and recommendations of the HAIP, however, can be applied more broadly to other managed 

and protected species.
6

• Contribute to ecosystem-based fi shery management (EBFM), integrated ecosystem assessments (IEA’s), and coastal and 

marine spatial planning (CMSP).

Loss of marine habitats can lead to decreased fi shery production (Hutton et al., 1956; Zimmerman and Nance, 2001). However, the signifi cance of marine habitats in providing the essential ecosystem services that support the social and economic 

well-being of the nation is poorly understood. Th is lack of knowledge is of growing concern, especially because our increasing 

demands for energy, shipping, seafood, and development exert untold impacts on our nation’s marine and coastal habitats. 

Added to these stresses are the potentially large impacts to fi shery habitats that are related to climate change, including increased ocean temperatures, sea level rise, ocean acidifi cation, changes in freshwater fl ow, and alterations to weather patterns. 

Furthermore, confl icting demands on limited marine resources challenge our ability to balance fi sheries quotas and habitat 

conservation with industrial growth. 

We urgently need to improve our management of ocean resources. Our ability to manage these resources from an ecosystem 

perspective requires an understanding of the linkage between marine habitats and living marine resources (LMR). Th e lack 

of knowledge about the signifi cance of marine habitats to LMR’s currently prevents managers from incorporating impacts of 

habitat change into stock assessments and management plans, despite considerable demand for this information from fi shery 

managers and many other stakeholders. For this reason, the U.S. Commission on Ocean Policy (COP, 2004) and other independent review bodies have called for NOAA to implement a coordinated national habitat science program to better understand the relationships between managed fi shery species and their habitats.

Ensuring the sustainability of our fi sheries, LMR’s, and ecosystems is a major national goal. Commercial and recreational fi shing contribute billions of dollars to the U.S. economy each year. In 2006, commercial fi shing in the United States generated an 

estimated $4.1 billion in dockside revenues alone (NMFS, 2009a). Th eir contribution to local economies adds considerably 

to this value. Additionally, sport fi shermen spent $5.8 billion on recreational trips in 2006, which generated $82 billion in 

associated sales and supported over 500,000 jobs (NMFS, 2009a). Healthy coastal and ocean habitats also provide numerous 

indirect benefi ts such as maintenance of water quality and protection from storm damage and erosion, which can save coastal 

communities billions of dollars in reconstruction and restoration costs.

OAR/National Undersea Research Program

Habitats provide a wide variety of important ecosystem 

services. In addition to protecting coastal areas from 

erosion and storm surge, 

mangrove roots provide important habitat for a number 

of commercially important 

fi shery species. 
7

Major U.S. Habitat-Related Legislation

• Magnuson-Stevens Reauthorization Act

• Endangered Species Act

• Marine Mammal Protection Act

• Coral Reef Conservation Act

• Marine Protected Areas Executive Order

1

U.S. Public Law 109-479.

2

16 U.S.C. 1801(a)(9).

3

U.S. Public Law 104-297.

4

16 U.S.C. 1802(10).

Th e HAIP provides guidance to develop the sound science needed to ensure the success of NOAA’s mandate of sustainable 

fi sheries and healthy marine ecosystems. Fulfi lling NMFS’ mandates to manage fi shery species and other LMR’s must be based 

on a scientifi c understanding of the relationships among species and their habitats, and of the dependence of marine ecosystems, and ultimately sustainable fi shery yields, on the extent and condition of these habitats. In addition, full implementation 

of the HAIP ultimately should reduce the impacts of litigation to NOAA, thereby allowing decision-makers to focus limited 

resources on our most pressing scientifi c and management needs.

Defi ning NMFS’ Habitat Assessment Mandates

NOAA’s mission is to understand and predict changes in Earth’s environment and conserve and manage coastal and marine 

resources to meet our nation’s economic, social, and environmental needs 

(NMFS, 2007). NMFS, an agency of NOAA, is the principal steward of 

fi shes within the U.S. exclusive economic zone (EEZ; generally from 3 to 

200 nautical miles off shore). NMFS also provides advice on the conservation and management of fi shery species within territorial and international waters. 

NMFS receives its stewardship responsibilities from a number of Federal 

laws, many of which include legislation related to the protection, conservation, and restoration of marine, estuarine, and anadromous fi sh habitats 

(Appendix 1). Much of NMFS’ habitat-related research and science is directed by the MSRA of 2006,1 which states:

“One of the greatest long-term threats to the viability of commercial and recreational 

fisheries is the continuing loss of marine, estuarine, and other aquatic habitats. Habitat 

considerations should receive increased attention for the conservation and management of fishery resources of the United States.”2

To this end, the MSRA declares that any Fishery Management Plan (FMP) may include management measures to conserve 

target and nontarget species and habitats, considering a variety of ecological factors aff ecting fi shery populations. 

EFH provisions in the MSRA form the cornerstone of NMFS’ mandated habitat responsibilities with respect to fi sheries (Appendix 2). EFH provisions were added to the MSRA through the Sustainable Fisheries Act of 1996.3

 EFH is defi ned as “... 

those waters and substrate necessary to fi sh for spawning, breeding, feeding, or growth to maturity.”4

 Th e MSRA requires that 

FMP’s: 1) identify and describe EFH; 2) minimize adverse eff ects of fi shing on EFH to the extent practicable; and 3) identify 

other actions to conserve and enhance EFH. Th e MSRA further requires that Federal agencies consult with NMFS on actions 

that may adversely aff ect EFH, and that NMFS provide conservation recommendations to those agencies. 

Deep-sea coral (DSC) habitats receive special protections under the MSRA, which provides NOAA with additional science 

and management authorities related to these unique communities. Biogenic habitats such as DSC communities have been 

identifi ed as hot spots of biodiversity and as EFH for managed species in some regions. Th ese habitats can be particularly vulnerable to some types of fi shing gear in contact with the seafl oor. Understanding the distribution of DSC and their functions 

in benthic ecosystems will assist in the conservation and management of our fi sheries and LMR’s.
8

Th e MSRA requires NMFS to identify and rebuild those Federally managed stocks that are overfi shed (i.e. a stock whose biomass level is below its prescribed biological threshold), and to prevent further overfi shing. In the third quarter of 2009, 46 of 

the 519 Federally managed stocks and stock complexes were classifi ed as overfi shed, fi ve were approaching an overfi shed condition, and 16 were in a rebuilding status (Figure 1; NMFS, 2009b). While reduction in fi shing pressure is essential to rebuild 

these overfi shed stocks, characterization and protection of EFH also are important to aid in rebuilding eff orts and to encourage 

enhanced stock production and recovery. However, the information necessary to designate EFH for many Federally managed 

stocks oft en is insuffi cient to support meaningful management measures (COP, 2004). 

NMFS’ mandates require adequate stock assessments be conducted to determine the status of Federally managed species, with 

respect to biomass and fi shing levels. In the third quarter of 2009, 221 of the 519 Federally managed stocks and stock complexes had an unknown or undefi ned status with respect to overfi shing, and 264 stocks/stock complexes had an unknown or 

undefi ned overfi shed status (Figure 1; NMFS, 2009b), which highlights the need for additional data and resources to successfully meet the mandates of our agency. In particular, habitat-specifi c information on abundance and distribution at higher spatial and temporal resolutions is necessary to accurately assess the status of many of these stocks, several of which live in complex 

habitats that are not easily or eff ectively surveyed with conventional methods (e.g. bottom-trawl gear). In addition, nearly all 

of the 135 stock assessments that currently are considered adequate under NOAA’s stock assessment performance measure (R. 

Methot, Personal communication5

) are based solely on demographically derived indices. Stock assessments of only a few of the 

best-studied species currently use any ecosystem and habitat information beyond simple stratifi cation of the surveys by depth 

and geographic province, which can be considered crude proxies for more appropriate habitat variables.

5

Richard Methot, NMFS Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA, 98112.

Not Overfishing (n=207)

Overfishing (n=38)

Unknown/Undefined (n=221)

Excepted (n=53)

Not Overfished (n=135)

Rebuilding (n=16)

Approaching Overfished (n=5)

Overfished (n=46)

Unknown/Undefined (n=264)

Excepted (n=53)

Figure 1

Status of FMP stocks in quarter 3 of 2009. Left, overfi shed 

status (relative to biomass 

targets). Right, status with respect to overfi shing (relative 

to fi shing mortality targets). 

Stocks classifi ed as unknown 

and undefined have been 

combined into a single category, as have stocks that 

have an exception to the 

application of overfishing 

criteria.
9

Recommendations from Independent Reviews

Several independent scientifi c reviews have emphasized the importance of improved habitat research and data collection to 

the conservation and management of marine fi sheries, habitats, and ecosystems. Th e U.S. Commission on Ocean Policy (COP, 

2004) asserts that, while the NMFS science program has done well in providing biological information to manage single species, agency research has not adequately addressed many pressing questions beyond traditional stock assessment science and 

fi shery biology (e.g. issues related to habitat and multispecies interactions). Th e COP states that coastal habitat conservation 

and restoration should be integral to ocean and coastal management, and should be strengthened through: 1) the development of national, regional, and local goals; 2) the institution of a dedicated program for coastal and estuarine conservation; 3) 

better coordination of Federal habitat-related activities; and 4) improved research, monitoring, and assessment. Coordinated 

and comprehensive habitat inventories and assessments are considered essential for identifying critical habitats, evaluating the 

causes of habitat loss and degradation, and setting priorities for conservation and restoration eff orts. 

Th e COP (2004) also recommends that NMFS designate EFH using an ecosystem-based approach (Recommendation 19-21). 

Th ey note that the current single-species approach to designating EFH, with “scant legislative guidance and little scientifi c 

information available on habitat requirements,” requires the Fisheries Management Councils (FMCs) to be overly broad when 

defi ning EFH. Our lack of information on species-habitat associations, coupled with this single-species approach, has resulted 

in the designation of so much EFH in some cases that the original purpose of identifying areas that deserve focused attention 

and protection (i.e. truly essential habitats) has not been realized. A new approach will require enhanced research programs to 

improve existing data collection and analytical methods, and to develop additional means of identifying those habitats critical

to sustainability and biodiversity goals. 

Th e National Research Council (NRC) has produced a number of reports that consider the current state of habitat information 

and research, as relevant to NMFS mandates. Th e authors of “Dynamic Changes in Marine Ecosystems” (NRC, 2006) contend 

that spatial analyses, in particular, may be one of the greatest challenges to fi sheries managers, and that new developments in 

measurement and analytical methods will allow for explicit consideration of spatial variability in marine systems. Collection of 

spatially explicit biological data is becoming essential for assessing and monitoring both broad- and fi ne-scale population trends 

(NRC, 2006). Furthermore, the NRC report on marine protected areas (MPA’s; NRC, 2001) notes that MPAs can function 

as living research laboratories in which habitat status can be monitored and the sustainability of biological communities and 

associated fi sheries can be evaluated. 

Many coastal states have developed action plans to address marine habitat issues of common interest to NMFS and other Federal agencies. Th e Gulf of Mexico Alliance, including Texas, Louisiana, Mississippi, Alabama, and Florida, released the “Governors’ Action Plan for Healthy and Resilient Coasts” (GOMA, 2006). Th is plan prioritizes identifi cation and characterization 

of Gulf habitats as one of fi ve key issues. Th e Gulf of Maine Council on the Marine Environment, representing the governors 

and premiers of Massachusetts, New Hampshire, Maine, New Brunswick, and Nova Scotia, released a similar plan that identifi es habitat conservation as one of three major goals (GOMC, 2008). Th e “West Coast Governors’ Ocean Action Plan” (West 

Coast Governors, 2008) includes three recommendations regarding habitat: 1) protect the health of ocean and coastal habitats by mapping ecological communities and human uses and characterizing coastal and marine habitats in a comprehensive 

geographic database; 2) identify key habitats that could benefi t from additional or innovative conservation measures; and 3) 

restore estuarine habitats, including coastal wetlands, to achieve a net increase in habitats and their functions. Th ese and other 

regional plans highlight the need for ecosystem-level policies that will maintain healthy habitats and species with critical ecological roles in all coastal states. 
10

From this meeting, the need for an HAIP having a format similar to the successful “Marine Fisheries Stock Assessment Improvement Plan” (SAIP) (NMFS, 2001; Appendix 3) was identifi ed. An HAIP writing team was appointed, comprising one 

or two representatives from each of the six NMFS Science Centers, F/ST, and F/HC; the fi rst meeting of the new HAIP Team 

was held in July 2008.

Given the complexity of this task, the scope of the HAIP was restricted to the 519 Federally managed stocks or stock complexes that are included in FMP’s, with a particular focus on the 230 stocks or complexes in the Fish Stock Sustainability Index 

(FSSI) (Figure 2; Appendix 4). FSSI stocks represent about 90% of all commercial and recreational U.S. landings. While the 

team based the analysis of resource needs on these important stocks, the conclusions and recommendations of the HAIP are 

relevant to and can be applied more broadly to other managed and protected species. Th ese species occur in marine, estuarine, 

and freshwater ecosystems that oft en are aff ected by signifi cant change to habitats and about which little is known. For example, under the Federal Power Act,7

 NMFS protects diadromous fi shes from hydropower development, yet managers do not 

have even baseline assessments on current or historic habitats. While these species were not specifi cally included in the HAIP, 

a better understanding of all habitats will facilitate our ability to implement the best management actions for all LMR’s. Future 

planning eff orts should address specifi c habitat science needs for those LMR’s not included in the HAIP (e.g. marine mammals, 

sea turtles, and non FSSI fi sh and invertebrate species).

Th e HAIP builds on the concepts that improvement of the stock assessment process is a high priority for fi sheries researchers, 

and that high-quality habitat science will enhance our ability to identify and implement appropriate management actions to 

sustain viable fi sheries. Th e HAIP emphasizes the importance of improving survey strategies and stock assessment models and 

their data input. Th e recommended research should: 1) determine habitat factors related to spatial and temporal variation in 

stock production, focusing on life history processes (e.g. dispersal and movement patterns, reproduction, feeding, growth, 

mortality) that occur during the most critical developmental stages; 2) describe in quantitative terms the role of habitat quality 

on these critical life history processes and overall stock production; 3) provide scientists with useful habitat information at appropriate spatial and temporal scales to improve design of stock surveys; and 4) provide scientists with habitat information to

be used in current stock assessment models or to support model improvements. Th ese activities also will support NMFS manScope of the Habitat Assessment Improvement Plan

A meeting of experts was held in April 2008 to address the lack of fi nancial 

support for habitat research within NOAA. Participants included members 

of the NOAA Habitat Program, NMFS Offi ce of Habitat Conservation 

(F/HC), NMFS Offi ce of Science and Technology (F/ST), representatives 

of each of the NMFS Science Centers, NOAA Sea Grant, and others. John 

Boreman, then Director of F/ST, presented the rationale for much-needed 

fi sheries habitat research and emphasized the necessity to deliver sound habitat assessment science in a form that can be readily applied by fi shery managers. He suggested that:

• Habitat science be linked to stock assessments and eventually to 

IEA’s;

• Habitat-related impacts shape natural mortality6

 rates (M); and

• An estimate of the fractional reduction in year class strength due to the 

source of mortality under study is needed from habitat scientists.

6

For a fi sh stock, Z (total mortality) = F (fi shing mortality) + M (natural mortality). 7

16 U.S.C. 791-828c.

Demersal

(n=145)

Coastal Pelagic

(n=21)

Highly Migratory

(n=36)

Benthic Invertebrate

(n=28)

Figure 2

Number of FSSI stocks in four life history categories.
11

agement needs to delineate EFH, identify HAPC’s, establish and monitor MPA’s and similarly managed marine areas, select 

sites, design and monitor habitat restoration and mitigation eff orts, and determine the eff ects of climate change on fi sheries. 

Gathering Information for the Plan

Th e HAIP Team developed two questionnaires to assist in identifying the most important factors hampering NMFS’ ability to 

provide accurate, precise, valid, and defensible habitat assessments and the resources needed to produce such assessments. Th e 

fi rst questionnaire was directed at NMFS habitat and ecosystem scientists, population/stock assessment scientists (those who 

conduct stock assessments and/or surveys of stock abundance), and resource managers from NMFS’ six Regional Offi ces; these 

scientists and managers should have a clear idea of the primary defi ciencies in habitat-related input data and spatially explicit 

models. One hundred thirty-three scientists and managers responded to all or part of the fi rst questionnaire. Th e second questionnaire was directed at science program managers, those best suited to give an overview of each Science Center’s habitat and 

population/stock assessment programs. Th is second questionnaire specifi cally was designed to determine the resources (e.g. 

data collection programs, assessment scientists, survey personnel, technicians, database managers, and computer programmers) 

needed to improve our ability to develop habitat assessments. One response to the second questionnaire was submitted from 

each Science Center.

Th e HAIP Team gathered additional input on direction and content of the HAIP during discussions specifi cally with stock 

assessment scientists and several briefi ngs to NMFS’ leadership, Habitat Assistant Regional Administrators, some FMC’s, and 

other staff of Science Centers and Headquarters. Th ese groups also were given the opportunity to review the draft HAIP.

13

What Is Habitat?

Habitat is the place where an organism lives, and species defi ne their habitat by their spatial and temporal distributions. It is 

commonly misconstrued that fi sh habitat refers only to benthic substrata, yet few species are strictly benthic or pelagic but 

rather use multiple habitat types even within a single stage in their life history. Th us, we recognize that habitat for any single 

species or group of species could include the physical, chemical, biological, and geological components of both benthic and 

pelagic realms.

Section 2: The Nature of Habitats

At a Glance

• Habitats, or the place where fi shery species live, can be characterized by the physical, chemical, biological, and 

geological components of our oceans. 

• Habitat science is the study of relationships between species and their environment. 

• Habitat information is needed in almost every program within NOAA, yet habitat science has received relatively little programmatic support. 

• A habitat assessment is both the process and the products associated with consolidating, analyzing, and reporting the best available information on habitat characteristics relative to the population dynamics of fi shery 

species. 

• Indicators of habitat value can be developed through a habitat assessment by understanding the relationship 

between habitat, the productivity of fi shery species, and type and magnitude of various impacts. 

• Habitats form the structural matrix of ecosystems, and habitat science can be the bridge between single-species 

stock assessments and multispecies IEA’s. 

• Understanding and predicting the eff ects of climate change and other anthropogenic impacts on marine resources and associated ecosystem services will require an increased emphasis on habitat science.

Habitat includes the physical, chemical, biological, and geological components of both benthic 

and pelagic realms.

SWFSC

Th e boundaries of an ecosystem are defi ned 

by combining the habitats of a community 

of organisms. Accordingly, habitats form the 

structural matrix of an ecosystem. Although 

species defi ne their own habitats, we identify 

important habitat characteristics by observing 

associations between the species and their environment.

Measuring the associations among species 

and their habitats on various spatial and temporal scales is essential to determine the relative importance of types and combinations 

of habitats in structuring communities. For 

example, geomorphology, depth, and rugosity 

explain much of the variability found in the 

local distribution and abundance of demersal 

fi shes (Love and Yoklavich, 2006; Stephens 
14

et al., 2006), and the habitat of highly migratory species of billfi shes is delineated by gradients in dissolved 

oxygen in the upper ocean (Prince et al., 2009). Species respond to their environment at various spatial and 

temporal scales (Anderson and Yoklavich, 2007; Ault 

and Johnson, 1998), thereby making a range of choices 

in occupying specifi c habitats. In this way, habitats can 

modify the distribution and movement of a species and 

the interactions among species, and ultimately can provide ecological benefi ts to their reproduction, growth, 

and survival.

What Is Habitat Science? 

Habitat science is the study of relationships between 

species and their environment. Th e relative importance 

of habitat characteristics for a species can be identifi ed by 

distribution and abundance patterns in time and space 

and by rates of growth, mortality, and reproduction. All 

of these measures can be related to fi shery productivity 

and used as indicators of habitat value.

Habitat science is not synonymous with ecosystem science, but habitats form the structural matrix of ecosystems, and an understanding of geospatial associations of 

species and their habitats can be one of the fi rst steps 

in producing IEA’s. Th e HAIP team considers habitat 

science and assessments as a bridge between single-species stock assessments and multispecies IEA’s (Figure 

3). Despite this conceptual linkage, systematic integration of these three central scientifi c endeavors of NMFS 

– stock, habitat, and ecosystem assessments – has been 

Habitat Characteristics Important to Marine Species

Seafl oor Structure

Vegetation

Emergent epifauna

Biogenic reefs (e.g. coral, oyster, sponge)

Geomorphology (e.g. rocky outcrops, pinnacles)

Physiography (e.g. seamount, submarine canyon)

Sediments

Grain size

Organic content

Rugosity

Stability

Slope

Hydrodynamic Processes

Currents/boundaries/fronts

Tidal dynamics

Wave dynamics

Upwelling

Hydrology

Depth/bathymetry

Salinity/haloclines

Temperature/thermoclines

Density/pycnoclines

Turbidity

Nutrients

Dissolved oxygen/oxyclines

pH

Anthropogenic Alterations

Pollutants/contaminants

Artificial structures (e.g. artificial reef, oil platform)

Created habitats (e.g. restored salt marsh, planted seagrass bed)

Fishery impacts

Marine debris

lacking. Without planning and coordination among these eff orts, the strength of collective results is greatly diminished.

Habitat science, while currently conducted on a limited basis throughout NOAA, is an integral component of almost every 

program (Figure 3). NOAA’s ability to conserve trust resources and assess potential environmental impacts requires an understanding of how habitats support LMR’s. Habitat science directly informs NMFS’ eff orts to identify and protect EFH. Eff ective habitat restoration depends on habitat science to identify appropriate sites, to design functional habitats, and to monitor 

habitat response. Similarly, habitat science is used to understand potential eff ects of MPA’s, climate change, and coastal and 

off shore energy and aquaculture development.

Improving habitat science is a major goal of many NMFS strategic planning documents. “Expand science-based knowledge to 

more eff ectively assess, protect, and restore important coastal and marine habitats” is one of four primary goals in the “NOAA 

Habitat Program: NMFS Strategic Plan 2009-2013” (NMFS, 2009c). A goal of “NMFS’ Strategic Plan for Fisheries Research” 

(NMFS, 2007) is to provide scientifi cally sound information in support of EBFM. Habitat science is vital to such an ecosystem-based approach to management, and considerable research will be needed to implement holistic EBFM. Most particular 
15

to NMFS, there has been little habitat research directed toward improving stock assessments. Th e availability of habitat data 

will help achieve the highest tier (SAIP Tier 3) of stock assessments, which calls for the explicit incorporation of ecosystem 

considerations (e.g. multispecies interactions and environmental eff ects, fi sheries oceanography, and spatial and seasonal analyses; NMFS, 2001). 

Th e HAIP specifi cally addresses these shortcomings and presents a focused habitat research program to provide the science 

that will help to integrate stock assessments into ecosystem assessments. Successful EBFM, as well as improved EFH conservation and management, depend on NMFS making this connection. 

What Is a Habitat Assessment? 

A habitat assessment (Figure 4) is both the process and the products associated with consolidating, analyzing, and reporting 

the best available information on habitat characteristics relative to the population dynamics of fi shery species and other living 

marine resources. Th e ultimate goal of a habitat assessment is to determine the function of habitats in relation to fi shery production and ecosystems, thereby supporting management decisions that are a mandated responsibility of NOAA. 

In a habitat assessment, spatial and temporal relationships of environmental data (e.g. ocean and climate properties, seafl oor 

substratum types, water depth) with species by life stage are used to determine types, distribution, and amount of habitats that 

support fi shery stocks. Evaluating the function of these habitats ultimately can include measures of habitat-specifi c vital rates 

such as growth, maturity, fecundity, and mortality, as well as patterns and rates of species movement among habitats.

Important habitat components can be identifi ed from these data and linked to sources of impacts and associated management 

options. Th e establishment of meaningful baseline conditions is critical to understand environmental impacts but can be diffi cult, largely due to lack of historic data. However, this should not forestall the advancement of habitat assessments. One key

EFH

Stock

Assessment

Coastal and Marine 

Spatial Planning &

Integrated

Ecosystem

Assessment

Habitat

Science &

Assessment Energy

Habitat

Restoration

Protected

Resources

Climate

Change

MPAs

Aquaculture

Ecosystem

modeling

Natural mortality

Catch efficiency

Survey design

Site selection

Environmental impacts

Site selection

Monitoring

Project design

Critical habitat

designation

Design

Site selection

Monitoring

Site selection

Environmental impacts

Forecasting

biological

response

Figure 3

Linkages among habitat science and 

assessments and other components of 

ecosystem-based fi shery management 

within NOAA. Examples of how habitat 

information can be used in these components are listed along the arrows and 

in circle intersections.
16

outcome of an assessment is a gap analysis, by which research and data necessary to improve the assessment are identifi ed and 

prioritized. Th e habitat research that improves assessments and the periodic review of assessments both lead to adaptive management.

Th ese assessments should provide the basis for sound habitat management and policy. To ensure quality and integrity, the 

science side of the process should be the domain of the Science Centers, while Regional Offi ces and FMCs determine management policy (Figure 4). A science-based assessment should be independently developed to feed into the separate public 

policy process, similar to the approach used for stock assessments that inform FMC decisions (see Figure 7, p. 23) and marine 

mammal assessments that inform fi ndings following from the Marine Mammal Protection Act and the Endangered Species 

Act (ESA). Given that management decisions oft en are contentious, and can have important eff ects on ocean activities, independent defensible assessments are critical. Feedback from the policy side of this process can be used to direct research and 

fi ne-tune future assessments.

Habitat Assessments and Climate Change 

Climate change is aff ecting coastal and marine ecosystems and the habitats they contain, and it is highly probable that the rates 

of these changes will increase in the foreseeable future (Intergovernmental Panel on Climate Change, 2007). Impacts attributable to climate change include: increasing ocean temperatures; sea level rise and subsequent inundation of low-lying habitats; 

ocean acidifi cation; loss of sea ice; changes in the quantity, quality, and delivery of fresh water; and severe alterations to weather 

patterns and possibly to ocean circulation (Griffi s et al., 2008). Furthermore, the geographic range of some fi sh stocks are 

shift ing as a result of climate-driven change to habitat conditions (Murawski, 1993; Perry et al., 2005), which may result in the 

development of new fi sheries in places like the Arctic. Consequently, habitat assessments need to be placed in the context of 

the varied eff ects of climate change. 

Habitat

Assessment

Science

Application

Policy Development

Stock

Assessments

•Spatially explicit environmental data

 -ocean and climate properties

 -seafloor substratum types

 -water depth

•Fish-habitat associations

 -types of habitat

 -distribution of habitat

 -abundance of habitat

 -ecological value of habitat

•Habitat-specific vital rates

 -growth, maturity, fecundity

 -natural mortality

 -fish movement

•Habitat type & area (maps)

•Habitat status or condition

Essential

Fish

Habitat

Reporting

Data Collection & Consolidation

Data Processing

Review & Validation

Data Modeling & Analysis

Data Interpretation

Data Products

Integrated

Ecosystem

Assessments

Feedback

•Adaptive management needs

•Identify key issues

•Identify key data gaps

•Identify ways to improve 

 habitat assessments

Figure 4

Flow diagram of the mechanics (development, application, and improvement 

through feedback) of a habitat assessment. Dotted line 

illustrates the distinct separation of science and policy 

development during the 

assessment process.
17

As consensus on the reality of climate change has emerged, mandates and programs of many science and management agencies 

are evolving to meet the new challenges. Concurrent with the development of the HAIP, NOAA has begun developing strategies to better meet its mandates as both a producer and a user of climate information. NOAA’s needs, as relevant to climate 

change, have been identifi ed as: baseline information, including integrated biological and climate observations; research and 

modeling of adaptive capacities of species and ecosystems and of physical and chemical changes of the oceans; and enhanced 

integration and capacity of programs within and beyond NOAA, including new tools for risk assessment and scenario planning to evaluate management options (Griffi s et al., 2008). Many of these needs are directly related to habitat science and assessments.

To serve fi shery management needs, NMFS’ habitat assessments must consider the consequences of climate change to the affected habitats and on the fi shery resources that depend on these habitats. Th e pace, scale, and ecological impacts of climate 

change could introduce additional levels of uncertainty, leading to an increased need for habitat assessments. To address these

issues, habitat scientists will need to:

• Establish fi eld and laboratory programs necessary to monitor long-term indicators for key habitats and species;

• Understand the eff ects of change in environmental factors (e.g. temperature and acidifi cation) on habitats and species 

distribution, reproduction, growth, and survival; 

• Synthesize the data in integrated physical, chemical, and biological models; and

• Provide advice and tools to inform managers of climate impacts on habitats and managed species.

Loss of sea ice and other impacts of climate change may 

be extreme in the northern 

seas and result in shifts in 

the geographic range of fi sh 

stocks and the possible development of new fi sheries 

in places like the Arctic.

Commander Richard Behn, NOAA Corps

19

Section 3: How NMFS Can Use Habitat Assessments

At a Glance

• Habitat assessments and associated data products can and should be used for: EFH designation; habitat conservation and management (including implementation of MPA’s); improved fi shery-independent population 

surveys and stock assessments; and CMSP and IEA’s. 

• Limited habitat data constrain NMFS’ ability to eff ectively designate EFH and prioritize habitat protection, 

restoration, and mitigation. 

• Most stock assessments currently lack integration of habitat data, despite the potential for habitat data to reduce uncertainty in estimates of species abundance and in the way population dynamics are modeled. 

• Most stock assessment biologists surveyed by the HAIP Team thought that habitat-specifi c stock assessments 

would require at least some modifi cation of existing models, if not entirely new models. 

Habitat assessments should form the underlying scientifi c basis for decisions on habitat management and protection. Data 

products from habitat assessments include maps of habitat type, extent, and condition; these products, combined with habitatspecifi c fi sh distribution (EFH Levels 1-2 as described in the EFH regulatory guidelines; Appendix 2) and vital rates (EFH 

Levels 3-4) support EFH designations and protection. Components of habitat assessments also can assist in advancing our 

ability to accurately assess fi shery stocks, particularly by: 1) using associations of fi sh densities, size distributions, and habitat 

characteristics to improve the design of fi shery resource surveys and resultant estimates of population abundance; 2) developing catchability coeffi cients (q) for diff erent habitats; and 3) estimating habitat eff ects on natural mortality (M) to improve 

population dynamic models. Th ese and other components of habitat assessments can be incorporated into Tier 3 – Next Generation Stock Assessments as prescribed in the SAIP (NMFS, 2001). 

Habitat assessments and the science supporting them have a major role in the design and management of MPA’s, which are 

intended for conservation of fi shery resources and the ecosystems that support them. Documenting and monitoring the extent 

and condition of habitat types, and the relationships between fi sh population dynamics and habitats, are necessary to ensure 

eff ective MPA’s. Once an MPA is established, it can have signifi cant eff ects on the behavior of associated fi shing fl eet(s) and 

on the dynamics of aff ected stocks. Th e redistribution of fi shing eff ort can introduce a new component of spatial heterogeneity into the vital rates of fi sh stocks, including fi shing mortality, size and age distribution, and fecundity. Th ese new aspects of 

spatial heterogeneity should be included in stock assessments, which in turn will drive new requirements for fi sh surveys and 

stock assessment models.

Ultimately, CMSP and the development of IEA’s will greatly benefi t from information produced in habitat assessments, and 

EBFM necessitates an understanding of the associations among the habitats and species in the ecosystem. All of these uses of 

habitat assessments (i.e. EFH, stock assessments, CMSP, and IEA’s) have the potential to incorporate information relevant to 

climate change and other anthropogenic impacts on habitats, associated ecosystem services, and management options.

Resource managers are turning increasingly to the concept of ecosystem services as part of their decision-making processes 

(Daily et al., 2009; NRC, 2005). Examples of services derived from functional coastal and marine habitats include: food from 

fi sheries; nursery grounds; coastal protection from erosion or inundation; value of recreation and tourism; energy from waves 

and tides; carbon storage and sequestration; water fi ltration; phyto-remediation; and aesthetic and existence values. Habitat 

science and habitat assessments hence should provice fundamental inputs to ecosystem models and their application in projecting ecosystem services.
20

EFH Level 1 for even one life stage of one species. Th is limited information 

and the precautionary approach adopted by most FMC’s, combined with 

the large number of managed species and all life stages, have resulted in initial EFH designations that extend over most of the EEZ and coastal waters. 

Given that information on EFH in FMPs forms the basis for NMFS’ habitat management actions related to fi shing and nonfi shing activities, such 

broad EFH designations make it diffi cult to prioritize management eff orts. 

Better habitat data and assessments will improve our ability to distinguish 

EFH from all other habitats for each managed stock/species.

Improved habitat assessments also are important to the FMC’s and NMFS 

as they implement requirements to minimize fi shing eff ects on EFH. Th ese 

measures may include gear modifi cations, reduction in fi shing eff ort, and 

fi shing gear restrictions in particular areas. In order to recommend such 

measures, resource managers need scientifi c assessments to demonstrate the 

temporal and spatial eff ects of fi shing gear on habitats and the severity of 

those eff ects on LMR’s. Integration of these analyses of gear impacts into 

broader assessments of habitat extent, condition, function, and threats will 

result in more eff ective habitat protection.

As an example, NMFS conducted a habitat assessment as part of the fi nal 

Environmental Impact Statement on EFH designation and minimization 

of adverse impacts to the habitats of 82 species of west coast groundfi shes, 

including 40 FSSI stocks (NMFS, 2005a). Th is assessment included innovative habitat suitability and risk models, an internet-based habitat-use 

database, and the fi rst step in the development of seafl oor habitat maps for 

the entire west coast (Figure 5; Copps et al., 2007). Th is assessment also 

represented a compilation of information on the status of habitats important to groundfi shes and the impact of fi shing on those habitats (Figure 6). 

Habitat Management

EFH Identifi cation and Conservation

Human-induced impacts on fi sh habitat can be direct or indirect, and may stem from activities such as fi shing, shipping, aquaculture, mining, coastal development, and climate change. To conserve and protect these habitats, the MSRA requires NMFS 

and the FMC’s to designate EFH for Federally managed species and to minimize fi shing eff ects on EFH as practicable in 

FMP’s. NMFS and the FMC’s also are required to review the science that supports EFH management actions every fi ve years, 

and to consult with other Federal agencies on actions that may adversely aff ect EFH. More robust and comprehensive habitat 

assessments will directly result in improved EFH identifi cation and conservation.

EFH regulatory guidance8

 provides an approach to organize and use the best available science for describing and identifying 

EFH. Th ese guidelines recognize a wide range in types of available information. While the most elementary designation of 

EFH is based on the distribution of species and habitat types from presence/absence data (EFH Level 1), more developed designations address the value of habitats to fi sheries production and require information on habitat-specifi c densities, growth, reproduction, and survival (EFH Levels 2-4). Information beyond EFH Level 1 currently exists for only a handful of fi shery species, and oft en for only a subset of their life stages (NMFS, In press). Less than half of Federal FMP’s contain information above 

8

50 CFR 600.905.

Figure 5

Coast-wide seafl oor habitat map used in a risk assessment 

of groundfi sh EFH on the Pacifi c Coast (produced by TerraLogicGIS, Stanwood, WA, with data and interpretations 

from Goldfi nger et al., 2003 and Greene et al., 2003.).
21

Habitat

• Geology (GIS)

• Bathymetry (GIS)

• Latitude (GIS)

• Other structural

 considerations (GIS)

• Biogenic habitat (GIS)

Habitat Use

• Fish life histories

• Habitat Use

 Database

• Fish distributions;

 NOAA Atlas (GIS)

• NMFS surveys (GAM)

• Habitat Suitability

 Probability

• Species/life stage

 assemblages

Fishing Effects

• Gear descriptions

• Impacts literature

 review

• Habitat sensitivity

 and recovery indices

• Fishing effort data

 (logbooks, fish

 tickets, focus 

 groups), spatial 

 analysis (GIS)

Nonfishing Effects

• Impacts literature 

 review

• Habitat sensitivity 

 and recovery indices

• Spatial information

 (GIS)

Existing Habitat

Protection

• MPA inventory (GIS)

• Other regulatory

 areas (GIS)

EFH Model HAPC Model Impacts Model

Model Validation

Policy Development

Modeling Data Consolidation

While lacking information on the contribution of habitats to the productivity of fi sh populations and the capacity of specifi c 

habitats to recover from various types of fi shing impacts, the assessment provided the scientifi c justifi cation for proposing and 

implementing several signifi cant management measures to protect EFH from fi shing. Th ese include a long-term reduction in 

fi shing pressure and the designation of large fi shery closures along the U.S. west coast, which will improve our understanding of 

the use of MPA’s to manage fi sheries and result in increased protection of sensitive seafl oor habitats and associated species. 

Similar but more qualitative or less spatially explicit approaches to the compilation of scientifi c information on habitat vulnerability and sensitivity have been used by the North Pacifi c, New England, Gulf, and Caribbean FMC’s. Th ese assessments 

oft en were limited by the lack of data on the spatial distribution of habitats, the value of habitats to fi sh production, and the 

distribution and magnitude of fi shing eff ort. More comprehensive habitat assessments are needed nationwide to support the 

protection of EFH from fi shing impacts. Th ere will be opportunities to design new habitat assessments or augment existing 

ones as NMFS and FMC’s conduct regular fi ve-year reviews of EFH information.

Th e MSRA also requires NMFS to address nonfi shing impacts to marine habitats through consultations with other Federal 

agencies on permitted or authorized activities that may adversely aff ect EFH. NMFS has the opportunity to provide conservation recommendations to avoid, minimize, or mitigate those impacts. Th e ability of NMFS to convince other agencies to 

implement our conservation recommendations oft en depends on direct, quantifi able evidence of impacts based on habitat 

recovery rates, habitat availability to fi sheries, and signifi cance of habitat loss to fi sheries. 

Such information is sometimes not available for impacts that have been occurring for years, for example dredge and fi ll activities, dock and pier construction, beach renourishment, mining, and oil and gas development. In addition to these types of 

on-going impacts, NMFS anticipates a whole new category of nonfi shing impacts to habitat, about which we know very little. 

In 2005, the emergence and widespread application of a new technology to regasify liquid natural gas (LNG) illustrated the 

consequences of insuffi cient science to NMFS’ eff ectiveness at conserving fi sh habitat. Th e lack of adequate information on the 

association between the vital rates of fi shes and their habitats impaired NMFS’ ability to quantify the environmental impacts 

of off shore LNG processing facilities on fi sh stocks in the Gulf of Mexico (Appendix 5). Th is exposed NMFS to considerable 

political scrutiny of our precautionary and protective recommendation to replace the proposed open-loop system with a less 

damaging and more expensive closed-loop system. Synthesizing existing information through more rigorous, quantitative habiFigure 6

Decision-making framework 

to guide the science-based 

habitat assessment (efforts 

below the dotted line) and 

policy development for 

West Coast Groundfi sh EFH 

(modifi ed from Copps et al., 

2007).
22

Rozas, 2002). Furthermore, habitat-specifi c abundances and vital rates could provide the quantitative information managers 

need to evaluate potential increases in stock production as a result of habitat restoration (Rozas et al., 2005). Demonstrating

the impact of restoration eff orts in terms of increased number or biomass of fi shes has more ecological signifi cance than the 

current measures of eff ectiveness based on program eff ort (e.g. number of projects funded, number of stream miles opened). 

Habitat assessments also may form the basis for mitigation recommendations that support EFH consultations or Damage Assessment, Remediation and Restoration Program studies and decisions. Th ese eff orts require data on the economic and ecological value of aff ected habitats. Products of habitat assessments, such as accurate mapping of habitats, are essential for managers to 

determine habitat loss and identify appropriate areas for mitigation eff orts. Habitat-specifi c abundance and vital rates provide 

the data needed to calculate change in fi sh productivity due to environmental damage. Because these data form the basis for 

requests for mitigation (e.g. compensation required, identifi cation of similarly productive habitats for protection and restoration), well-founded habitat assessments ultimately will result in more eff ective, defensible management actions.

Habitats and Stock Assessments

As described in the Marine Fisheries Stock Assessment Improvement Plan (SAIP) (NMFS, 2001; Appendix 3), a stock assessment is: 

“...the process of collecting, analyzing, and reporting demographic information for the purpose of determining 

the eff ects of fi shing on fi sh populations [Figure 7]. Th e production of stock assessments requires quantitative 

information on relative or absolute magnitude of a fi sh population, estimates of the total removals due to human activities (due to fi shery landings, discarded bycatch, and cryptic mortality due to encounters with fi shing 

gear), life history data including rates of growth, average age of onset of sexual maturity, maximum longevity, 

and the proportion of each age group dying each year due to natural causes, and other factors that aff ect stock 

productivity. Th ese data are combined using simple or complex mathematical models to derive best estimates of 

vital statistics such as historical and recent trends in the number and biomass of the resource, recruitment levels 

tat assessments will help NMFS protect EFH from nonfi shing 

impacts and identify science needs for future research. Th e effectiveness of NMFS’ eff orts to protect EFH depends on the 

quality of information on habitat value and condition.

Other Habitat Management Applications

Habitat assessments and associated products will support many 

other management eff orts and programs in addition to EFH 

designation. Assessments are particularly needed to identify, 

prioritize, and design habitats for restoration (e.g. habitats of 

declining condition, limited in extent, and/or associated with 

high fi sheries productivity) because the scale of such eff orts 

has recently increased (e.g. $167 million to NMFS under the 

American Reinvestment and Recovery Act of 20099

). For 

example, understanding the dynamics of salt marshes in the 

northern Gulf of Mexico has infl uenced the incorporation of 

marsh edges into the design of created wetlands (Minello and 

Habitat restoration of a Louisiana salt marsh. The native smooth cordgrass has been replanted to encourage rapid colonization of the area and 

prevent erosion.

Jed Brown, NOAA Restoration Center

9

U.S. Public Law 111-5.
23

Fishery-Dependent Data

Commercial and Recreational

Logbooks and Observers

Catch per unit of effort

Age/length information

Total catch

Fishery-Independent Surveys

Density

Abundance

Age-Length Composition

Life History Information

Growth

Maturity and Reproduction

Fecundity

Natural mortality

Stock structure

Habitat and Ecosystem Information

Spatial & seasonal analyses

Climate and environmental effects

Fisheries oceanography

Trophic structure, multispecies interactions

Population Assessment

(mathematical model)

Biomass, Recruitment & Exploitation Rate

Policy Development and

Management Strategy Evaluation

Allowable Biological Catch

Optimum Yield

Rebuilding Analysis

Status Determination Criteria

Stock Status

Science (Peer) Review

Data Collection and Input Modeling Policy

Improves and Informs

(number of small fi sh entering the fi shery each year), and the fi shing mortality rate or the fraction of the stock 

alive at the beginning of the year that are killed by fi shing (commonly referred to as the exploitation rate). Th e 

results of stock assessment calculations provide information necessary to estimate the current abundance and 

exploitation rate of resources in relation to predefi ned goals for these two attributes, also termed ‘status determination criteria’. ...In addition, assessment results provide the technical basis for setting the level of biologically 

acceptable yield for healthy stocks, and the expected rate of rebuilding for depleted stocks.... Th e quality of a 

particular stock assessment (i.e. the accuracy and precision of stock size and exploitation rate estimates) is directly related to the quality and completeness of the input data used for the assessment. ...improving the quality 

of fi sh stock assessments primarily involves improving the quality of basic input data on catches, abundance and 

life history...”

In the absence of rigorous quantitative data, qualitative information on habitat and ecosystem considerations can be used to 

inform stock assessments and guide management decisions. However, such qualitative data sets have not been fully incorporated into many stock assessments. One exception is the Ecosystem Considerations Report included in Stock Assessment and 

Figure 7

Diagram outlining the fi sheries stock assessment process, with data collection 

and modeling on the science 

side (below the dotted line) 

and policy development 

and management strategy 

evaluation above the line. 

Habitat and ecosystem information, while not yet 

commonly used, can inform 

and improve assessments 

for many stocks.
24

Fishery Evaluation reports published for each FMP under the jurisdiction of the North Pacifi c FMC. Th ese reports include 

information on fi shing eff ects on ecosystems, trends in climate and physical environment, and climate eff ects on ecosystems. 

Improved habitat data, even if not at a level or resolution that can be directly integrated into a stock assessment model, will

contribute signifi cantly to qualitative assessments of stock and ecosystem health.

Th e precautionary approach is a guiding principle in marine resource management. Th is approach prescribes conservative 

management when scientifi c uncertainty is high. Improved information on the value of habitats for fi shery species will reduce 

this uncertainty. However, certain types of scientifi c data will reduce uncertainty in habitat, stock, or ecosystem status more 

than others (Figure 8a), and an important challenge will be the determination of the costs and benefi ts of data acquisition. 

For example, the SAIP (NMFS, 2001) recommends monitoring of catch, life history data, and fi sheries-independent surveys 

of abundance as information that will strongly reduce uncertainty in a stock assessment. Other types of data might fall in the 

zone of diminishing returns, whereby the cost of collecting such information surpasses any reduction in uncertainty. Th e SAIP 

notes that habitat and ecosystem information potentially is useful, moving stock assessments from SAIP Tier 2 to Tier 3. While 

habitat data can improve many stock assessments, the utility of this information varies for diff erent stocks.

Life history variation will infl uence the value of diff erent types of habitat data. For example, benthic habitat characterization 

naturally should be more predictive of stock status for demersal fi shes, while oceanographic characteristics such as sea surface 

temperature (SST) likely would be more predictive for pelagic fi shes. Both demersal and pelagic fi shes may be sensitive to hydrodynamic patterns (e.g. currents) at certain periods of their life cycles, and therefore this information might have intermediate utility for both (Figure 8b). By extension, certain approaches to integrating these types of data into stock assessments could 

reduce uncertainty better than others. 

Fishery species exhibit a wide range of life histories and have developmental stages that occur in very diff erent habitats, both of 

which have consequences for the incorporation of habitat data into stock assessments. For example, penaeid shrimp in the Gulf 

of Mexico, like many estuarine-dependent species, have a life cycle that is relatively short in duration (approximately 1 year) but 

extends over a large geographic range (Cook and Lindner, 1970). Th e adults spawn off shore and the demersal eggs and planktonic larvae occur in shelf waters. Larvae are carried by currents and tides to shallow estuarine habitats where postlarvae settle 

and grow through the juvenile stage. Subadults then migrate into open bays and return to off shore habitats. Survival rates vary 

Figure 8

a) The level of uncertainty in 

stock size can be reduced by 

various types of information, 

including habitat data. 

b) Particular types of habitat 

data may be more effective 

than others in reducing the 

level of uncertainty in stock 

size, depending on the life 

history (e.g. pelagic vs. demersal) of the stock.

Level of Uncertainty

Information

Catch monitoring

Life history data

Fishery-independent surveys

Recruitment forecasts

Diminishing returns iminishing returns

Habitat data?

Minimum

critical

information

SST

Hydrodynamics

Benthic structure Pelagic species

Benthic structure

Hydrodynamics

SST

Demersal species

•

•

•

•

•

•

A. B.
25

be vastly diff erent (Houde, 1987; Cortés, 2000). Similarly, the eff ects of habitats on fi shery populations can be quite variable 

because of their relation to life history patterns. Th us, uncertainty related to habitat use and habitat change may vary greatly 

among stocks. Further, understanding habitat associations on the spatial and temporal scales relevant to the stock will assist in 

the interpretation of variability in our generally broad-scale survey data.

Th ree Tiers of Assessment Excellence to improve our Nation’s stock assessments have been described in the SAIP (NMFS, 

2001; Appendix 3). Th e highest tier (SAIP Tier 3) calls for explicit incorporation of ecosystem considerations, such as multispecies interactions, environmental eff ects, fi sheries oceanography, and spatial and seasonal analyses, into stock assessments. 

Improvements in the collection and availability of habitat and ecosystem data will help us achieve SAIP Tier 3 assessments. 

Below, we discuss several ways that habitat information can inform, and hopefully improve, stock assessments. We stress that 

habitat data will not necessarily reduce uncertainty for all stocks in all the ways described. Not all approaches are appropriate 

for every stock, and other improvements, independent of habitat data, will likely improve stock assessments. Th ese caveats 

point to a need to prioritize those stocks assessments that are likely to benefi t from habitat data, and to an independent eff ort 

to clarify requirements for SAIP Tier 3 stock assessments.

Habitats, Survey Design, and Estimates of Stock Size

Many fi sh stocks have strong affi nities to specifi c characteristics of their habitat, resulting in patchy spatial distributions in 

abundance. Sample stratifi cation or otherwise explicitly incorporating these habitat characteristics into survey design can increase precision and accuracy of estimated densities (Anderson et al., 2005; Ault et al., 1999). Coupling these habitat-specifi c 

fi sh densities with maps of habitat across large areas can be used to improve estimates of stock size (Ault et al., 2005; Yoklavich 

et al., 2007). 

for each stage, and associated habitats can aff ect these rates. Fishing mortality generally does 

not occur until the subadult and adult stages, but a life history analysis suggests that over 

99.99% of shrimp mortality occurs before they recruit to the fi shery (Baker et al., 2008).

In contrast, most of the 65+ species of rockfi shes (genus Sebastes) off the U.S. west coast and 

Alaska have a relatively long life cycle, with some species living over 100 years. Rockfi shes, 

in general, are highly fecund live-bearers that go through larval, juvenile, and adult stages 

in approximately the same geographic location but in diff erent habitats (Love et al., 2002; 

Tolimieri and Levin, 2005). Most larvae are pelagic over continental shelf waters, settling 

to benthic habitats in relatively shallow water and moving deeper as they grow and mature. 

Older segments of the population for many of these species live in high-relief rocky areas that 

are inaccessible to standard trawl gear, while the younger segments are more easily sampled 

during such surveys. 

Sharks and other elasmobranchs provide yet another example of fi shery species with widely 

diff erent life histories. While many sharks are long-lived (like rockfi shes) and range over large 

geographic areas during their life cycle (like shrimp), their life history strategy is quite diff erent from teleosts or crustaceans. Sharks generally have low fecundity rates with annual litters 

of only a few off spring, and natural mortality in early developmental stages is relatively low. 

Th us, habitat-related changes in mortality can be quite diff erent from other species (Garcia 

et al., 2007; Heppell et al., 1999). In addition, vulnerability of these stocks to exploitation 

can strongly depend on vital rates during diff erent life stages (Cortés, 1998, 2002).

It is apparent from just these three types of stocks that life histories of fi shery species can 

Examples of fi shery species with 

a wide variety of life histories. Top, 

white shrimp; middle, cowcod 

(rockfi sh species); bottom, nurse 

shark.

NOAA SWFSC FKNMS
26

Improved geophysical methods and remote sensing have resulted in detailed maps of surfi cial seafl oor geology. Within U.S. 

large marine ecosystems, there are ongoing or developing eff orts to create geographic information systems (GIS) databases for 

benthic habitats interpreted from these maps (e.g. Greene and Bizzarro, 2003; Lundblad et al., 2006; NCDDC, 2009; Noji et 

al., 2004; Parke, 2007; Poppe et al., 1989; Romsos et al., 2007; Sheridan and Caldwell, 2002). Th ese GIS databases capitalize 

on many years of data collection and mapping from numerous sources. Th ese databases represent some of the fi rst coast-wide 

delineations of seafl oor habitat types and, at a minimum, indicate the distribution of rocky and unconsolidated substrata. Th ese 

maps and underlying GIS databases are critical to NMFS’ eff orts to incorporate habitat into survey design and stock assessments.

A variety of census techniques and stratifi cation strategies may be required, depending on the species and habitat associations 

(Table 1). Traditional bottom-trawl surveys are conducted by NMFS in several regions and provide critical fi shery-independent data on the distribution, abundance, size- and age-structure, and reproductive status of many demersal stocks. For example, trawl surveys of walleye pollock in the Gulf of Alaska have as many as 49 strata based on habitat features (Dorn et al.,

2008). Even in the absence of detailed habitat data, trawl catches are expanded to abundance based on coarse habitat zones (i.e. 

Eastern Bering Sea shelf, Eastern Bering Sea slope, and Aleutian Islands) in the stock assessment of skates in the Bering Sea and 

Aleutian Islands (Ormseth et al., 2008).

Advancements in technology allow scientists to collect new types of data during traditional NMFS surveys. Environmental 

sensing packages increasingly are being attached to trawls and record a full array of environmental parameters (e.g. depth, temperature, salinity, dissolved oxygen, chlorophyll fl uorescence, and turbidity). Additional sensors for light parameters also are 

being used on trawls (Kotwicki et al., 2009). Th e new series of state-of-the-art Fishery Survey Vessels (FSV’s) currently being 

Stock Assessment

Parameters or Equations

Examples of 

Relevant Stock

Assessment Models

Effects

of Habitat

Examples from Stock

Assessments or Other Studies

Observations

Abundance CPUE All Stratifi cation across habitats Habitat-based visual survey for cowcod 

(Yoklavich et al., 2007)

Habitat-stratifi ed visual census for mutton 

snapper (SEDAR, 2008)

Catchability q ASPIC

SS

ADAPT

Unfi shable areas

Gear selectivity

Migration; vertical and horizontal 

movements

Temperature-dependent q for arrowtooth 

fl ounder (Wilderbuer et al., 2008a) and 

other fl atfi sh stocks

Biological Processes

Natural mortality M ASPIC

SS

ADAPT

Variation in mortality rate within a 

life stage

Age- or size-specifi c variation due 

to ontogenetic change in habitat 

use

Habitat-dependent mortality of red drum 

(Levin and Stunz, 2005)

Mortality varies with habitat-dependent life 

stages (Boreman, 1997; Houde, 1987, 1997)

Density dependence Logistic, Beverton-Holt, or 

Ricker functions

ASPIC

ADAPT

SS

Variation in productivity

Variation in carrying capacity

Habitat-dependent recruitment in sablefi sh 

(Schirripa, 2007)

Migration and other 

movements

Constrained logistic 

function specifying agespecifi c migration

SS Spatial heterogeneity

Ontogenetic shift in habitat use

Integrating MPAs into stock assessments 

depends on movement (Field et al., 2006)

Growth Von Bertalanffy equation SS Environmental variation in growth 

rate

Effects of SST and chlorophyll on growth of 

anchovy (Basilone et al., 2004)

Table 1

The relation of habitat data to observations and biological processes tracked in stock assessment models.
27

added to the NOAA fl eet are equipped with a variety of technologically-advanced survey tools including high resolution, multibeam sonar that can be used to image both the water column and the seafl oor. Th ese tools, if fully employed, will signifi cantly 

increase capacity for acoustic surveys and benthic habitat mapping as well as improve environmental data collection during 

fi sheries surveys. Across all of the Science Centers, improved environmental sensing capabilities during both bottom trawl 

surveys and pelagic acoustic surveys have led to collaborations with academic partners and with developers and manufacturers 

of advanced sampling technologies.

Further, survey and habitat scientists are collaborating on the collection of oceanographic habitat data along with trawl survey data. For example, in addition to recording vertical profi les of temperature and salinity in the Northeast (e.g. Taylor and 

Bascunan, 2001), continuous surface sampling for these variables and fl uorescence is regularly conducted during trawl surveys. 

Plankton also is collected for the entire region, typically 6 times per year; the chief platform for these collections is the trawl 

survey. Th e Northeast Fisheries Science Center (NEFSC) also dedicates two to four “habitat cruises” to augment collections of 

benthic habitat data (e.g. multibeam bathymetry and bottom rugosity), which are accompanied by bottom trawling. Advanced 

technologies, such as remotely operated vehicles (ROV) and autonomous underwater vehicles (AUV) with acoustic sonar and 

ichthyoplankton sampling capabilities, oft en are used during these habitat cruises. Notably, the Ship-of-Opportunity Program 

(SOOP) at the NEFSC not only collects Continuous Plankton Recorder data ( Jossi et al., 2003) but also profi les of salinity, 

temperature, and pCO2

 for climate studies (Pershing et al., 2005). Although the SOOP program is conducted in partnership 

with commercial shipping vessels, incorporating this type of program into trawl survey protocol is a consideration. Such opportunities to calibrate stock assessments with habitat data off er a feasible way to forecast and hindcast eff ects of habitat variation 

on stocks (Link et al., 2008a).

A challenge common to trawl surveys is the potential bias and uncertainty in estimating fi sh biomass in high-relief untrawlable 

habitats. Two recent independent reviews have criticized the data obtained from trawl surveys that do not adequately sample 

untrawlable habitats along the west coast of North America (GAO, 2004; Mohn, 2006). Consequently, an expanding number 

of research groups are developing and refi ning alternative direct-count visual techniques using human-occupied submersibles 

(Yoklavich and O’Connell, 2008), scuba (Bohnsack et al., 1999), and dropped video camera arrays (Gledhill et al., 2005) to 

assess fi sh abundance in habitats that are diffi cult or impossible to survey with trawls or in areas (e.g. MPA’s) where damage to 

habitat by trawling should be avoided. ROV’s and AUV’s (Tolimieri et al., 2008) are being evaluated as alternative sampling 

tools for monitoring fi sh abundance under some circumstances. 

Rockfi shes in high-relief rocky habitat are diffi cult to survey using traditional 

methods such as bottom trawls.

NWFSC FRAM Division

In the eastern Gulf of Alaska, the Alaska Department of 

Fish and Game has been conducting habitat-based stock assessments for several species of the rockfi sh complex since 

1989 (O’Connell et al., 2007). Biomass is derived from the 

product of estimated fi sh density for all rocky habitats, estimated area of rocky habitat, and average weight of fi shes 

from port samples. Density is based on direct-count, line 

transect surveys conducted from a human-occupied submersible. High-resolution multibeam echosounder data 

are used to delineate the rocky habitats, thereby reducing 

uncertainty in the assessment. Other habitat-specifi c assessments using direct-count survey methods and interpreted 

habitat maps have been conducted for cowcod in the 

Southern California Bight (Dick et al., 2007; Yoklavich et 

al., 2007), spiny lobster in the southeastern United States 

(SEDAR, 2005), and mutton snapper in the South Atlantic 

and Gulf of Mexico (SEDAR, 2008). Th ese habitat-based 
28

assessments are being used by FMC’s to set catch quotas and, in some cases, to support stock rebuilding programs. Th ese 

surveys need to be repeated over time in order to develop temporally informative assessments that can be used in forecasting 

population abundance.

Semi-demersal schooling species inhabiting rocky untrawlable habitats present a diff erent challenge to habitat and stock assessment scientists, and several Science Centers are evaluating new approaches to this sampling problem. At the Northwest 

Fisheries Science Center (NWFSC), scientists recently demonstrated the use of local fi shermen’s knowledge in conjunction 

with combined acoustical and optical technologies to survey widow rockfi sh along the U.S. west coast (Ressler et al., 2009). 

Th is approach could be applied to other diffi cult-to-assess schooling species.

Habitats and Catchability 

Stock assessment models (e.g. Virtual Population Assessment and Stock Synthesis [SS]) typically use catch, catch rate, and 

biological information (e.g. length-frequency, age-frequency, fecundity, and maturity) from fi shery samples and fi shery-independent surveys, as well as auxiliary information on stock-recruitment parameters, ageing uncertainty and bias, and natural 

mortality (Ianelli and Fournier, 1998; Methot, 1990; Methot, 2009; Somerton et al., 1999) to calculate year- and age-specifi c 

survival for each cohort and determine annual change in fi sh abundance. Fishery-independent surveys of fi sh stocks (e.g. trawl, 

acoustic, and direct-count surveys) are essential for estimating fi sh biomass, modeling the structure of stocks, and setting catch 

quotas. Most surveys, however, provide information only on relative changes in fi sh abundance. To estimate true population 

size, stock assessment models include a critical parameter, the catchability coeffi cient (q; Sanchez, 1996). Th is coeffi cient is a 

proportionality constant that relates relative abundance to actual stock size. Uncertainty in q can signifi cantly aff ect the accuracy and precision of biomass estimates. A realistic catchability coeffi cient likewise is important to alternative approaches, such 

as estimating biomass empirically from direct-count surveys. Th is uncertainty weakens management decisions.

Catchability is infl uenced by several factors, including stock availability and the probability of either being caught or counted 

directly, depending on the type of survey. Each stock has its own inherent availability and each gear or survey type has its own 

inherent catchability; both can be modulated by habitat, including an array of environmental variables such as depth, substratum, temperature, dissolved oxygen, and currents. Quantifying the infl uence of habitat will reduce uncertainty in q and could 

improve stock assessments by explaining some of the temporal and spatial variability in catch (or absolute counts). A number 

of stock assessments include habitat-dependent catchability coeffi cients (Table 1). Several assessments of fl atfi sh stocks in the 

Bering Sea and Aleutian Islands region of Alaska integrate bottom temperature as a covariate of q (e.g. arrowtooth fl ounder 

[Wilderbuer et al., 2008a]; fl athead sole [Stockhausen et al., 2008]; northern rock sole [Wilderbuer and Nichol, 2008]; yellowfi n sole [Wilderbuer et al., 2008b]). In the stock assessment of Atlantic swordfi sh, generalized additive models were used 

to relate catch to environmental variables (convergence zones and depth of mixing) in pelagic areas of the South Atlantic (ICCAT, 2007).

Habitats and Population Dynamics

Most stock assessments rely on models that simulate population dynamics and forecast size of the population (Methot, 2009). 

Habitat data potentially can be used in population dynamic models in several ways (Table 1): 1) habitats can aff ect variation in 

vital rates and changes in body size; 2) habitats can be linked to productivity and capacity parameters in stock-recruit models; 

and 3) habitats can aff ect a species’ movement. Th ese methods hold promise to advance stock assessments to SAIP’s Tier 3 

status and to provide an explicit link to the requirements of MSRA for managing stocks and their habitats.

Habitats and Vital Rates: Th e management of fi shery stocks historically has focused on fecundity (how many animals are 

born) and fi shing mortality (how many are harvested), while natural mortality (M) oft en is assumed to be constant. However, 

both fecundity and survival strongly depend on size and age (growth); changes in these parameters need to be age- or size-
29

structured and may plateau or decline at extremely high population densities. Th ese vital rate parameters vary among life stages 

and habitats.

Over the lifetime of a fi shery species, natural mortality is much higher than fi shing mortality, and both growth and mortality 

vary among and within life stages due to changing habitat conditions from human and natural infl uences. In determining acceptable levels of fi shing mortality for exploited populations, natural mortality oft en is assumed to be constant, mainly because 

of inadequate information on the causes and extent of this variability. An important component of a habitat science program is 

the evaluation of habitat eff ects on fecundity, growth, and natural mortality of fi shery species. Th e initial goal of such an evaluation should be to determine the usefulness of additional information on habitats and these vital rates in stock assessments.

Th e general approach to such an evaluation involves: 1) identifying habitat-specifi c vital rates within life stages of a species; 2) 

developing a stage-structured matrix model that requires basic information on vital rates for each stage; 3) using the model to

identify life history stages that are sensitive to changing vital rates; and 4) examining relationships among habitats and vital 

rates for these sensitive life stages. 

A stage-based matrix model (Caswell, 2000) is a convenient way to organize information on habitat-specifi c vital rates for 

a species. Th e matrix model requires estimates of fecundity, growth, and mortality (natural and fi shing) for each life stage. 

Growth is used to determine stage duration, and the matrix then provides estimates of survivorship for each life stage. For most 

managed species, stock assessments have estimated many of the vital rates for stages undergoing fi shing. Th e stage-based matrix 

model also provides a framework for examining the sensitivity of a population to changes in vital rates during any particular 

stage (Greene and Beechie, 2004; Levin and Stunz, 2005; Mangel et al., 2006; Quinlan and Crowder, 1999). Information on 

how habitats aff ect growth and mortality can be derived from laboratory and fi eld experiments or by measuring these vital rates 

in populations occupying diff erent habitats. With appropriate information on the eff ect of habitats on these vital rates, such a 

model can be used to estimate the population’s responses to likely or projected habitat change. Studies that use this approach 

oft en have identifi ed early mortality as having a higher impact on a stock’s productivity than fi shing mortality (Greene and 

Beechie, 2004; Levin and Stunz, 2005), and hence lend support for integration into stock assessment models. Existing stock 

assessment modeling environments (e.g. SS) already can include age-, stage-, and space-specifi c variation in natural mortality, 

and thereby allow for the complexity demanded by a stage-based matrix approach. 

Th is approach could work for those species that have strong affi nities to habitat, occupy geographically well-defi ned habitats 

during large portions of their life cycle, and can be sampled in their habitats in a relatively straightforward manner. As such, 

these models may be more appropriate for short-lived species in coastal habitats where it is relatively easy to obtain estimates of 

habitat-specifi c abundance. Conversely, these models may be diffi cult to apply to long-lived species that are less tied to specifi c 

habitats during their entire life cycle, and to deepwater species whose abundance across habitats is diffi cult to assess.

Habitats and Stock-recruit Functions: Populations cannot increase in size indefi nitely. Limited resources, such as food or 

shelter from predators, control population size. Th is limitation results in a habitat-specifi c carrying capacity that constrains a 

population’s maximum productivity. Th e limitation on population growth usually is inversely related to population size and 

is referred to as density dependence. Density dependence can occur during any part of an animal’s life cycle and theoretically 

can be examined from the relationship between abundance of the adults (the stock) and the abundance of some life stage in a 

subsequent cohort (the recruits). Stock assessments oft en refl ect this assumption by incorporating stock-recruit functions like 

Ricker and Beverton-Holt relationships (Table 1), but these oft en are not linked conceptually to the availability of habitat and 

oft en do not recognize relationships at multiple life stages.

In their seminal paper, Beverton and Holt (1957) recognized the importance of density dependence at diff erent life stages, 

and formulated a relationship that summed across habitat- or life-stage-specifi c stock-recruit relationships to increase the utility of the function. Subsequently, Mousalli and Hilborn (1996) reformulated the Beverton-Holt function to refl ect multiple 
30

life stages. More complex models using this reformulation (Greene and Beechie, 2004; Scheuerell et al., 2006) provide ways 

to predict the infl uence of diff erent habitats on fi sh populations. In the absence of data on survival rates, abundance or density 

estimates obtained for diff erent life stages might be used to generate simple life-stage-specifi c stock-recruit curves and thereby 

provide a starting point for estimating habitat-specifi c productivity and capacity. Integrating such curves across life stages or 

among diff erent habitat types could help reduce parameter uncertainty, which is usually very high in these models.

In addition, temporal fl uctuations in habitat may help explain the variation that exists around these relationships. For example, 

in the west coast sablefi sh stock assessment, sea surface height (SSH) and two zooplankton anomalies were included as covariates for recruitment deviations from the fi tted stock-recruitment relationship (Schirripa, 2007). Recruitment deviations 

strongly correlated with all three indices, particularly with SSH. Th is example points to the need for models that can include 

temporally dependent habitat data to inform observations for fi sh stocks. Recent advances in stock assessment models, such as 

SS, could readily incorporate such variation.

Habitats, Movement, and Spatial Variation: Habitat availability and productivity vary geographically. Spatially explicit models and associated habitat data, therefore, hold promise to better understand abundance and productivity of stocks at the large

spatial scales on which fi sheries oft en are managed. With a few exceptions, many of these spatially explicit models currently are 

of heuristic value only (i.e. they provide insight on the potential infl uence of spatial variation on stock attributes), partly due 

to the large amount of required data. In addition to area-specifi c estimates of survival or fecundity, spatially explicit models 

require information on dispersal patterns of the species (i.e. movements among habitats). From a more practical standpoint, 

the increase in the spatial resolution of surveys over time may hinder comparisons among current and older periods. For these 

reasons, stock assessments have usually ignored spatial heterogeneity.

However, as noted by Field et al. (2006), the increasing use of MPA’s for management of LMR’s creates important spatial structure relevant to the demographic characteristics of the stock. Similar arguments apply to some habitat types (e.g. untrawlable 

habitats; Zimmerman, 2003). Consequently, stock assessments that integrate habitat-specifi c spatial information stand to improve accuracy in estimates of abundance.

Th e development of models like SS (Table 1), which can specifi cally incorporate spatial variability (Methot, 2009), makes 

habitat-informed stock assessments feasible. Th e challenge is to populate spatially explicit models with data that can reduce 

uncertainty of the assessment. Th is challenge is two-fold because the models require: 1) data on each spatial element; and 2) 

rules for linking spatial elements (e.g. movement matrices). While the fi rst issue primarily depends on the extent of habitat 

observations, the second issue deserves more attention and could serve as a starting point for future research. Habitat-patchspecifi c information is not obtainable for most species, but general habitat classes, their relative availability, and how they aff ect 

demography may be suffi cient to improve stock assessments. Likewise, certain rules-of-thumb (e.g. abundance or residence 

time is proportional to independently assessed habitat quality; Fretwell, 1972) may simplify incorporation of habitat variation

and also reduce the uncertainty of the stock assessment. For some stocks, such rules-of-thumb might be suffi cient to overcome 

uncertainty in movement rates among habitats. 

For highly migratory species (HMS) such as tunas and billfi shes, tagging eff orts can explicitly inform movement rules in pelagic habitats. For example, pop-up tags that transmit high-resolution data via satellite have enabled scientists to describe pelagic 

habitat for Atlantic billfi shes (Hoolihan et al., 2009). Further, chemical fi ngerprinting of fi sh tissues and otoliths have been 

used to understand the migratory patterns of Atlantic bluefi n tuna (Dickhut et al., 2009). Defi ning habitat for HMS is an important challenge, particularly as the United States seeks the strongest possible management to conserve Atlantic bluefi n tuna. 

Tagging eff orts coupled with habitat assessments can elucidate the infl uence of habitat heterogeneity on age- or stage-specifi c 

movements of these and many other species.
31

Capability of Stock Assessment Models to 

Include Habitat Data

Th e inability of stock assessment scientists to 

incorporate habitat data directly into assessment models potentially could be a signifi cant 

impediment to advancing to SAIP Tier 3 stock 

assessments. In the questionnaire developed by 

the HAIP Team, NMFS scientists having stock 

assessment and population biology expertise (n 

= 46) were asked to rate the potential of stock 

assessment models to accommodate specifi c 

types of habitat data. Respondents could rate 

these types of data as: 1) requiring new stock 

assessment models; 2) requiring some modifi -

cation of existing models; or 3) not necessitating changes to models because existing models 

would readily accommodate the habitat data.

Respondents indicated that some types of 

habitat data would be more diffi cult to integrate into stock assessment models than others 

(Figure 9). In particular, a majority of scientists 

indicated that habitat-specifi c vital parameters 

and information on habitat associations by life 

stage would require modifi ed or new models. 

Most scientists also responded that incorporation of maps of dynamic oceanographic features (e.g. chemical, temperature, or current 

variation) and of anthropogenic impacts would 

require modifi cation or creation of new models. In contrast, respondents generally reported 

that time series of oceanographic and climate 

variation, and to a lesser extent bathymetry 

and habitat-specifi c catch, eff ort, and biomass 

data, could be incorporated with little or no 

modifi cation to existing models.

Th ese perceptions were clearly infl uenced by 

Figure 10

The capability of stock assessment models to accommodate any type of habitat 

data, by responses from stock assessment scientists who study demersal and 

pelagic stocks. Bars indicate the percent frequency of questionnaire respondents 

who thought: 1) new models are required to integrate each type of habitat data; 2) 

changes to existing models are suffi cient; or 3) existing models can accommodate 

the data.

Percent Response

80 100

Demersal stocks

Pelagic stocks

New models are required 

Changes to existing models are required 

Existing models can accommodate data

0 20 40 60

both the species studied and the geographic region in which the scientist worked. Scientists that studied demersal stocks were 

more optimistic of the capability of models to integrate habitat data than scientists working with pelagic stocks (Figure 10). 

Interestingly, scientists from the NWFSC were more optimistic about the capability of models to incorporate habitat data at 

some level than scientists from any other region, and scientists from the NEFSC were more skeptical (Figure 11). Th is pattern 

could be a consequence of the species assessed by the respondents and the types of stock assessment models used by scientists 

in diff erent regions. 

Figure 9

The capability of stock assessment models to accommodate different types of habitat 

data. Bars indicate the percent frequency of questionnaire respondents (n = 46) 

who thought: 1) new models are required to integrate each type of habitat data; 2) 

changes to existing models are suffi cient; or 3) existing models can accommodate 

the specifi c type of data.

Percent Response

80 100

Time series of oceanographic/climate data

Habitat-specific catch/effort data

Bathymetry

Habitat-specific biomass/abundance

Maps of benthic substratum

Habitat-specific vital parameters

Habitat associations by life stage

Maps of oceanographic habitat variation

Maps of anthropogenic disturbance

New models are required

Changes to existing models are required

Existing models can accommodate data 

0 20 40 60
32

In addition to querying opinions of stock assessors, the HAIP Team reviewed some of the 

core tools in the Stock Assessment toolbox and 

found elements in the models that could incorporate habitat data (Table 1). Several models 

have entry points by which habitat data could 

be integrated, including habitat-specifi c vital 

rates (i.e. natural mortality and growth), stockrecruit parameters, and movement formulations. In fact, SS provides all such capabilities 

and all parameters can exhibit spatio-temporal 

variation. Th e greatest challenges to be met are 

the lack of useful habitat data and the synthesis 

of the observations. Currently, data oft en are 

not collected or integrated in a habitat-specifi c 

manner and, until such eff orts are made, advances in linking habitat and stock assessments 

will proceed very slowly.

Habitats, Integrated Ecosystem 

Assessments, and Coastal and 

Marine Spatial Planning

Percent Response

80 100

NEFSC

SEFSC

SWFSC

NWFSC

AFSC

PIFSC

New models are required 

Changes to existing models are required 

Existing models can accommodate data 

0 20 40 60

Figure 11

The capability of stock assessment models to accommodate any type of habitat 

data, by responses of stock assessment scientists from each NMFS Fisheries Science Center. Bars indicate the percent frequency of questionnaire respondents 

who thought: 1) new models are required to integrate each type of habitat data; 2) 

changes to existing models are suffi cient; or 3) existing models can accommodate 

the data.

One of NOAA’s goals is to “protect, restore, and manage the use of coastal and ocean resources through an ecosystem approach 

to management” (NOAA, 2008). EBFM requires a comprehensive framework for making decisions about LMRs. In contrast 

to single-species or single-issue management, EBFM considers a wider range of relevant ecological, environmental, and human 

factors bearing on societal choices regarding resource use. In this context, EBFM is adaptive, is geographically specifi ed, takes 

account of ecosystem knowledge and uncertainties, considers multiple external infl uences, and strives to balance diverse societal objectives (Murawski and Matlock, 2006). 

Ecosystem-based fi sheries management requires managers to consider all interactions that a fi sh stock has with predators, 

competitors, and prey species; the eff ects of weather and climate on fi sheries biology and ecology; the complex interactions 

between fi shes and their habitat; and the eff ects of fi shing on fi sh stocks and their habitat (EPAP, 1999). While ocean and 

coastal resource managers recognize the ultimate use of an EBFM approach, implementation for fi sheries, habitat, and coastal 

watersheds presents substantial challenges. Little practical experience is available to assist managers in achieving EBFM (Levin 

et al., 2009). Likewise, limited ecosystem data are available to derive decision support tools that facilitate the selection and 

testing of alternatives to EBFM. NOAA is in the process of establishing the scientifi c underpinning for EBFM of ocean and 

coastal LMR’s so that complex management actions are based on comprehensive, cumulative, and reliable science (Murawski 

and Matlock, 2006).

IEA’s are an emerging tool for NMFS to use in meeting EBFM objectives for U.S. coastal waters. An IEA is the synthesis and 

quantitative analysis of information on ecological and human processes relevant to a specifi ed set of EBFM objectives (Levin 

et al., 2009). IEA’s combine biological, physical, chemical, and geologic data and socioeconomic information to quantitatively 

assess a range of possible management objectives that could aff ect ecosystems (Levin et al., 2009). While this approach is still 

in its infancy, four promising IEA’s (Chesapeake Bay, the Gulf of Mexico, the California Current, and Puget Sound) are under 

development.
33

Habitat science and habitat assessments are at the core of an IEA (Table 2) and, by extension, EBFM. Habitat assessments furnish information on the structure and function of the ecosystem in which fi shing activities occur, thereby increasing awareness 

of both the eff ects of management decisions on the ecosystem and the eff ects of other components of the ecosystem on fi sheries. Th e abundance, spatial arrangement, and quality of habitats aff ect the integrity of ecological systems and critical population 

metrics, such as encounter rates between predators and prey, availability of refuges from predation, vital rates, productivity,

incidence of disease, and many other processes that potentially infl uence the sustainable yield of exploited populations (Breitburg and Houde, 2006; Walters and Martell, 2004). As such, the link between habitat science and IEA’s deserves further 

investigation and refi nement.

IEA’s comprise a fi ve-stage process for EBFM: 1) scoping; 2) developing ecosystem indicators; 3) risk analysis and assessment 

of ecosystem status; 4) management strategy evaluation; and 5) monitoring (Table 2). Th ere are several entry points through 

which habitat assessments can improve IEA’s. During the scoping stage, habitat assessments can help in identifying threats to 

EBFM goals in at least two ways. First, EBFM goals can include fi sheries sustainability, which can be infl uenced by impacts to 

habitats and associated population dynamic functions. Second, EBFM goals can include the importance of habitat integrity in 

and of itself. In this case, habitat assessments can support EBFM even in the absence of certainty in the causal mechanisms that 

link habitat impacts to stock production.

Once habitat integrity is incorporated into EBFM goals, indicators of stock or habitat status need to be developed. Observations of habitat processes, distribution, and impacts should be evaluated in the context of other ecosystem indicators (e.g. surveys of species abundance, socioeconomic indicators) in order to develop realistic management targets related to these indicators. Scientists oft en rely on driver-pressure-state-impact-response (DPSIR) conceptual models to help clarify which indicators 

will be most useful (Niemeijer and de Groot, 2008). Some of the most successful DPSIR models have well-developed habitat 

modules in which anthropogenic pressures aff ecting habitat are explicitly incorporated, changes in habitat state are assumed, 

and both habitat and species impacts are identifi ed. Successful conceptual modeling supports the risk analysis stage of an IEA, 

in which ecosystem targets are examined in light of uncertainties in estimating current and historic habitat characteristics and 

level of impact. 

Habitat assessments can be incorporated into the fourth stage of an IEA (i.e. evaluating management strategies) using spatially

explicit ecosystem models. Th e Atlantis model (Figure 12; Fulton et al., 2005) is one successful example, whereby users specify 

habitat “boxes” that correspond to three-dimensional units of analysis. While habitat composition can be varied within the 

boxes, the total number of boxes in such a model is a compromise among confl icting issues, including realistic match to number 

of distinct habitats and their boundaries; data availability within each model cell; and computation speed. Overcoming such 

challenges is an emerging area of research in habitat science. In the fi nal ecosystem monitoring stage of an IEA, scientists verify 

predictions and determine the eff ectiveness of management. Habitat assessments are reevaluated in light of new data. Th is last 

step closes the feedback loop necessary for eff ective EBFM. 

Table 2

The role of habitat assessments in an integrated ecosystem assessment (components modifi ed from Levin et 

al., 2009).

Components of IEA Role of Habitat Assessments

Identify goals of EBFM and threats to achieving 

those goals

Identifi cation of goals for, and threats to, fi sheries or habitat

Develop ecosystem indicators and targets Determination of the use of habitat observations in ecosystem 

monitoring

Risk analysis and assessment of ecosystem 

status

Determination of uncertainty associated with habitat impacts and habitat 

observations

Management strategy evaluation Construction of spatially explicit ecosystem models that incorporate 

habitat heterogeneity

Monitoring indicators and management 

effectiveness

Evaluation of multiple habitat assessments over time
34

NMFS has become an active participant in CMSP, an eff ort to allocate compatible human uses of the oceans while sustaining important ecological, socio-economic, and cultural functions for the future (NOAA Ecosystem Goal Team et al., 2009). 

CMSP is a comprehensive, ecosystem-based process that involves many components of NOAA as well as numerous other Federal agencies and stakeholders. It is intended to reduce impacts of human activities in ecologically sensitive areas and confl icts 

among incompatible activities, while maintaining ecosystem services. 

Th e Interagency Ocean Policy Task Force (2009a) has draft ed an interim national policy “that ensures the protection, maintenance, and restoration of the health of the ocean, coastal, and Great Lakes ecosystems and resources...”. Th e objectives for 

implementing this policy include ecosystem-based management, CMSP, and science-based regional ecosystem protection and 

restoration. Th e Task Force (2009b) is also currently developing a government-wide framework for CMSP. Th e concept underlying this eff ort is that the current sectoral allocation of ocean space will evolve into an ecosystem-based, adaptive management 

process in a manner similar to the transition from single-species fi sheries management to EBFM and IEA’s. Th e Framework 

describes benefi ts, governance, a phased process for implementation, and needs for scientifi c knowledge, data integration, research, management, and access to the CMSP information.

Many of NOAA’s legal authorities, functions, and capabilities are relevant to CMSP. NOAA collects a wide range of spatial 

data on ocean resources, uses, and characteristics, develops and uses decision-support tools, and conducts spatial analyses of 

marine data to support regional planning and management. Habitat maps and information on the relationships between living 

marine resources and their habitats are major components of the information upon which eff ective CMSP will depend.

Many of NMFS’ stewardship mandates result in regulation of marine areas, including designation of EFH and HAPC’s for 

fi shery species and Critical Habitat for ESA-listed species. Th ese regulations can lead to restrictions in fi shing and nonfi shing 

activities for conservation purposes. Such regulations are based on habitat science and assessment. Th e NOAA Ecosystem Goal 

Team et al. (2009) identifi ed CMSP functions, all of which are signifi cantly linked to habitat science and assessment (Table 3). 

Biogeochemistry

Climate and Oceanography

Habitat

Fisheries

submodel

Ecology

submodel

Hydrographic

submodel

Figure 12

Schematic of the Atlantis 

ecosystem model, which 

simulates oceanography, 

ecology (including habitat 

effects), and fishing (from 

Brand et al., 2007).
35

CMSP Functions Contributions of NMFS Habitat Science and Assessments

Spatially explicit ecosystem 

information

NMFS generates, analyzes, and interprets data on important habitats, species, and 

ecological processes for designation of EFH and Critical Habitat of ESA-listed species and 

for development of fi shery regulations

Spatially explicit assessment 

 of ocean uses

Habitat assessments and maps of EFH, fi shery regulations, and Critical Habitat

Decision support tools NMFS generates, analyzes, and interprets data of fi shery species and associated habitats

Interagency coordination Federal agencies must consult on actions that potentially impact EFH and ESA-listed species

Policy framework CMSP legislation and policies will be based on sound scientifi c principles to conserve habitats and ecosystem function and services

Table 3

The contributions of NMFS 

habitat science and assessments to the various functions of coastal and marine 

spatial planning (NOAA 

Ecosystem Goal Team et 

al., 2009).

37

Section 4: Data for Habitat Assessments

At a Glance

• Habitat assessments require both collection and synthesis of multiple types of data at a variety of temporal and 

spatial resolutions.

• Research eff orts to collect habitat data have been fragmented and limited, with our greatest success demonstrated by the physical characterization of habitats.

• A survey of NMFS scientists indicated that most habitat data occur at low resolution based on inadequate 

information.

• Primary challenges to the eff ective management of habitat data are: the multiplicity of data types and the large 

volume of imagery data; the lack of appropriate metadata and accessibility to research data; and the means to 

effi ciently collect and process data and produce the required products.

• Habitat data collection eff orts and data management initiatives should be coordinated across NOAA and its 

partners.

• NMFS data management systems and integration applications should be expanded, and the number of NMFS 

technical staff should be increased.

Habitat assessments require input data that vary not only on spatial and temporal scales of resolution, but also in complexity 

relative to the ecosystem processes being studied. Th e foundation of a habitat assessment requires information at increasing levels of understanding or resolution from three major categories: 1) habitat type and area (i.e. characterization and delineation of 

habitats); 2) ecological value of habitat (i.e. habitat-specifi c species abundance, growth, mortality, reproduction, and production) and the functional relationships within and among habitats; and 3) habitat status or condition (Figure 13). Critical to the 

synthesis of these three categories of habitat data are the levels of data integration and the frequency at which assessments are 

conducted to monitor habitat change. A habitat assessment includes all of these components.

While a variety of habitat data have been collected by NMFS and others, most of these data have been gathered for disparate, 

project-specifi c purposes and do not lend themselves to the type of integration and synthesis required for habitat assessment. 

Our ability to conduct habitat assessments will remain hampered until systematic habitat research eff orts are coordinated and 

implemented at appropriate spatial and temporal scales using methodologies that facilitate integration of the diverse physical,

biological, and socioeconomic data needed for these assessments. Enterprise data management initiatives, such as NOAA’s 

Integrated Ocean Observing System (IOOS) and a system being developed by NMFS F/ST, will facilitate data management 

and integration eff orts in the future. Th ese systems, however, are still relatively undeveloped, especially as relevant to habitat 

and life-cycle data for fi shery species.

Characterization and Delineation of Habitats

Marine habitats are characterized and delineated using physical, chemical, and biological data. Th ese data are collected using a 

variety of survey instruments and methods, collated, analyzed, and translated into maps for use in habitat or stock assessments. 

Due to limitations of the surveys, data, and analyses, most habitat maps are usually not explicit and oft en are derived from a 

reasonable environmental proxy (e.g. depth, grain size, rugosity, and water temperature; Figure 14). Th e acceptability and usability of habitat maps based on such proxies depend on the resolution and quality of the sampling, the method of inferential 

interpolation, the classifi cation analyses, and the degree to which other important functional characteristics (e.g. properties 
38

most critical to distribution, spawning, growth, and mortality of fi shery species) of the habitat have been delineated. Appropriate spatial statistics, habitat classifi cation schemes, and mapping conventions, therefore, are essential to reduce uncertainty and 

facilitate the explanation and mapping of functional relationships.

Data types that are commonly used to characterize habitats are listed in Section 2 (p. 13). Scientists have imperfectly, but oft en 

usefully, organized habitat characteristics into hierarchical classifi cation schemes, several of which have been proposed for U.S. 

coastal and ocean systems. For example, NOAA’s Coastal and Marine Ecological Classifi cation Standard (Madden et al., 2009) 

has three distinct components (i.e. benthic, water column, and geoform) that together provide a framework and standard terminology for describing marine and coastal habitats. Greene et al. (2007) emphasize the importance of schemes with fl exibility 

to meet the needs of various users both within and across regions.

Th e absence of consensus on habitat classifi cation schemes has not impeded habitat mapping. In fact, there has been a rapid 

increase in the interest of mapping marine benthic habitats over the past two decades (e.g. Noji et al., 2004; Todd and Greene,

2007). While large amounts of bathymetric and geomorphological data have been collected (for instance, see Brown and Th omas, 2008), these data are most suitable for habitat delineation and assessments when collected and verifi ed (groundtruthed) 

specifi cally for such purposes. Recent eff orts to increase collection effi ciency using ROV’s, AUV’s, and unmanned aircraft 

systems, coupled with improvements to data collection instrumentation (e.g. synthetic aperture sonar, laser line scan imaging, and high-resolution video imaging), could provide useful data on multiple scales (centimeters to kilometers) to improve 

habitat delineation. Most of these emerging technologies are relatively expensive at present, require specially trained operators, 

and create signifi cant challenges in data processing and storage. Partnerships among multiple users, such as that recently forged 

in NOAA’s Integrated Ocean and Coastal Mapping Program (IOCM) (Appendix 6), are critical to realize the full benefi ts of 

these technologies for practical resource management.

Mapping pelagic ecosystems also is fundamental to habitat assessments for many managed species. Pelagic habitats occur in a 

three-dimensional dynamic fl uid medium where vertical and horizontal boundaries of the system are far less static with regard 

to temporal and spatial scales than are the boundaries of a benthic system. Th e oceanographic disciplines (i.e. physical, chemical, geological, and biological) provide a description of the properties of this fl uid environment (e.g. temperature, salinity, chlo-

 Integration of habitat data Frequency of habitat assessment

 Habitat products in map or GIS format Baseline assessment complete

 Habitat products with stock data by lifestage Periodic assessments conducted

 Habitat products for growth/survival by lifestage Standardized monitoring in place

 Habitat products that address multiple species,

 ecological value & trophic interactions

 Habitat type & area Ecological value Status or condition

 Bathymetric charts Presence/absence Impact of fishing activities

 Multibeam acoustics Density Impact of pollution

 Seafloor & water column Growth/survival Impact of climate change

 Abiotic & biotic components Interspecific competition Impact of invasive species

 Production 

High

High

Habitat Assessment

Data

Synthesis

Low

Low

Complexity/

Certainty

Complexity/

Certainty

Figure 13

Flow of information from the 

Data Block to the Synthesis 

Block, which together produce a habitat assessment.
39

rophyll), the currents, and water masses. Data at the sea surface are collected on a regional scale by a variety of satellite-borne 

sensors. Moored and drift ing buoys collect and transmit temperature, salinity, pressure, and current profi les at multiple ocean 

depths. Research vessels also are used to collect environmental data, as well as associated biological samples, at specifi c stations. 

Archival and pop-up tags attached to fi shes, turtles, and mammals collect data on geo-location, light, temperature, and depth 

that are used to model both pelagic habitats and the organism’s movement over time.

Habitats are delineated for management purposes even in the absence of meaningful environmental and biological data. Bathymetric data oft en have been used to defi ne management boundaries for EFH, HAPC, MPA’s, and other political or management zones (National Marine Protected Areas Center, 2008). In other cases, noticeable landmarks, treaty agreements (e.g. 

EEZ’s), or relatively arbitrary distance units are used to delineate habitat boundaries. Th ese political boundaries usually are 

determined without regard to habitat types or ecological function. Coastlines, population maps, hydrologic and hydrographic 

maps, draft Environmental Impact Statement alternatives, socioeconomic census data, digital elevation models, and sediment 

maps also could infl uence habitat delineation. 

Ecological Value of Habitats

Information on the distribution, abundance, and life history of managed stocks is commonly based on fi shery-dependent sampling of catch and on fi shery-independent surveys using various fi shing gears. Fishery-independent trawl surveys are among the 

highest quality data sets in NMFS, generally being conducted under controlled conditions using standardized sampling protocols and gear. Th ese data oft en are collected as individual samples that integrate over broad (kilometer) spatial scales. Little 

or no concomitant habitat information is collected during these surveys, with the exception of broad-scale, low-resolution data

on depth, location, and perhaps temperature that are integrated over the entire sample and used to document a range of biogeographical and depth patterns of associated species (Williams and Ralston, 2002). 

 Various methods, ranging from fi eld observations to laboratory experiments, have been used to quantify habitat value. Visual 

survey techniques using scuba and various types of underwater vehicles, combined with large-scale remote acoustic surveys, 

have been used successfully to quantify habitat associations for some species at the spatial scales of fi sheries (Section 3, p. 19). 

A number of collaborative teams of fi sheries biologists, marine ecologists, and marine geologists have advanced this approach 

Figure 14

Example of a habitat map 

of the Hudson River Canyon 

off New York and New Jersey, based on depth as an 

environmental proxy. Map 

courtesy of Vincent Guida, 

NEFSC.
40

to the level of a recognized discipline, as illustrated by two recently published volumes on mapping seafl oor habitats and fi sh 

associations (Reynolds and Greene, 2008; Todd and Greene, 2007). At much smaller spatial scales, laboratory, mesocosm, and 

fi eld caging studies also are used to document interactions between fi shes and biotic and abiotic features of habitats, and measure habitat use under diff ering structural complexity and predation pressure. Th ese types of studies can provide information 

on vital rates such as mortality and growth for certain life stages under diff ering environmental conditions.

Habitat is the context in which species interact. Habitat-specifi c life history data and information on the interdependence 

of fi sh stocks, including both physical and biological relationships (e.g. food webs or shared habitats), are relatively sparse. 

Stomach content analyses, consumption rates, food preference studies, nutritional analyses, stable-isotope analyses, otolith 

microchemistry, forage fi sh abundance measures, predator-prey dynamics, spatial diff erences in stock distribution as measured 

by catch and DNA analysis, home-range fi eld observations, and analyses of bycatch are used to understand the functional relationships among ecosystem components. Th ese eff orts, although not prolifi c, will be key in developing food web models for 

IEAs (Link et al., 2008b). Research on interactions at multiple trophic levels is even less well developed. While stock assessment models are being developed to include these interactions and models of ecosystem-wide food webs are being calibrated 

with such information, the data needed to advance these investigations are substantial. Habitat information will be essential in 

understanding the signifi cance of predator-prey interactions. 

Th us far, however, we have achieved more success in mapping physical features of potential habitats (e.g. distribution of rocky 

seafl oor, kelp beds, and upwelling plumes) than in conducting the biological sampling necessary to defi ne and delineate critical ecological relationships specifi c to those habitats. Th e functional relationships between species and habitats have yet to be 

elucidated largely because of the diffi culty in obtaining datasets at relevant spatial and temporal scales commensurate with 

distribution and abundance of important life stages. Th e identifi cation of habitat properties critical to growth and survival 

remains a large gap, particularly in our understanding of sensitive life stages and of nontargeted species.

Status or Condition of Habitats

Th e changing status (or condition) of habitats is another challenging aspect of a habitat assessment. Changes that result from 

indirect infl uences at the community level or across the wider ecosystem are least understood and can infl uence the habitat’s 

ecological relevance. Physical, biological, and chemical degradation can alter the ecological services provided by habitats, and 

can be an important consideration in maintenance of the biochemical balance of the ecosystem and subsequent responses of 

fi shery stocks. Physical impacts, such as disturbance to seafl oor communities from bottom-contact fi shing gear (Barnes and 

Th omas, 2005) or eff ects of sedimentation from coastal runoff , can be identifi ed and oft en quantifi ed with direct or remote observations. Changes to biodiversity associated with introduced and invasive species can be diffi cult to recognize, and chemical 

and other water quality impacts to the ecological balance may be the hardest to identify and measure for many reasons. NonBoth fi eld observations and 

laboratory experiments are 

important to quantify habitat 

value.

Left: Doris Alcorn, AFSC; right: NEFSC.
41

point source pollution is oft en ubiquitous, our 

perception of climate change can be that it is 

gradual or episodic, and physiological impacts 

may only be discernible over long monitoring 

periods. Furthermore, little or no baseline information is available on community structure 

in most ecosystems that we manage.

Visual methods to monitor the status or condition of benthic habitats include scuba, manned 

submersibles, towed and drop cameras, laser 

line scanners, AUV’s, ROV’s, and aerial/satellite sensors. Data products from these tools 

oft en are in the form of video or other imagery. 

Interpretation of such data requires substantial 

funding and trained personnel (Somerton and 

Gledhill, 2005), and NMFS programs that 

characterize biological components of benthic habitats oft en rely opportunistically on 

external funding and rarely include long-term 

monitoring. 

Visual methods using underwater tools such as the Phantom ROV are important in monitoring 

the status and condition of habitats, but can present challenges in terms of data interpretation 

and storage.

Scott Mau, SWFSC

NMFS Science Centers and Regional Offi ces operate limited water quality monitoring programs that collect chemical, physical, 

and biological data that may refl ect habitat condition. Th ese programs operate primarily in estuarine and near-shore environments, which can be subject to substantial anthropogenic impacts; these programs are rarely spatially or temporally adequate 

for habitat assessments. NOAA’s National Ocean Service (NOS) and National Centers for Coastal Ocean Science (NCCOS) 

operate the National Status and Trends Program, the National Estuarine Eutrophication Assessment Program, the Coral Reef 

Ecosystem Monitoring Program, the Monitoring and Event Response for Harmful Algal Blooms Research Program, and the 

National Marine Sanctuaries habitat monitoring programs. Water quality monitoring programs also are conducted by other 

government entities such as U.S. Geological Survey (USGS), Environmental Protection Agency, and the coastal states, and 

usually are focused on rivers, estuaries, and coastal beaches. NOAA’s Offi ce of Oceanic and Atmospheric Research (OAR) and 

NCCOS conduct limited monitoring programs on invasive species, generally through state and nonprofi t partners. 

Monitoring the impacts of climate change on marine habitats will be especially demanding. Changes to sea level, sea temperature, salinity, carbonate chemistry, ocean currents, ocean structure, wave dynamics, storm frequency and intensity, and rainfall 

all will have considerable eff ects on habitat distribution over various time scales. NOS and NOAA’s National Environmental 

Satellite, Data, and Information Service currently use a combination of satellite and buoy measurements to assess the impacts 

of climate change on a limited number of habitats in coastal and ocean ecosystems.

Even when considered together, these programs do not constitute a comprehensive, coordinated national enterprise to eff ectively evaluate and monitor marine habitats. Funding constraints limit the number and diversity of sampling sites, as well as the 

frequency of sampling. Th e absence of a national program precludes assessments of water quality and biological condition of 

coastal and marine habitats (COP, 2004).

Management of Habitat Data

Even cursory habitat delineations and assessments demand a variety of data; systematic eff orts to achieve acceptable levels of 
42

data quality and to manage these data are limited. In addition, data integration remains a substantial challenge regardless of 

the collection and accessibility of appropriate data. Th ree of the most vexing challenges to the eff ective management of habitat 

data are: 1) the multiplicity of data quality and types, defi nitions, and resolutions, and the large volume of imagery data; 2) the 

general lack of appropriate metadata, base maps, and geospatial frameworks; and 3) the limited ability to collect, store, access, 

integrate, analyze, and distribute data in a consistent, coherent, and effi cient way. While some progress has been made in developing data management and integration systems for habitat science at some Science Centers, these are relatively isolated eff orts. 

Many of the Science Centers and their partners have engaged in the opportunistic collection of specifi c types of habitat data, 

while few have had the necessary resources to pursue systematic collection and analysis of such data for habitat delineation and 

assessment. Data are collected on various temporal and spatial scales with a variety of instruments and protocols, aggregated 

and analyzed with multiple methodologies and classifi cation schemes, and archived (oft en without appropriate metadata) in 

a perplexing array of information systems and data formats. All of these defi ciencies in data quality control, compatibility, and 

analytical methods hamper the eff ective and effi cient integration and distribution of NMFS’ habitat data. Consideration of 

NOAA’s IOOS data management standards and protocols could alleviate some of the problems associated with many disparate 

physical data sets, but the management and delivery of NMFS’ biological data present signifi cant challenges.

Adequacy of Habitat Data

As noted earlier (Figure 13, p. 38), the foundation of a habitat assessment requires data from three major categories: 1) habitat 

type and area; 2) ecological value of habitat; and 3) habitat status or condition. Th e HAIP Team polled 133 NMFS habitat and 

ecosystem scientists, population/stock assessment scientists, and resource managers to assist in identifying the level of complexity and certainty in data that is currently available for each of these categories. Our descriptions of the types of available data, 

while not mutually exclusive, were designed to represent a series of increasing complexity and certainty (from low to high) in 

our comprehension of habitat data. Our survey was not intended to capture all dimensions in habitat data, but instead serves 

as a measure of habitat data currently available to support habitat and stock assessment goals and emerging issues in ecosystem

management. Respondents were asked to score the adequacy of each type of data availability as having: 1) no information; 2) 

insuffi cient information; 3) or adequate information. Progress is needed in each of the three data categories to develop successful habitat assessments, and thus there should be concurrent eff orts to advance our level of understanding in each category.

Data on type and area of habitat (listed fr om low to high complexity and/or certainty)

• Bathymetric charts or other sources of information on water depth, which are used with fi eld sampling and 

observations to infer the distribution of managed species. 

• High resolution, multibeam acoustic survey data (e.g. acoustic backscatter data to discern hard and soft areas of 

the seafl oor) that improve our characterization of seafl oor substrata are used to infer distribution of managed 

species. 

• Water-mass features (e.g. currents, eddies, vertical structure of temperature) associated with topography (e.g. 

seamounts, island masses, banks, canyons) are identifi ed as infl uential attributes of habitat. 

• Surveys of habitat, including abiotic components (e.g. substratum type, hydrographic variables) and associated 

biotic components (e.g. kelp, coral, sea grass, sponges), result in an improved understanding of community and 

ecosystem structure and function. 

Data on ecological value of habitat (listed fr om low to high complexity and/or certainty)

• Th e distribution of the managed stock is predictable based on presence/absence by habitat types (depth, temperature, or other attributes of habitat). 

• Habitat-specifi c abundance (e.g. density, biomass, CPUE) of the stock is known.

• Habitat-specifi c vital parameters such as growth and mortality are known. 

• Direct and indirect roles of habitat as prey, shelter, and inter-specifi c competition for managed stocks and 
43

other ecosystem taxa have been assessed by survey or experimental methodologies. 

• Projections of production are linked to the quality and availability of habitat types. 

Data on habitat status or condition (listed fr om low to high complexity and/or certainty)

• Th e degree that habitat is altered from trawling, longlines, trapping, and other fi shing activities is known. 

Note: As regulation of fi shing is the mandate of NMFS, it is possible to address fi shing impacts more directly 

than the following issues.

• Information is available on the degree that habitat is altered by point and nonpoint source pollution.

• Information is available on the rates that climate is altering habitat (e.g. change in temperature, sea level, salinity, pH, etc.) for managed stocks and the ecosystem. 

• Th e degree to which invasive species alter habitat form and function is known, as well as the consequences to 

the managed stock and ecosystem.

Most survey respondents divided their answers between the choices of none and insuffi cient to describe the state of knowledge 

for the three data categories ( Figure 15). Some survey respondents indicated that they chose insuffi cient over the none category 

because some very basic information was available even though the amount oft en was extremely limited. A clear minority of 

respondents indicated that there were adequate data in each of the data categories, and the proportion of these respondents 

diminished with increasing levels of data complexity. Patterns of response were consistent for both the early life stages and harvest stages of managed taxa, with uncertainty generally larger in early life stages. Insuffi cient was the dominant response for the 

type-and-area data category, with only the lowest level (bathymetric charts) given an equal proportion of responses as adequate. 

For the ecological value data category, insuffi cient was the dominant response and the proportion of none responses increased 

at higher data levels. Th e habitat status data category was dominated by the insuffi cient response, except for data concerning 

invasive species where none was the most frequent response.

Th e overall response of the survey indicates an overwhelming inadequacy of habitat data to support even rudimentary habitat 

assessments. Th ese patterns persisted when the data were evaluated in the context of pelagic versus demersal stocks and by the 

noted discipline of the respondents (e.g. stock assessors, habitat scientists, and managers). 

Adequacy of the Synthesis of Habitat Data

Critical to the synthesis of the three categories of habitat data discussed above (i.e. type and area; ecological value; and status or 

condition) are the levels of data integration and the frequency at which assessments are conducted to monitor change in habitat

status or condition. Th e synthesis element of a habitat assessment will vary with each application. 

Integration of habitat data (listed fr om low to high complexity and/or certainty)

• Habitat products are in map or GIS format. 

• Habitat products include data on stock abundance by life stage. 

• Habitat products include growth and survival of stock by life stage.

• Habitat products include multiple species, ecological value, and trophic interactions. 

Frequency of habitat assessment (listed fr om low to high complexity and/or certainty)

• Baseline assessments are available. 

• Periodic assessments are being conducted.

• A plan for standardized long-term monitoring is in place.

Th e majority of survey responses for adequacy of data integration and frequency of assessments were either none or insuffi cient 
44

 Figure 15

Proportion of scores from respondents on the adequacy 

of information in three habitat data categories (type and 

area; ecological value; and 

status) by life stage (early vs. 

harvested) of FSSI stocks.

(Figure 16). Very few respondents indicated that either integration of habitat data or the frequency of habitat assessment was 

being conducted at an adequate level. Th e proportion of the none response notably increased with the level of data integration and assessment frequency for both the early life and harvest stages of taxa. Integration of habitat data with ecosystem 

considerations was completely absent. In summary, responses to the survey indicate very little synthesis of habitat data has been 

conducted, which is likely tied to the limited availability of data. 

Habitat Type & Area

Early Life Stages

Bathymetric charts

Multibeam acoustics

Seafloor & water column features

Abiotic & biotic components

Harvested Stages

Ecological Value

Early Life Stages

Presence/absence by habitat type

Density by habitat type

Growth/survival by habitat type

Role of habitat in interspecific competition

Habitat-specific production models

Harvested Stages

Habitat Status

Early Life Stages

Impacts from fishing activities

Impacts from pollution

Impacts of climate change

Impacts from invasive species

None 

Insufficient 

Adequate 

Harvested Stages

High

Low

Resolution

High

Low

Ecosystem

Understanding

Proportion

High

Low

Uncertainty of

Human-Induced

Impacts
45

Adequacy of Staffi ng 

Many demands are placed on habitat assessment scientists aside from the basic duties required to conduct habitat and ecosystem research. In fact, few scientists are actually dedicated to a single discipline; consequently a team of scientists with diverse 

skills typically carries out habitat research. Within a given year, an individual habitat assessment scientist may be expected to: 1) 

participate in fi shery-independent surveys or other fi eld work; 2) provide input on data collection objectives and protocols for 

observer programs and other fi shery-dependent activities; 3) quality control data; 4) conduct habitat assessments; 5) conduct 

research to advance approaches to habitat assessment and fi sheries management; 6) present assessment results and scientifi c 

advice to Regional Offi ces, FMC’s, and others; 7) participate in FMP development; 8) defend habitat assessments in a court 

of law; 9) produce and peer-review scientifi c manuscripts for publication; 10) undertake training or train others on new methodologies; 11) participate in national and international conferences; and 12) undertake administrative duties depending on 

supervisory level. With limited exceptions, there is insuffi cient opportunity for individual scientists to focus on just one or a 

few of these activities due to an overall shortage of habitat scientists.

Th e HAIP Team surveyed NMFS habitat and ecosystem scientists, population/stock assessment scientists, and resource managers on the actual and optimal allocations of their time associated with various components of habitat assessments. Stock 

assessment scientists were asked to participate in the survey because many conduct habitat-related research and because of the 

HAIP’s emphasis on habitat and ecological considerations in fi sheries stock assessments. Scientists and managers were asked 

to estimate the percentage of their time, averaged over the previous two years, spent in each of ten activities: 1) the mechanics 

of habitat assessments; 2) modeling research to improve assessment methodology; 3) other research to improve habitat assessIntegration of Assessment

Early Life Stages

Habitat products in map or

GIS format

Habitat products with stock data

by lifestage

Habitat products for growth &

survival by lifestage

Habitat products that address

multiple species, ecological value

& trophic interactions

Harvested Stages

Frequency of Assessment

Early Life Stages

Baseline assessments complete

Periodic assessments conducted

Standardized monitoring in place

None 

Insufficient 

Adequate 

Harvested Stages

High

Low

Integration

High

Low

Frequency

Proportion

 Figure 16

Proportion of scores from 

respondents on the adequacy of data integration and 

frequency of habitat assessments, by life stage (early vs. 

harvested) of FSSI stocks.
46

ment methods and tools; 4) participation in 

collection, analyses, and management of data; 

5) provision of scientifi c advice to FMC’s; 6) 

participation in FMP development, evaluation of alternative management strategies, and 

other FMC-related activities; 7) other interactions with constituents; 8) professional development including producing manuscripts, 

reading journals, attending conferences, and 

training; 9) administrative duties; and 10) 

other. Respondents were also asked to estimate 

the ideal percentage of time that should be allocated to these activities.

Overall, habitat and ecosystem scientists spend 

about 83% of their time on habitat-related activities. Population/stock assessment scientists 

and resource managers spend about 38% and 

71% of their time, respectively, on habitat-related activities. All three groups agree that ideally they could spend 3-7% more time on these 

activities (Figure 17). 

All respondents (averaged across disciplines) 

similarly spend the most time on tasks such 

as data collection, professional development, 

administrative duties, and other habitat-related research (Figure 18). Diff erences did exist, however, among regions on the amount of 

time available to spend specifi cally on habitatrelated tasks. For example, habitat and ecosystem scientists from the Southwest and Northeast Science Centers spend 100% of their time 

on habitat-related tasks, while researchers at 

the other Science Centers allocated 50-94% of 

their time to those duties. Th is emphasizes that 

some Science Centers have teams dedicated to 

ecosystem and habitat research, while teams at 

other Science Centers comprise a mix of staff 

that perform functions other than those relatFigure 17

Percent of time (averaged from all respondents in each discipline) currently and 

ideally spent on all habitat-related activities by NMFS staff in three disciplines.

0

10

20

30

40

50

60

70

80

90

100 Current 

Ideal 

Ecosystem/Habitat

Scientists

Population Biologists/

Stock Assessors

Resource

Managers

Percent

of time

n = 52

n = 36

n = 14

Figure 18

Percent of time (averaged from respondents across all regions) currently and ideally 

spent on specifi c habitat-related tasks for all regions combined.

Percent of Time

0 2 4 6 8 10 12 14 16 18 20

Other activities

Modeling research

FMP development

Constituent interactions

Assessment mechanics

Scientific advice

Other research

Administrative activities

Professional development

Data collection

Ideal 

Current 

ed to habitat assessment. Resource managers spend the majority of their time on other activities, such as EFH consultations, 

habitat restoration and protection, nonfi shing-related eff ects on habitat, and strategic planning. Th ey also spend a fair amount 

of time on FMP development and data collection. All three groups agree that they require more time to accomplish most habitat-related tasks and spend too much of their available time performing administrative duties.

Th ere were no substantial diff erences between the current allocation of time and the surmised ideal situation. Th is is an indication that the time of NMFS staff , regardless of discipline, is fully committed. NMFS staff have little occasion to shift duties or 
47

responsibilities, and they have limited time for habitat assessments and much less time to improve them. Th e conclusion of the 

HAIP Team is that additional staff will be necessary to achieve improvements to habitat assessments. 

49

Section 5: Resource Requirements

At a Glance

• Major obstacles to producing and using credible habitat assessments include: lack of habitat-specifi c abundances and biological parameters; insuffi cient staff to collect, process, analyze, and model habitat data; and 

insuffi cient research on environmental and multispecies eff ects.

• Three Tiers of Excellence for Habitat Assessments include the essential elements of a comprehensive habitat 

assessment and monitoring program: habitat-specific biological information, geospatial information on habitat characteristics, and development and application of indices to monitor habitat condition related to fish 

production.

• About 5% of total NMFS staff are currently working on habitat-related activities at the Science Centers, and 

an alarming average of 33% of those staff working on habitat are contractors and students supported with 

transient, non NMFS funds.

• Full implementation of the HAIP will require a 250% increase in staff and a substantial increase in funds for 

program operations, tools, technology, and infrastructure.

Programmatic Needs

Th e HAIP team asked NMFS habitat and ecosystem scientists, population/stock assessment scientists, and resource managers 

to identify the most important factors hampering their ability to provide accurate, precise, valid, and defensible habitat assessments (including data collection, analyses, and reporting) that would assist in improving accuracy and precision of stock assessments and EFH/HAPC designations. From their average responses, habitat-specifi c abundance, the quantity of staff to collect 

necessary habitat-related data, and research on multispecies interactions were ranked as major obstacles to producing and using

credible assessments, and were relatively high priorities for improvement of assessments (Figure 19). Taken as a whole (i.e. responses across all disciplines), research on environmental eff ects and habitat-specifi c biological parameters, and the quantity of 

staff to develop better habitat assessment models and to produce habitat analyses also ranked as major impediments to producing and using quality assessments. Th ese seven categories also were consistently scored among the six Science Centers as being 

the greatest impediments to producing and using credible assessments and the highest priorities for improvement. On average, 

the population/stock assessment scientists identifi ed fewer obstacles to quality habitat assessments than the other two groups, 

and the resource managers scored more topics as being major impediments to quality habitat assessments than the other two 

groups (Figure 19). Resource managers alone identifi ed inadequate number of staff to communicate habitat-related results as 

one of the greatest obstacles to producing and using quality habitat assessments. 

While not graphically depicted, some diff erences in average scores occurred among the Science Centers. For example, the 

Southeast Fisheries Science Center (SEFSC) considered more topics to be major obstacles to quality assessments, while the 

Alaska Fisheries Science Center (AFSC) and NWFSC scored fewer topics as high priorities. In addition, collection of habitatspecifi c commercial catch and eff ort data was considered a relatively high priority by researchers at the Pacifi c Islands Fisheries 

Science Center (PIFSC) and SEFSC, but not as much by the other four Centers. Across all the Centers, and regardless of discipline, the current quantity of scientists to communicate habitat-related results to NMFS constituents generally was thought 

to be adequate and a low priority for improvement. 

Considering fi shery-independent data needs, there were some diff erences in the average scores between respondents who work 
50

on pelagic stocks and those who focus on demersal stocks (Figure 20). Respondents working on demersal species scored direct 

observation survey methods as a relatively high priority (especially as related to survey design, fi sh-habitat associations, and 

habitat-specifi c abundance or biomass from quantitative transects), while those respondents working on pelagic species did 

not need improved data from this type of survey. Respondents who work on either pelagic or demersal species did not need 

improved data from trawl surveys, and neither group thought that additional training courses on species identifi cation for underwater surveys or for operation of multibeam acoustic equipment were needed.

While not graphically depicted, respondents from all six Science Centers identifi ed increased sampling frequency (including 

habitat-specifi c, seasonal, and spawning surveys) as the highest priority fi shery-independent data needed in order to enhance 

their ability to produce accurate, precise, and timely habitat assessments. More habitat-specifi c recruitment surveys and tagging 

studies (particularly archival and sonic tags) also were scored as top fi shery-independent data needs by the Science Centers in 

general. Additionally, increased numbers of data managers, sample processors, and statistical staff were important to a majority 

of responders from all Science Centers.

Th e HAIP Team also asked managers of habitat and population assessment programs at the six Science Centers to identify the 

resources (e.g. data collection programs, assessment scientists, survey personnel, technicians, database managers, and computer

programmers) needed to improve NMFS’ habitat assessments. Th eir responses (one from each Center) reinforced those of 

their staff scientists; across all Science Centers, program managers ranked habitat data processing, habitat-specifi c biological 

parameters, and habitat-specifi c fi shery independent indices of abundance as the three types of data or activity most needed 

to improve NMFS’ habitat assessments (Figure 21). Increasing the number of scientists to develop improved habitat-related 

assessment models and habitat-specifi c commercial catch and eff ort data also ranked high for most Science Centers.

Th ree Tiers of Assessment Excellence 

Th e quality of habitat assessments is represented using a series of tiers in a manner similar to other NMFS assessment improvement plans (NMFS, 2001; Appendix 3). Th e three tiers of the HAIP include the essential elements of a comprehensive habitat 

assessment and monitoring program: habitat-specifi c biological information, geospatial information on habitat characteristics, 

Habitat-specific commercial catch & effort data

Habitat-related communication staff

Habitat-specific recreational catch & effort data

Population and genetic structure

Fine-scale data for regulatory analyses

Training to improve habitat-related skills & tools

Database programmers/managers

Habitat-specific biological parameters

Habitat assessment modelers

Research on multispecies interactions

Research on environmental effects

Habitat analyses staff

Habitat data collection staff

Fishery-independent habitat-specific abundance

Habitat/Ecosystem Scientists (n = 65)

Population/Stock Assessment Scientists (n = 53)

Resource Managers (n = 14)

Minor obstacle

Lowest priority

Major obstacle

Highest priority

Figure 19

Obstacles to producing 

and/or using quality habitat assessments, averaged 

over responses from NMFS 

staff of three disciplines 

(habitat/ecosystem science; 

population/stock assessment science; and resource 

management).
51

Multibeam Training

Species Identification Training

Survey Cost-Benefit Analyses

Statistical Staff

Sample Processors

Data Managers

Sonic tagging studies

Tag recovery studies

Tag retention studies

Archival tags

Tagging Efforts

Increased Sampling Density

Vital rates/habitat selection

Expand oceanographic data collection programs

Process Studies

Analysis of habitat associations

Analysis of habitat-specific fishing properties

Recruitment Indices

Demersal fish-habitat associations

Benthic impact studies

Evaluate effectiveness of survey tools

Evaluate survey design

Quantitative transects

Direct Observation Surveys

Habitat-specific species availability

Groundtruthing of acoustic signals

Analysis of habitat-specific fishing properties

Acoustic Surveys

Fish-oceanographic associations

Benthic fish-habitat associations

Analysis of habitat-specific fishing properties

Longline Surveys

Benthic impact studies

Trawl mortality studies

Fish-oceanographic associations

Benthic fish-habitat associations

Analysis of habitat-specific fishing properties

Trawl Surveys

Habitat-specific spawning studies

Seasonality studies

More frequent surveys in appropriate habitats

Sampling Frequency

Pelagic species

Demersal species

Less important

Lower priority

More important

Highest priority

and development and application of indices to monitor habitat condition related to fi sh production. Th e tiers indicate increasing levels of resolution in assessment data and an increased understanding of the functioning of fi shery habitats.

Progress can be made, and already is being made in a limited manner, simultaneously on all three tiers of habitat assessment. 

Th e accomplishments in the lower tiers will enhance the success in the higher tiers, but this process does not preclude working 

on tasks identifi ed in multiple tiers. Respondents to the HAIP Team’s questionnaire indicated that research needs vary across 

Science Centers, and thus the order in which the three tiers are addressed and the rate of advancement through the tiers will 

be Center-specifi c and depend on the research emphasis, staff expertise, and available infrastructure at each Science Center. 

Fundamental to the three-tier assessment structure is a feedback loop that uses results from studies in the higher tiers to inform 

the prioritization process of the lower tiers (Figure 22).

Figure 20

Fishery-independent data 

needs (grouped by bolded 

categories) as identifi ed by 

132 NMFS staff from six 

NMFS Fisheries Science 

Centers and three research 

disciplines (habitat/ecosystem scientists; population/

stock assessment scientists; 

and resource managers), 

averaged by two fi sh stock 

life styles (pelagic and demersal).
52

Tier 1 includes a comprehensive evaluation and synthesis of existing habitat information for FMP/

FSSI stocks by life stage. Tier 1 habitat assessments can be developed at any level of specifi city, 

depending on the available information. A minimum requirement is habitat-specifi c presence/absence species distribution, similar to EFH Level 1 data (Appendix 2). Tier 1 habitat assessments 

will result in limited improvements to EFH designations, associated risk assessments, and stock 

assessments (e.g. stock assessment analysts could have more information to identify, and perhaps 

adjust for, the eff ects of habitat on survey design and catch data). Completing Tier 1 habitat assessments will improve the knowledge base used to protect and conserve habitat, and will provide the 

much-needed basis for determining priorities for future research and development of assessment 

and monitoring capabilities. Tier 1 habitat assessments will be more thorough, timely, better quality-controlled, and better communicated than are the current assessments. 

In Tier 2, new or expanded data collection and research initiatives will be required to achieve a 

higher level of habitat assessments. Th e minimum biological data requirement is habitat-specifi c 

densities of species and life stages, similar to EFH Level 2 data (Appendix 2). Habitat maps for each 

region will provide relevant detail for all life stages of all species. Th ese maps and spatially explicit 

fi sh densities will be used to determine habitat-specifi c abundance or biomass. Habitat theory and 

proxies will be developed and applied to data-poor stocks. Habitat-specifi c coeffi cients of catchability will be developed for some species. 

Th e surveys and monitoring required for Tier 2 habitat assessments should be conducted at appropriate temporal resolutions (i.e. monthly, seasonally, annually, or longer), depending on the 

vulnerability of specifi c habitat types to natural and anthropogenic impacts. Developing indices of 

habitat condition and evaluating impacts of habitat change on the abundance of stocks by life stage 

will be part of Tier 2 assessments, and sources of uncertainty will be identifi ed for future research. 

Tier 2 products will be used in EFH amendments, improved fi shery-independent surveys, stock 

assessments, and analyses related to habitat protection and conservation.

 

Staff to process habitat data

Habitat-specific biological parameters

Habitat-specific commercial catch/effort data

Habitat-specific recreational catch/effort data

Habitat-specific fishery-independent abundance

Population and genetic structure

Fine-scale data for regulatory analyses

Research on environmental effects

Research on multispecies interactions

Staff to collect habitat-related data

Scientists to produce habitat assessments

Scientists to develop habitat assessment models

Habitat-related training to improve skills/tools

Staff to communicate results/conduct follow-up

Less needed

Lower priority

Most needed

Highest priority

PIFSC AFSC NWFSC SWFSC SEFSC NEFSC

Figure 21

Resources most needed to 

produce and/or use quality 

habitat assessments, as identifi ed by program managers 

at each of the six NMFS Fisheries Science Centers (one 

response per Center).

Figure 22

An illustration of the progress and feedback achieved 

among the three Tiers of 

Excellence for habitat assessments.

Tier 3

Tier 2

Tier 1
53

Tier 3 is the most challenging level of the HAIP, and will require substantial new or expanded data collection and research 

initiatives and the interdisciplinary cooperation among stock assessment scientists and habitat biologists and ecologists. Tier 3 

habitat assessments will incorporate habitat-specifi c vital rates (e.g. growth, reproduction, survival, and production) of FMP/

FSSI stocks by life stage, which is equivalent to EFH Levels 3 and 4 data (Appendix 2). Quantitative maps of habitat distribution and condition, which refl ect appropriate temporal resolution, also will be required. Priorities identifi ed in Tier 1 and Tier 

2 will guide new studies of vital parameters and community interactions linked to habitat types or condition. To fully achieve 

Tier 3, these inputs of geospatial biological and physical habitat data will need to be obtained through regular monitoring, such 

that the dynamics of the stocks, habitats, and ecosystems can be tracked through space and time. Both Tier 2 and Tier 3 will 

require new ways to combine geospatial data, and advances in data analyses, display, and modeling that can incorporate diverse 

data into assessments.

Tier 3 habitat assessments will provide quantitative estimates of fi sh productivity by habitat and ecosystem considerations (such 

as multispecies interactions, environmental eff ects, and spatial and seasonal analyses) for incorporation into stock assessments, 

thereby helping to meet the SAIP Tier 3 goals (NMFS, 2001; Appendix 3). Tier 3 habitat assessments and the SAIP Tier 3 

stock assessments they support will promote the development of meaningful IEA’s. Understanding the relative importance and 

the functional mechanisms of the major factors that aff ect productivity of stocks is fundamental to the goals and indicators, 

ecosystem models, and monitoring programs that comprise the IEA process. Findings from Tier 3 habitat assessments will 

contribute to a body of habitat theory that is integral to the formulation and implementation of EBFM. 

Timefr ames and Relationships Among Tiers 

Habitat assessments will vary by FMP stock, geographic scope, and application. It is likely that eff ort spent on a habitat assessment for one taxon may be relevant to taxa with similar habitat and life history traits. Even with this type of leveraging, Tier 2 

and Tier 3 assessments will require a signifi cant increase in staff and infrastructure for data collection and analyses.

Th e purpose of the HAIP tier system is to ensure that monetary investments and research eff orts result in the necessary information to improve NMFS’ habitat assessments. While there is some habitat data currently available in all three tiers, most are 

classifi ed as being in Tier 1 at best. Progress ideally should be made simultaneously in all three tiers. Implementing the HAIP 

over time, Tier 1 assessments for prioritized stocks will be completed in an estimated 3-5 years. Tier 2 assessments could be 

achieved within a 10-year timeframe, contingent on timely increases in necessary infrastructure and number of staff . Achieving 

Tier 3 assessments for prioritized stocks could be at least 10 years from full implementation of the HAIP and will be subject to 

revised projections based on Tier 2 fi ndings. Feedback from research results at the higher tiers to the prioritization process at 

the lower tiers will be necessary on a regular basis to realize an adaptive tiered framework. 

National Staffi ng Requirements to Meet Tier Goals 

Th e number of full-time staff currently assigned to habitat-related research activities and the number of additional staff required to achieve the objectives of each of the three Tiers of Excellence for habitat assessments have been summarized by type 

of habitat-related activity for each Science Center (Figure 23) and for all six Science Centers combined (Table 4); see Appendix 

7 for region-by-region descriptions of habitat programs and staffi ng requirements at the six Science Centers. Program managers 

estimate that the equivalent of 221 full-time staff are currently working on habitat-related activities throughout NMFS; this 

amounts to about 5% of total NMFS staff (estimated at 4,090). An alarming average of 33% of the 221 staff are contractors and 

students supported with transient, non NMFS funds. Th e pursuit of marine fi sheries habitat research in all the Science Centers 

has been possible due to the many successful partnerships with our academic colleagues and opportunistic funding from other 

NOAA offi ces, other Federal agencies, state agencies, and private foundations (Appendix 6). A comprehensive NMFS research 

program that is directly focused on the ecological value of marine habitats to fi shery stocks and on IEA’s will require signifi cant 

additional funding from NMFS.
54

Current Situation Tier 1 Requirements

80 100

PIFSC 

AFSC 

NWFSC 

SWFSC 

SEFSC 

NEFSC 

Tier 2 Requirements

Staff (including contractors and students)

Communicate assessment results

Improve habitat risk assessments

Refine/develop habitat models

Habitat into stock assessments

Refine/develop population models

Refine/develop survey methods

Determine habitat-specific vital rates

Produce habitat assessments

Process/convert raw habitat data

Collect habitat-related data

Tier 3 Requirements

Staff (including contractors and students)

0 20 40 60 80 100 0 20 40 60

0 20 40 60 80 100 0 20 40 60 80 100

Communicate assessment results

Improve habitat risk assessments

Refine/develop habitat models

Habitat into stock assessments

Refine/develop population models

Refine/develop survey methods

Determine habitat-specific vital rates

Produce habitat assessments

Process/convert raw habitat data

Collect habitat-related data

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NA

NMFS program managers have estimated that 557 additional staff devoted to habitat research and assessments will be required 

to fully implement and support the HAIP; this is about a 250% increase over current staffi ng levels. Additional staff for collecting, processing, and communicating habitat-related data and for producing habitat assessments is needed in each of the three 

Tiers of Excellence. Implementation of Tier 1 (i.e. improvements to habitat assessments using existing data) will require modest increases in staffi ng levels (100 new positions nationwide), particularly for database managers, statisticians, GIS specialists, 

and other analytical staff . Th e additional demands associated with Tier 2 (i.e. estimating habitat-specifi c densities of species 

and life stages; assessing spatial extent of habitats) call for another 169 staff over current levels throughout NMFS. To achieve 

Activity Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

Collect habitat-related data 97 30 64 94 72 166

Process and convert raw habitat data into usable products 46 34 32 66 44 110

Produce habitat-specifi c assessments 22 27 32 59 59

Determine habitat-specifi c vital rates over time 64 64

Refi ne existing habitat-related survey methods/tools and develop new ones 23

Refi ne existing population models and develop new habitat-related ones 16

Incorporate habitat and ecosystem information into stock assessments at SAIP Tier 3 41 41

Refi ne existing habitat and ecosystem models and develop new ones 28 28 28 56

Develop improved habitat risk assessments 22 22

Communicate improved assessment results and conduct other follow-up work 17 9 13 22 17 39

Total 221 100 169 269 288 557

Table 4

Number of additional full-time staff required to meet the three Tiers of Excellence by type of activity for all NMFS Fisheries Science Centers combined. Number of staff in each category does not necessarily refl ect the absolute number of individuals involved in these activities, because some 

individuals may divide their time between several activities. Estimated numbers of staff include permanent employees, as well as contractors and 

students that have only temporary funding. Grey cells indicate that an activity did not apply in a particular tier, according to the questionnaire. See 

Appendix 7 for staffi ng requirements at each of the six Science Centers. 

Figure 23

Current number of full-time 

staff, and the additional 

number of staff required to 

meet the criteria of the three 

Tiers of Excellence, for ten 

habitat-related activities at 

each NMFS Fisheries Science Center. Number of staff 

was estimated by program 

managers from each Center 

and includes permanent 

employees, as well as contractors and students that 

have only temporary funding. “NA” indicates that a 

habitat activity did not apply 

to a particular tier, according 

to the questionnaire.
55

Tier 1 and Tier 2 habitat assessments, 269 new staff will be needed. For Tier 3 assessments, another 288 staff will be required 

to determine habitat-specifi c vital rates and incorporate habitat and ecosystem information into stock assessments. As part of 

these staffi ng needs, the HAIP Team recommends the establishment of a Habitat Assessment fellowship program, similar to 

the Stock Assessment and Economics fellowship programs, which would provide funding for graduate students and post-doctoral associates of specifi c disciplines to advance habitat modeling, evaluation, and assessment eff orts. 

Th e NEFSC currently has the largest habitat program (54 staff ), followed by the SEFSC (47 staff ), the NWFSC (40), the 

Southwest Fisheries Science Center (SWFSC) (33), the PIFSC (30), and the AFSC (17; Table 5). Considering the sum of 

Tier 1 and Tier 2 staffi ng requirements, the NEFSC requires an additional 44% staff above the current situation; the SEFSC 

(168%); the NWFSC (160%); the SWFSC (97%); the PIFSC (123%); and the AFSC (194%). In addition to new staff , improvements to data management and communication systems, program support (e.g. vessel contracts; advanced technology 

survey and experimental tools and equipment), and infrastructure will be necessary to meet the requirements of the three tiers.

Th ese additional operational costs are roughly estimated to be equal to the expected increases in staffi ng funds that will be required to advance the quality of habitat assessments to the highest tier.

Th e estimated number of additional staff refl ects the ever-increasing demands being placed on NMFS to eff ectively conserve, 

protect, and manage fi shery species and other LMR’s within the U.S. EEZ; to consult on Federal actions that may impact marine habitats; to respond to threats to habitats, restore damaged habitats, and mitigate habitat loss; to understand the role of 

habitat in trophic and community interactions and other critical ecosystem processes; to provide increasingly fi ne-scale spatially explicit habitat data for improved stock assessment modeling; and to predict the eff ects of climate change on marine habitats 

and associated fi shery species. Additionally, the HAIP staff requirements will complement other NMFS plans, in particular 

the SAIP (NMFS, 2001; Appendix 3), which addresses the resources needed to improve NMFS fi shery stock assessments to 

an adequate or better level. Th e SAIP identifi es the need to include habitat and ecosystem information in stock assessments to 

advance to the “Next Generation” of assessment science, but makes few provisions for the resources necessary to accomplish 

this signifi cant task. Th ese and related plans, initiatives, and activities (such as those related to protected resources and other 

non FSSI stocks) should be integrated as one comprehensive approach to fi sheries stock assessments and EBFM.

Program Operation Needs: Tools, Technology, and Infrastructure 

In addition to increased support for staffi ng, the habitat science program presented in the HAIP can only be realized with concomitant funds for needed program operations, including the necessary tools, technology, and infrastructure. NMFS’ current 

level of available infrastructure and advanced technologies are inadequate to meet the needs for improved habitat assessments. 

Time on chartered vessels as well as on NOAA ships and advanced technology survey tools likely will be the most costly items 

needed to achieve improved assessments. Characterizing and delineating the area and boundaries of habitats for some stocks 

(e.g. west coast groundfi sh species in deep water or highly migratory tunas) will be an extensive undertaking that requires improved technologies and additional time at sea. Both remote and direct-observation technologies are needed to effi ciently and 

Center Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

PIFSC 30 22 15 37 63 100

AFSC 17 17 16 33 36 69

NWFSC 40 20 44 64 44 108

SWFSC 33 10 22 32 34 66

SEFSC 47 24 55 79 55 134

NEFSC 54 7 17 24 56 80

Summed Staff 221 100 169 269 288 557

Table 5

Number of additional full-time staff 

required to meet the three Tiers of 

Excellence for improved habitat 

assessments at each Science Center and for all Centers combined. 

Estimated number of staff includes 

permanent employees, as well as 

contractors and students that have 

only temporary funding.
56

accurately survey more area more frequently, and to accurately monitor important habitat attributes. Many of these technologies currently are being developed (for example, see Appendix 6), with emphasis on improving optical and acoustic sensors. 

Improved technology will integrate these sensors with more eff ective sampling platforms, such as increasing swath of area being surveyed by ships and aircraft in order to improve data collection effi ciencies and increase resolution of the observations 

to improve accuracy of the data. Optical and acoustic sensors also are being integrated into submersibles, ROV’s, and AUV’s 

to increase sampling capability and versatility. A signifi cant challenge in adopting enhanced sampling capabilities will be the 

management of the increased volume of data. Improved hardware and soft ware will be necessary to effi ciently process the data 

and to ensure data availability.

It will be important to assess the adequacy of current technologies and infrastructure that is available both nationally and regionally to support the goals established in the HAIP. By way of example, a careful inventory was conducted by the NEFSC to 

assess its current and future technology and infrastructure needs (Hare et al., 2007). Th ey identifi ed platforms and sampling 

devices that are appropriate to collect habitat data for various trophic levels of organisms. Th e HAIP Team recommends that 

similar assessments be conducted, perhaps through a series of regional and national workshops, in order to better estimate the 

level of operational (nonstaffi ng) support required to collect and analyze the habitat data identifi ed in the HAIP. 

Th e HAIP Team also recommends that a National Habitat Assessment Workshop (NHAW) be convened in the near future 

to begin implementation of the HAIP and to develop a prioritized agenda of current habitat topics to be addressed at small, 

focused workshops. Currently, NMFS supports biennial National Stock Assessment Workshops (NSAW) and National Economics and Social Science Workshops, which provide opportunities to build coordinated programs, address issues of national 

concern, and promote interdisciplinary research. Th e establishment of a comparable biennial national forum for habitat science 

would advance the implementation of the HAIP recommendations to develop a national habitat science program. Given that 

one of the major objectives of the HAIP is to integrate aspects of habitat into stock assessments, the HAIP Team recommends 

that the fi rst NHAW be held in conjunction with the NSAW.

In addition to a biennial NHAW, the HAIP Team recommends that focused workshops be convened periodically (perhaps in 

conjunction with NHAW or other annual national meetings such as that of the American Fisheries Society) to address specifi c research topics (e.g. incorporation of habitat variables into a specifi c stock assessment). Th ese workshops would provide 

a directed level of scientifi c discourse that could lead to the peer-reviewed publication of specifi c habitat assessments or to the 

development of budget initiatives. 
57

Section 6: Measuring Performance

At a Glance

• Performance measures will help NMFS monitor HAIP accomplishments and demonstrate eff ectiveness of the 

HAIP investments.

• Output-oriented performance measures for the HAIP should track the quantity and quality of biological and 

geospatial information and habitat condition indices that contribute to habitat assessments of FSSI stocks.

• Outcome-oriented performance measures for the HAIP should track the number (or percentage) of FSSI 

stocks for which the role of habitat in stock dynamics has been assessed at increasing levels of understanding.

Performance measures are necessary for eff ective management of LMR’s as well as the habitat assessment program, and are a 

requirement of the NOAA budget process. Th e formal adoption of performance measures is a function of the planning and 

budget process,10 but should be guided by the HAIP. Th e HAIP, therefore, will provide context for and describe characteristics 

of performance measures so that the eff ectiveness of the investments made to improve habitat assessments can be tracked. 

Development of performance measures begins with identifi cation of a strategic goal or ultimate purpose of a plan (Espinosa, 

2007). Th e strategic goal of the HAIP is to determine the function of habitats in the production of FSSI and other FMP stocks 

and related ecosystem processes in support of management decisions that are the mandated responsibility of NMFS. Th is 

information is interpreted through habitat assessment, defi ned as both a process and the products associated with obtaining, 

consolidating, analyzing, and reporting the best available information on habitat characteristics relative to the population dynamics of fi shery species.

Performance is measured by tracking progress made from the starting condition (baseline) toward a target over a defi ned time 

period. A useful performance measure contains an indicator to be measured, a unit of measure for quantifying the indicator, a 

baseline that establishes the initial condition, and a target for the desired level of performance (Cohen and Bortniak, 2009). 

Th ere is a hierarchy of performance measures, with numerous outputs (i.e. things that a program does, such as making observations) leading to a smaller number of outcomes (i.e. desired eff ects of the program). 

Outcome performance measures relate to a program’s mission and mandates and to the societal benefi ts they support, but these 

outcomes may be aff ected by many factors that are external to the program. Achieving and maintaining healthy and sustainable 

fi sheries is an example of an outcome that addresses the mandates of the MSRA. A successful marine fi sheries habitat science 

program will contribute to achieving this outcome, but other factors external to the program also play signifi cant roles. Output 

performance measures, by contrast, are focused internally on the program, and address the quantity, quality, and timeliness of a 

program’s products and services. Output measures relate to the program’s productivity and activities, and are primarily aff ected 

by factors closely controlled by the program. 

A coordinated suite of outputs and outcomes is needed to evaluate program performance and to justify continued growth of 

the program. In addition, both outputs and outcomes can be hierarchical. As a successful program grows, the outputs increase 

in quantity and sophistication, progressively contributing to more comprehensive outcomes that support NMFS’ mission and 

provide increased benefi ts to society.

10NMFS’ policy directive for developing and adopting performance measures can be found at https://reefshark.nmfs.noaa.gov/f/pds/publicsite/documents/policies/33-

102.pdf.
58

Performance measures for the HAIP should tie habitat assessments to NMFS mandates. Th e indicators must be quantifi able, 

respond to available resources, and track criteria relevant to the essential elements of a habitat science program. If possible, 

performance measure targets should refer to criteria that already have been formally adopted through legislation or regulations

(e.g. EFH regulations; see Appendix 2), rather than adopt new, and possibly ad hoc, criteria. Th e EFH fi nal rule requires that 

EFH information be reviewed and updated at least every fi ve years. To be consistent with this requirement, it is suggested that 

all data syntheses and assessments related to performance measures should be evaluated and updated, as necessary, at least every 

fi ve years.

Output-oriented performance measures for the HAIP (Table 6) should relate to the three Tiers of Excellence of habitat assessments (see Section 5, p. 49). Th ese three tiers, in turn, are related to EFH Levels 1-4 data, which refl ect the level of detail 

and sophistication of the underlying scientifi c information. Th e indicators for the output performance measures should track 

the scientifi c activities (e.g. habitat-specifi c surveys of fi sh stocks) and products (e.g. GIS maps of habitats) that are needed to 

produce habitat assessments at each tier. Outputs for Tier 1 would be based on the comprehensive discovery and synthesis of 

currently existing biological and geospatial information. Outputs for Tier 2 would be based on the development of quantitative 

data of habitat-specifi c densities and habitat availability, which provide statistically reliable stock abundance by habitat type. 

Outputs for Tier 3 would be based on the development of quantitative data of habitat-specifi c vital rates and monitoring data 

on habitat status, which will support statistically reliable assessments of stock productivity by habitat type. 

All three tiers of habitat assessments include the development and application of habitat condition indices. Th ese indices are 

numerical indicators for tracking the status and trends of habitat for each of the life stages of FSSI and other FMP stocks. 

Th ese indices will provide essential measures for assessing change in the amount and condition of habitat and the eff ects on the 

carrying capacity of the environment, productivity, and the level of sustainable fi shing. Examples of habitat condition indices 

include the area of an essential habitat for a particular life-history stage of an FSSI stock, such as salt-marsh edge for juvenile 

shrimp, or a measure of environmental quality, such as the volume of water with suffi cient dissolved oxygen for a species to 

maintain normal physiological functions. At the highest level, these indices will contribute to assessments of ecosystem sustainability. Determining baselines will require detailed analyses of the current scientifi c literature and datasets; progress toward 

targets will depend on the resources made available as the HAIP program develops.

Outcome performance measures appropriate for the HAIP (Table 6) should relate to the provision of information on the function of habitats in the production of FSSI and other FMP stocks and ecosystem processes in the form of habitat assessments 

that support the scientifi c and management decisions of NMFS. Th ese measures should be based on the graduated scale inherent in the three Tiers of Excellence of habitat assessments. Th e indicator and unit of the outcome performance measures would 

be the number (or percentage) of FSSI stocks for which habitat assessments address the role of habitats in determining stock 

dynamics at a given Tier of Excellence. Reaching these outcomes for each tier would provide fi sheries scientists, stock assessors, 

and fi sheries and habitat managers with comprehensive summaries of information on the role of habitat in determining the dynamics of FSSI stocks at the level of detail specifi c to each habitat assessment tier. For Tier 1, an outcome performance measure 

would be the number of habitat assessments that summarize the currently existing information on the relationships between 

the life stages of FSSI stocks and their habitats. For Tier 2, the outcome performance measure would be the number of habitat 

assessments that contain quantitative information on density of the life stages of FSSI stocks by habitat type. Outcome for Tier 

3 would be measured by the number of habitat assessments that are based on habitat-specifi c rates of growth, reproduction, 

survival, and, ultimately, production of FSSI stocks. At present, the baseline for Tier 3 habitat assessments is nearly zero (see 

Figure 15, p. 44), especially when all life stages are considered. Th e recommended target would be Tier 3 habitat assessments 

for all 230 of the FSSI stocks.
59

Tier 1: Comprehensive evaluation and synthesis of existing information on the habitat associations for all life stages of FSSI stocks

Outputs

Biological Information Number of life stages of FSSI stocks1

 for which existing habitat information has been assembled and interpreted. The minimum 

level of detail is presence/absence data by habitat type (EFH Level 1 data), but all levels of detail are relevant.

Geospatial Habitat Information Number of habitat types that have been identifi ed and described in suffi cient detail for interpreting and mapping existing 

biological information for every life stage of FSSI stocks. The minimum level of detail is qualitative text descriptions and the 

portrayal of habitat associations on generalized regional maps.

Habitat Condition Indices Number of life stages of FSSI stocks for which numerical indicators of the status and trends of habitat have been developed 

and applied in habitat assessments.

Outcome

Habitat Assessments Number of summaries of existing information on the relationships between life stages of FSSI stocks and their habitats, including application of habitat indices. The minimum level of detail is text description and portrayal, on generalized regional maps, of 

the distribution of these life stages and the occurrence of habitat types, but all levels of detail are relevant.

Tier 2: Quantitative estimates of habitat use by FSSI stocks and life stages

Outputs

Biological Information Number of life stages of FSSI stocks for which density data are available by habitat type (EFH Level 2 data).

Geospatial Habitat Information Area2

 for which geospatial information is available on the distribution of important habitat characteristics of the life stages of 

FSSI stocks, to be used with density estimates as relevant to stock assessments and related areas of fi sheries science (e.g. 

survey design, catchability coeffi cients, habitat characterization).

Habitat Condition Indices Number of life stages of FSSI stocks for which habitat condition indices have been developed and applied at the level of density by habitat type.

Outcome

Habitat Assessments Number of comprehensive summaries based on Tier 2 quantitative information on habitat-specifi c densitites of FSSI stocks.

Tier 3: Quantitative estimates of fi sh productivity by habitat for FSSI stocks

Outputs

Biological Information Number of life stages of FSSI stocks for which growth, reproduction, survival rates (EFH Level 3 data), or productivity (EFH 

Level 4 data) within habitats are available.

Geospatial Habitat Information Area of habitat of the life stages of FSSI stocks for which condition is monitored at spatial and temporal resolutions suffi cient 

to support status assessments based on habitat indices at the level of growth, reproduction, survival, or production by habitat

type.

Habitat Condition Indices Number of life stages of FSSI stocks for which habitat condition indices have been developed and applied at the level of 

growth, reproduction, survival, or production by habitat type, and which can contribute to the science underlying EBFM decisions.

Outcome

Habitat Assessments Number of comprehensive summaries of Tier 3 quantitative information on the growth, reproduction, survival, or production of 

FSSI stocks by habitat type.

1

Five life stages are recognized for most (but not all) of the 230 FSSI stocks: egg, larva, juvenile, adult, and spawning. Thus, the baseline and target would be assessed against approximately 

1,150 life stages.

2

Scale (e.g. square nautical miles, square kilometers, hectares) depends on life history of species and stage, type of habitat, and the scientifi c question being addressed.

Table 6

Potential output-oriented and outcome-oriented performance measures of the Habitat Assessment Improvement Plan.

61

Section 7: Connecting HAIP to Other Habitat 

Science Programs

At a Glance

• It is essential that NMFS continue to foster partnerships with other groups, both within and outside of 

NOAA.

• All partners will benefit from, as well as contribute to, the success of the HAIP.

• NMFS should unite with other NOAA line offices to develop a NOAA-wide strategic plan for habitat science 

and assessments.

Habitat science is conducted for a variety of reasons and with disparate objectives throughout NOAA, other Federal and state 

resource agencies, universities, and private institutions. Th e breadth of multidisciplinary expertise and the extent of physical 

resources necessary to conduct a coherent habitat science program have demanded that NMFS enter into partnerships not only 

with other NOAA offi ces but also with other governmental agencies (e.g. USGS, National Aeronautics and Space Administration) and nongovernmental entities (particularly academia). Most of these partnerships have been formed independently 

at each of the Science Centers on an ad hoc basis, drawing scientists together based on complementary research interests and 

needs. It is essential that NMFS continue to foster partnerships with other groups, both within and outside of NOAA.

To achieve its goals, the HAIP should especially complement, coordinate, and leverage the expertise found in existing NMFS 

programs. For example, NMFS’ Advanced Sampling Technology Working Group (ASTWG) (Appendix 6) currently supports 

the development of sampling technology for stock assessments and the SAIP (Appendix 3) and could similarly assist in meeting the goals and objectives of the HAIP. ASTWG already has identifi ed the characterization of benthic habitat as a key theme 

in its funding process, and has supported projects and workshops that contribute to improved habitat assessments (Somerton 

and Gledhill, 2005). HAIP also will coordinate with and enhance those programs focused on ecosystem synthesis, such as 

Fisheries and the Environment (FATE) (Appendix 6) and the Comparative Assessments of Marine Ecosystem Organization 

(CAMEO) (Appendix 6). Th e purpose of FATE is to encourage the inclusion of environmental data in the stock assessment 

process; this program potentially can play a signifi cant role in developing approaches to include habitat-related parameters in 

stock assessments. CAMEO is an emerging eff ort between NMFS and the National Science Foundation that supports research 

on the complex dynamics controlling productivity, behavior, population connectivity, climate variability, and anthropogenic 

pressures associated with living marine resources and critical habitats. 

 

Many potential non NMFS partners within NOAA have habitat-related interests and capabilities (see Appendix 6 for a more 

comprehensive synopsis). Within OAR, Sea Grant comprises 32 university-based programs, many of which conduct habitat 

research. Ocean Exploration and Research supports missions to explore unknown areas of the oceans aboard the dedicated 

vessel, Okeanos Explorer. Within the National Ocean Service (NOS), the National Centers for Coastal and Oceanic Science 

conduct and support research, monitoring, and assessments, focusing on estuaries, coral reefs, and National Marine Sanctuaries. NOS also manages programs that are integrated across line offi ces and can be important partners in HAIP-related activities. 

Habitat studies outlined in the HAIP will use and provide data in coordination with IOCM, as well the Integrated Ocean Observing System (IOOS) and regional subsystems. Th e integration and delivery of habitat data will adhere to IOOS standards 

for data-set descriptions (metadata), discovery, accessibility, and security.

Th e diverse data necessary for habitat delineation and assessment could be the fi rst test of the use of the enterprise data sys-
62

tems being proposed for NMFS. Habitat activities outlined in the HAIP would add value to, as well as benefi t from, ongoing 

NOAA matrix programs such as the Coral Reef Conservation Program (Appendix 6). Full implementation of the HAIP will 

contribute to both national and regional programs such as the National Status and Trends Program, the National Estuarine 

Eutrophication Assessment Program, the Monitoring and Event Response for Harmful Algal Blooms Research Program, the 

National Marine Sanctuaries habitat monitoring programs, and invasive species monitoring programs.

One partnership to which HAIP-directed research would be especially relevant is the National Fish Habitat Action Plan (NFHAP: http://fi shhabitat.org/), which is assessing the causes of declines in fi sh habitat with an emphasis on inland, freshwater 

systems. Led by the U.S. Fish and Wildlife Service, partners include the USGS, the National Fish and Wildlife Foundation, 

fi shing and conservation organizations and industry, and, more recently, NMFS. Th e NFHAP program has taken shape over 

the last several years, marked by the publication of the “Action Plan” in 2006 (Association of Fish and Wildlife Agencies, 2006) 

and the recent release of a draft report, “A Framework for Assessing the Nation’s Fish Habitat” (National Fish Habitat Science 

and Data Committee, 2008). Th e fi rst NFHAP national assessment will be completed in 2010, with updates planned at 5-

year intervals. NMFS’ participation in future assessments could provide vital coastal and marine components, given suffi cient 

resources, requisite data, and improved assessments generated by the HAIP. 

Despite the diversity of other habitat-related eff orts both within and outside of NOAA, the research proposed in the HAIP 

is unique in its focus on habitat functions in relation to fi shery productivity and in linking habitats with FSSI and other FMP 

stocks. Th is habitat science has been recognized as a need within NMFS for some time, and implementation of the HAIP will 

address gaps in the stock assessment process as well as provide a way forward for NOAA to develop EBFM. NMFS should 

unite with other NOAA line offi ces to develop a NOAA-wide strategic plan for habitat science and assessments.
63

Section 8: The Benefits of Implementing the HAIP

Th e Marine Fisheries Habitat Assessment Improvement Plan (HAIP) defi nes NMFS’ unique role in conducting habitat science and in developing habitat assessments to meet its mandated responsibilities to sustain marine fi sheries and associated habitats. A coordinated national program envisioned through the HAIP will result in improved science addressing the relationships 

between fi shery species and their habitats, which is fundamental to meeting the agency’s mandates and is a major goal of many 

NMFS strategic planning documents. Moreover, the habitat needs identifi ed in the HAIP concur with the priorities for habitat 

research that have been identifi ed by each Science Center in NMFS’ Our Living Oceans habitat report (NMFS, In press) and 

in the strategic plan for NOAA’s Habitat Program (NMFS, 2009c; Appendix 8).

Th rough the HAIP, NMFS off ers a guide to conduct its diverse habitat research, monitoring, and assessments and to develop 

budget alternatives and increased support for habitat science. A comprehensive NMFS research program that is directly focused on the ecological value of marine habitats to fi shery stocks and on integrated ecosystem assessments (IEA’s) will require 

signifi cant additional funding from NMFS.

Improved habitat science capabilities and products that result from a fully supported and implemented HAIP will meet the 

mandated needs of NMFS. Improved habitat data collection and analytical methods, and coordinated and comprehensive 

habitat inventories, assessments, and indicators are critical in understanding the role of habitat in fi sh and fi shery production. 

Developing this information through the HAIP and eff ectively communicating it to managers, stakeholders, and the general 

public will provide important benefi ts to the nation.

With full support and implementation of the HAIP:

0 NMFS will improve its capabilities to identify those habitats critical to the sustainability of our nation’s fi sheries, living marine resources, and ecosystems. Th is will lead to:

• More rigorous, quantitative habitat assessments that enable NMFS to more effi ciently and eff ectively identify and protect EFH and HAPC from fi shing and other impacts; 

• Reduced risks to fi sh production, and many other ecosystem services, due to habitat degradation or loss; and

• More eff ective habitat restoration projects that enhance fi sh production.

0 Scientists will have habitat information at appropriate spatial and temporal scales to improve design and interpretation of 

stock surveys and to use in current stock assessment models and support model improvements. Th is will lead to:

• Improved fi eld surveys; 

• Improved stock assessments; and

• Reduced need for high precautionary limits in fi sheries management.

0 NMFS will have the necessary information to deliver high-quality habitat science that can be readily applied by fi shery managers. Th is will lead to:

• A more comprehensive understanding of the role of habitat in trophic and community interactions and other critical 

ecosystem processes, resulting in successful ecosystem-based fi shery management (EBFM); and

• Fishery management decisions that have a greater positive impact on the long-term sustainability of habitats, fi sh production, and many other ecosystem services.

0 NMFS will better understand, monitor, and predict the eff ects of climate change and other anthropogenic impacts on marine 

habitats and associated species distribution, reproduction, growth, and survival. Th is will lead to:

• Signifi cant advancements in the implementation of EBFM; 
64

• Increased effi ciency in conducting and applying marine habitat science; and

• Fishery management decisions that are robust to the eff ects of climate change and other anthropogenic impacts.

0 Th e nation will be better able to address confl icting demands on limited marine resources through eff ective coastal and marine spatial planning and IEA’s. Th is will lead to:

• Reduced impacts to coastal and marine habitats and fi sh stocks; 

• Increased ecosystem health and sustainability; and

• Th e preservation of critical ecosystem services that support the social and economic well-being of the nation.

0 Controversy surrounding management decisions will be reduced, thereby allowing NOAA and NMFS to focus on the most 

pressing scientifi c and management issues and to reduce costs and delays associated with litigation. 

0 NMFS partnerships, both within and outside of NOAA, will benefi t in their mutual pursuits of habitat delineation and assessment eff orts.
65

Section 9: Recommendations

Th e HAIP is the fi rst step in building a comprehensive, coordinated national science-based enterprise to eff ectively evaluate, 

monitor, and manage habitats for coastal and marine fi shery species. To that end, the HAIP Team makes the following recommendations:

• NMFS and NOAA should develop new budget and staffi ng initiatives to fund habitat science that is directly linked to 

NMFS mandates.

• NMFS should develop criteria to prioritize stocks and geographic locations that would benefi t from habitat assessments.

• NMFS’ habitat and stock assessment scientists should work together to initiate demonstration projects that incorporate 

habitat data into stock assessment models, perhaps focusing on well-studied species. 

• NMFS should identify and prioritize data inadequacies for stocks and their respective habitats, as relevant to information 

gaps identifi ed in the HAIP. 

• NMFS should increase collection of habitat data on fi shery-independent surveys and develop a plan for better utilizing new 

technologies (e.g. multibeam sonars) aboard the expanding NOAA fl eet of Fishery Survey Vessels (FSV’s). 

• NMFS habitat scientists should engage partners within and outside of NOAA to exchange information about programs and 

capabilities. Habitat data collection eff orts and data management initiatives should be coordinated and data management 

systems and integration applications should be upgraded and expanded to improve data accessibility and syntheses.

• NMFS should convene regional and national workshops to develop strategies to integrate habitat science and assessments, 

stock assessments, and IEA’s. Workshops will advance the implementation of the HAIP and foster communication among 

habitat/ecosystem researchers, stock assessment scientists, and resource managers.

• NMFS should establish a habitat assessment fellowship program and provide funds to graduate students and post-doctoral 

associates of specifi c subdisciplines that would advance habitat modeling, evaluation, and assessment eff orts.

• NMFS should unite with other NOAA line offi ces to develop a NOAA-wide strategic plan for habitat science and assessments in support of the nation’s ocean policy priorities for EBFM, CMSP, and the use of IEA’s.

67

Anderson, T. J., and M. M. Yoklavich. 2007. Multispecies habitat associations of deepwater demersal fi shes off central California. Fishery 

Bulletin 105:168-179.

Anderson, T. J., M. M. Yoklavich, and S. L. Eittreim. 2005. Linking fi ne-scale groundfi sh distributions with large-scale seafl oor maps: issues 

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Islands (Compilers), Stock assessment and fi shery evaluation report for the groundfi sh resources of the Bering Sea/Aleutian Islands 

Regions, p. 707-776. North Pacifi c Fishery Management Council, Anchorage, AK.

Wilderbuer, T. K., D. G. Nichol, and K. Aydin. 2008a. Arrowtooth fl ounder. In Plan Team for the Groundfi sh Fisheries of the Bering Sea 

and Aleutian Islands (Compilers), Stock assessment and fi shery evaluation report for the groundfi sh resources of the Bering Sea/Aleutian Islands Regions, p. 643-706. North Pacifi c Fishery Management Council, Anchorage, AK.

Wilderbuer, T. K., D. G. Nichol, and J. Ianelli. 2008b. Yellowfi n sole. In Plan Team for the Groundfi sh Fisheries of the Bering Sea and Aleutian Islands (Compilers), Stock assessment and fi shery evaluation report for the groundfi sh resources of the Bering Sea/Aleutian Islands 

Regions, p. 521-592. North Pacifi c Fishery Management Council, Anchorage, AK. 

Williams, E. H. and S. Ralston. 2002. Distribution and co-occurrence of rockfi shes (family: Sebastidae) over trawlable shelf and slope habitats of California and southern Oregon. Fishery Bulletin 100:836-855.

Yoklavich, M., M. Love, and K. Forney. 2007. A fi shery-independent assessment of an overfi shed rockfi sh stock, cowcod (Sebastes levis), 

using direct observations from an occupied submersible. Canadian Journal of Fisheries and Aquatic Sciences 64:1795-1804.

Yoklavich, M. M., and V. O’Connell. 2008. Twenty years of research on demersal communities using the Delta submersible in the Northeast 

Pacifi c. In J. R. Reynolds and H. G. Greene (Editors), Marine habitat mapping technology for Alaska, p. 143-155. Alaska Sea Grant 

College Program, University of Alaska, Fairbanks.

Zimmerman, M. 2003. Calculation of untrawlable areas within the boundaries of a bottom trawl survey. Canadian Journal of Fisheries and 

Aquatic Sciences 60:657-669.

Zimmermann, R. J., and J. M. Nance. 2001. Eff ects of hypoxia on the shrimp fi shery of Texas and Louisiana. In N. N. Rabalais and R. E. 

Turner (Editors), Coastal hypoxia: consequenses for living resources and ecosystems, p. 293-310. American Geophyiscal Union, Washington, DC.
75

First and foremost, the HAIP writing team thanks John Boreman for recognizing NMFS’ immediate need to improve habitat 

science in support of fi sheries management decisions and for initiating the development of the “Marine Fisheries Habitat Assessment Improvement Plan”. We also greatly appreciate Steve Murawski, Pat Montanio, Ned Cyr, David Detlor, Brian Pawlak, 

and the NMFS Science Center directors for their continued support and guidance in developing the HAIP. Additionally, we 

acknowledge the valuable input received from Richard Methot throughout HAIP production. We thank each Science Center 

division director of the HAIP team members for recognizing the importance of these eff orts and allowing their staff the time to 

develop the Plan over the past 18 months. Our thanks also go to all NMFS scientists and managers who contributed essential 

responses to questionnaire surveys, informal focus group discussions, and periodic briefi ngs. In particular, Steve Copps, Steve 

Giordano, Karen Abrams, Garry Mayer, Jim Bohnsack, Tom Laidig, Phil Levin, Mary Ruckelshaus, and Jeff Fugioka assisted 

with writing and reviewing various sections of the Plan, and Rita Curtis off ered input on questionnaire development. Many 

NMFS scientists and managers, as well as the staff of several FMC’s and Commissions, improved draft s of the HAIP through 

the NMFS internal review process. Dave Stanton, Willis Hobart, and Fran Pfl eiger assisted with production and copyediting.

Acknowledgements

77

ADAPT: adaptive framework-virtual population analysis stock assessment model

AFSC: NMFS Alaska Fisheries Science Center

AKRO: NMFS Alaska Regional Offi ce

ASPIC: A Stock Production Model Incorporating Covariates

ASTWG: NMFS Advanced Sampling Technology Working Group

AUV: autonomous underwater vehicle

CAMEO: Comparative Assessments of Marine Ecosystem Organization

CFMC: Caribbean Fishery Management Council

COP: U.S. Commission on Ocean Policy

CMSP: coastal and marine spatial planning 

CPUE: catch-per-unit-of-eff ort

DIDSON: dual-frequency identifi cation sonar

DPSIR: driver-pressure-state-impact-response

EBFM: ecosystem-based fi sheries management

EEZ: Exclusive Economic Zone

EFH: essential fi sh habitat

EIS: Environmental Impact Statement

ESA: Endangered Species Act

F/HC: NMFS Offi ce of Habitat Conservation

F/ST: NMFS Offi ce of Science and Technology

FATE: Fisheries and the Environment program

FMC: Fishery Management Council

FMP: Fishery Management Plan

FRAM: NWFSC Fishery Resource Analysis and Monitoring division

FSSI: NMFS Fish Stock Sustainability Index

FSV: Fishery Survey Vessel

GAM: generalized additive model

GMFMC: Gulf of Mexico Fishery Management Council

GIS: geographic information systems

GOMC: Gulf of Maine Council on the Marine Environment

HAIP: “Habitat Assessment Improvement Plan”

HAPC: habitat areas of particular concern

HMS: highly migratory species

IEA: integrated ecosystem assessment

IOCM: Integrated Ocean and Coastal Mapping

IOOS: U.S. Integrated Ocean Observing System

LIDAR: light detection and ranging

LME: large marine ecosystem

LMR: living marine resource

LNG: liquefi ed natural gas

M: natural mortality for a fi sh stock

MAFMC: Mid-Atlantic Fishery Management Council

MPA: marine protected area

MSRA: Magnuson-Stevens Conservation and Management Reauthorization Act of 2006

List of Acronyms
78

NCCOS: NOAA’s National Centers for Coastal Ocean Science

NEFMC: New England Fishery Management Council 

NEFSC: NMFS Northeast Fisheries Science Center

NFHAP: National Fish Habitat Action Plan

NHAW: National Habitat Assessment Workshop

NMFS: NOAA’s National Marine Fisheries Service

NOAA: National Oceanic and Atmospheric Administration

NOS: NOAA’s National Ocean Service

NPFMC: North Pacifi c Fishery Management Council

NRC: National Research Council

NSAW: National Stock Assessment Workshop

NURP: NOAA’s National Undersea Research Program

NWFSC: NMFS Northwest Fisheries Science Center

OAR: NOAA’s Offi ce of Oceanic and Atmospheric Research

OE: Offi ce of Ocean Exploration in OAR

PFMC: Pacifi c Fishery Management Council

PIFSC: NMFS Pacifi c Islands Fisheries Science Center

q: catchability coeffi cient

ROV: remotely operated vehicle

SAFMC: South Atlantic Fishery Management Council

SAIP: “Marine Fisheries Stock Assessment Improvement Plan”

SEAMAP: Southeast Area Monitoring and Assessment Program

SEFSC: NMFS Southeast Fisheries Science Center

SOOP: Ship-Of-Opportunity Program

SS: Stock Synthesis

SSH: sea surface height

SST: sea surface temperature

SWFSC: NMFS Southwest Fisheries Science Center

USGS: U.S. Geological Survey

WPFMC: Western Pacifi c Fishery Management Council
79

Acts / 

Executive Orders Summary

NOAA 

Lead Date

Magnuson-Stevens 

Fishery Conservation and 

Management Act

• Established U.S. management authority over the U.S. Exclusive Economic Zone (generally 

3-200 nautical miles from shore). Also established eight Regional Fishery Management 

Councils (FMC’s) with responsibility for the preparation of fi shery management plans (FMP’s) 

to sustainably manage fi shery stocks and their habitats within their regions.

• States that any FMP may include management measures in the plan to conserve target and 

nontarget species and habitat, considering the variety of ecological factors affecting fi shery 

populations.

• Defi nes essential fi sh habitat (EFH) and includes provisions for conserving EFH through 

the following: 1) identify and describe EFH for managed species in FMP’s; 2) minimize the 

adverse effects of fi shing on EFH to the extent practicable; and 3) identify other actions 

to conserve and enhance EFH. The Act further requires that Federal agencies consult with 

NMFS on actions that may adversely affect EFH and that NMFS provide conservation recommendations to those agencies. 

• Directs Secretary of Commerce to establish a Deep-Sea Coral Research and Technology 

Program that will identify existing information; map locations of deep-sea coral habitats; 

monitor activities in these habitats; conduct research; develop technologies to reduce interactions between fi shing gear and deep-sea corals; prioritize activities; and provide information 

to FMC’s to aid in the conservation and management of these important habitats. The Act 

further authorizes FMC’s to designate zones to protect deep-sea coral habitats from damage 

caused by fi shing gear under FMP discretionary provisions.

NMFS 1976 (as amended 

by the Sustainable Fisheries Act 

in 1996 and the 

Magnuson-Stevens 

Reauthorization Act 

(MSRA) in 2006)

Endangered Species Act 

(ESA)

Provides for the protection and conservation of endangered and threatened species as well as 

the habitats and ecosystems upon which they depend. Requires the identifi cation and protection of Critical Habitat (defi ned as habitat necessary for breeding, spawning, rearing, migrating, feeding, or sheltering) for every species listed under the ESA, and issuance of Biological 

Opinions for all Federal actions that may impact the critical habitat of any listed species. 

NMFS 1973

Marine Mammal Protection 

Act

Provides for the protection of all species of marine mammals, regardless of their status under 

the ESA. Restricts any alterations to habitat that could adversely impact stocks of marine mammals through disruption of behavioral patterns that include, but are not limited to, migration, 

breathing, nursing, breeding, feeding, and sheltering.

NMFS 1972 (as amended)

Coral Reef Conservation Act Provides NOAA with additional authority to undertake a number of activities (including mapping, monitoring, assessment, research, and restoration) to understand, manage and protect 

coral reef ecosystems. Authorizes the establishment of the Coral Reef Conservation Fund and 

provides matching grants for coral reef conservation projects. 

NOAA 2000

Marine Protected Areas 

Executive Order 13158

Purposes are to: strengthen the management, protection, and conservation of existing marine 

protected areas (MPA’s) and establish new or expanded MPA’s; develop a scientifi cally based, 

comprehensive national system of MPA’s representing diverse U.S. marine ecosystems, and 

the Nation’s natural and cultural resources; and avoid causing harm to MPA’s through Federally 

conducted, approved, or funded activities. Establishes a MPA Center tasked with the development of a framework for a national system of MPA’s and providing the information, technologies, and strategies to support the system.

NOAA 2000

Clean Water Act (Federal 

Water Pollution Control Act)

Aims to prevent destruction of aquatic ecosystems, including wetlands, by authorizing water 

quality and pollution research and addressing a number of other water quality issues. Provides 

for Federal regulation of water quality through measures such as water quality standards, discharge limits, and permits, as well as permits to dredge and fi ll waters of the United States. 

NMFS 1972

National Environmental Policy 

Act

Requires Federal agencies to analyze the potential effects of any proposed Federal action that 

would signifi cantly affect historical, cultural, or natural aspects of the environment. The required 

analysis must include consideration of the environmental effects of a range of alternatives.

NOAA 1969

Note: Th ere are many U.S. legislative mandates pertaining to habitat. Th is list includes the major mandates that apply to the National Marine Fisheries Service (NMFS); the summaries are of specifi c aspects that apply to habitat conservation, protection, and recovery.

Appendix 1: Summary of Major U.S. Habitat Conservation 

Legislation
80

Acts/

Executive Orders

Summary NOAA

Lead

Date

Federal Power Act Provides authority to issue mandatory fi sh passage prescriptions and recommend hydropower 

license conditions to protect, mitigate damages to, and enhance anadromous fi sh. Applies to 

licenses issued by the Federal Energy Regulatory Commission for non Federal hydropower 

projects.

NMFS 1920

Coastal Zone Management 

Act

Provides for the management of the nation’s coastal resources, including the Great Lakes, and 

balances economic development with environmental conservation. Establishes the National 

Coastal Zone Management Program and the National Estuarine Research Reserve System. The 

Act also enables states to conserve habitat through the Federal permitting process.

NOS 1972 (as amended)

Comprehensive Environmental Response, Compensation, 

and Liability Act (Superfund 

Act)

Requires NOAA to seek damages from those who have released hazardous substances that 

have caused injury to natural resources (e.g. habitats). Accordingly, NOAA (NOS) determines 

injuries to natural resources and seeks recoveries from the potentially responsible parties to 

restore, replace, or acquire the equivalent of natural resources and to cover the costs of damage assessment. NMFS assists in developing and implementing restoration in certain cases; 

however, the assessment of injuries, development of the economic claim, development of the 

damage assessment, and restoration plan is a function of NOS. The Offi ce of General Council 

for Natural Resources reviews all documents, advises, and negotiates the claim–hence this is a 

multiline offi ce effort within NOAA.

NOS 1980

Estuary Restoration Act Established the Estuary Habitat Restoration Council that includes NOAA, and authorizes funding 

for a comprehensive program to restore habitat in America’s estuaries.

NOAA 2000

Fish & Wildlife Coordination 

Act

Requires Federal Agencies to consult with NMFS (also U.S. Fish and Wildlife Service and state 

resource agencies) concerning any project that may affect waters of the United States to 

ensure fi sh and wildlife resources are given equal consideration in water resource development.

NMFS 1958

Coastal Wetlands Planning, 

Protection, and Restoration 

Act

Established task force that includes NOAA (represented by NMFS) to develop a comprehensive 

approach to restoring and preventing loss of coastal wetlands in Louisiana.

NOAA 1990

Coral Reef Protection Executive Order 13089Established the interagency U.S. Coral Reef Task Force, which is charged with developing and 

implementing a comprehensive program of research and mapping to inventory, monitor, and 

identify the major causes and consequences of degradations of coral reef ecosystems. The 

order also directs Federal agencies to do the following: 1) avoid harm to coral reef ecosystems 

through Federal actions; 2) expand their own research, preservation, and restoration efforts; 3) 

support international coral reef conservation efforts; and 4) address the U.S. role in international 

trade of coral reef species. 

NMFS 

and NOS 

share 

lead

1998

National Marine Sanctuaries 

Act (Title III of the Marine 

Protection, Research, and 

Sanctuaries Act)

Provides for protection of areas designated as marine sanctuaries due to their special natural or 

cultural resource qualities by the following methods: 1) requiring NOAA to issue regulations and 

providing for civil penalties; 2) requiring NOAA to seek damages from those who have injured 

sanctuary resources (NOAA uses the money mainly to restore the injured resources); and 3) 

requiring other Federal agencies to consult with NOAA if they are proposing an action likely to 

injure sanctuary resources and, should they fail to follow NOAA’s recommendations, to restore 

any injured sanctuary resources.

NOS 1972 (as amended)

Oil Pollution Act Requires NOAA to seek damages from those who have released oil and caused injury to natural 

resources. Accordingly, NOAA (NOS) determines the injuries to natural resources and seeks 

recoveries from the potentially responsible parties to restore, replace, or acquire the equivalent 

of natural resources and to cover the costs of damage assessment.

NOS 1990

Atlantic Coastal Fisheries 

Cooperative Management Act 

(Atlantic Coastal Act)

Requires the development, implementation, and enforcement of coastal fi shery management 

plans to promote interstate conservation and management of Atlantic coastal fi shery resources. 

The Act provides a mechanism to ensure Atlantic coastal state compliance with mandated conservation measures in FMP’s approved by the Atlantic States Marine Fisheries Commission.

NMFS 1993 (as amended)
81

Th e Magnuson Fishery Conservation and Management Act was originally passed in 1976 and added amendments in 1986 that required 

FMC’s to evaluate the eff ects of habitat loss or degradation on their fi shery stocks and take actions to mitigate such damage. In 1996, this 

responsibility was expanded to ensure additional habitat protection with the addition of EFH provisions in the Sustainable Fisheries Act,1

which, among other things, amended the habitat provisions of the Magnuson Act. Th e renamed Magnuson-Stevens Act called for direct 

action to stop or reverse the continued loss of fi sh habitats and mandated the identifi cation of habitats essential to managed species and 

measures to conserve and enhance this habitat. Th e Act required cooperation among the NMFS, the FMC’s, fi shing participants, Federal 

and state agencies, and others in achieving the goals of habitat protection, conservation, and enhancement.

EFH is defi ned as “... those waters and substrate necessary to fi sh for spawning, breeding, feeding, or growth to maturity”.2 For the purposes 

of interpreting the defi nition of EFH, “waters” include aquatic areas and their associated physical, chemical, and biological properties that 

are used that are used by fi sh and may include aquatic areas historically used by fi sh where appropriate; “substrate” includes sediment, hard 

bottom, structures underlying the waters, and associated biological communities; “necessary” means the habitat required to support a sustainable fi shery and the managed species’ contribution to a healthy ecosystem; and “spawning, breeding, feeding, or growth to maturity” 

covers a species’ full life cycle.3

FMC’s must identify and describe in their Fishery Management Plans (FMP’s) the habitats used by all life history stages of each managed 

species in their fi shery management units. EFH that is judged to be particularly important to the long-term productivity of populations of 

one or more managed species, or to be particularly vulnerable to degradation, should be identifi ed as “habitat areas of particular concern” 

(HAPC) to help provide additional focus for conservation eff orts. Aft er identifying and describing EFH, FMC’s must assess the potential 

adverse eff ects of all fi shing activities and gear types to EFH and must include management measures to minimize adverse eff ects, to the 

extent practicable, in FMP’s. Th e FMC’s are also directed to examine nonfi shing sources of adverse impacts that may aff ect the quantity or 

quality of EFH and to consider actions to reduce or eliminate the eff ects. FMC’s are further directed to identify proactive means to further 

the conservation and enhancement of EFH.

FMC’s are required to obtain information to describe and identify EFH from the best available sources, including peer-reviewed literature, 

unpublished scientifi c reports, data fi les of government resource agencies, fi sheries landing reports, and other sources. FMP’s should identify gaps in habitat data and defi ciencies in data quality (including considerations of scale and resolution; relevance; and potential biases 

in collection and interpretation) and must demonstrate that the best scientifi c information available was used in the identifi cation and 

description of EFH, consistent with National Standard 2. Th e information necessary to identify and describe EFH is organized according 

to a series of data levels:

• Level 1: Distribution data are available for some or all portions of the geographic range of the species. At this level, only distribution data are available to describe the geographic range of a species (or life stage). Distribution data may be derived from 

systematic presence/absence sampling and/or may include information on species and life stages collected opportunistically. In the event that distribution data are available only for portions of the geographic area occupied by a particular life

stage of a species, habitat use can be inferred on the basis of distributions among habitats where the species has been found 

and on information about its habitat requirements and behavior. Habitat use may also be inferred, if appropriate, based 

on information on a similar species or another life stage.

• Level 2: Habitat-related densities of the species are available. At this level, quantitative data (i.e. density or relative abundance) are available for the habitats occupied by a species or life stage. Because the effi ciency of sampling methods is oft en 

aff ected by habitat characteristics, strict quality assurance criteria should be used to ensure that density estimates are 

comparable among methods and habitats. Density data should refl ect habitat utilization, and the degree that a habitat 

is utilized is assumed to be indicative of habitat value. When assessing habitat value on the basis of fi sh densities in this 

manner, temporal changes in habitat availability and utilization should be considered.

• Level 3: Growth, reproduction, or survival rates within habitats are available. At this level, data are available on habitatrelated growth, reproduction, and/or survival by life stage. Th e habitats contributing the most to productivity should be 

Appendix 2: Summary of Essential Fish Habitat (EFH) 

Regulations and Programs

1

U.S. Public Law 104-297.

2

16 U.S.C. 1802(10).

3

EFH Final Rule, 67 FR 2375.
82

those that support the highest growth, reproduction, and survival of the species (or life stage).

• Level 4: Production rates by habitat are available. At this level, data are available that directly relate the production rates of 

a species or life stage to habitat type, quantity, quality, and location. Essential habitats are those necessary to maintain fi sh 

production consistent with a sustainable fi shery and the managed species’ contribution to a healthy ecosystem.

FMC’s should strive to obtain data suffi cient to describe habitat at the highest level of detail (i.e. Level 4). 

Th e EFH components of FMP’s should be reviewed periodically by the FMC’s and NMFS to ensure that information is current and applicable. Each EFH FMP amendment is required to include a provision requiring review and update of EFH information and preparation of a 

revised FMP amendment if new information becomes available. Th e schedule for this review is based on an assessment of both the existing 

data and expectations of when new data will become available. Th is information is reviewed as part of the annual Stock Assessment and 

Fishery Evaluation Report preparation. A complete review of EFH information should be completed by the FMC’s as recommended by the 

Secretary of Commerce, but at least once every fi ve years. 

Th e Magnuson-Stevens Act requires all Federal agencies to consult with NMFS on all actions, or proposed actions, authorized, or funded, 

or undertaken by the agency, that may adversely aff ect EFH. An EFH consultation consists of three steps:

1) Th e Federal action agency must submit a complete EFH Assessment to NMFS with information on the eff ects of the 

action on EFH. Such assessments must contain: a description of the proposed action; an analysis of the eff ects (including cumulative eff ects) of the proposed action on EFH, the managed species, and associated species; the agency’s views 

regarding the eff ects of the actions on EFH; proposed mitigation, if applicable; and additional information such as the 

results of an on-site inspection to evaluate the habitat and site-specifi c eff ects of the project, the views of recognized experts on the habitat or species that may be aff ected, a review of pertinent literature and related information, an analysis 

of alternatives to the proposed action, and other relevant information. 

2) NMFS responds to the Federal action agency with formal EFH conservation recommendations. 

3) Th e action agency will then respond in writing to NMFS with a description of measures proposed by the agency for 

avoiding, mitigating, or off setting the impact of the activity on EFH. In the case of a response that is inconsistent with 

NMFS conservation recommendations, the Federal agency must explain its reasons for not following the recommendations, including the scientifi c justifi cation for any disagreements with NMFS over the anticipated eff ects of the proposed 

action and the conservation measures needed. 

For additional information on the Essential Fish Habitat Program and Regional EFH contacts, please visit the EFH homepage at: http://

www.nmfs.noaa.gov/habitat/habitatprotection/efh /index.htm.
83

• Th e Stock Assessment Improvement Plan is the report of the National Marine Fisheries Service (NMFS) National Task Force for Improving Fish Stock Assessments, and is a component of the Science Quality Assurance Program. Th e Task Force consisted of one representative 

from NMFS Headquarters and 1-2 representatives from each of the fi ve NMFS Science Centers. Th e report also addresses recommendations made in the National Research Council study on Improving Fish Stock Assessments (NRC 1998a). 

• Improvements in stock assessments area required for several reasons, including: that management entities are “managing at the edge” for 

many species, and therefore require the most accurate and precise stock assessments possible; it is no longer permissible to overfi sh; and 

there are currently increased demands for adopting a “precautionary approach” and incorporating “ecosystem considerations” into stock 

assessments and fi sheries management. Th is report discusses these and other factors that defi ne NMFS’ stock assessment mandate.

• Although the NRC study on Improving Fish Stock Assessments (NRC 1998a) focused on improving assessment methodology, the Task 

Force agreed that the greatest impediment to producing accurate, precise, and credible stock assessments is the lack of adequate input data, 

in terms of the quantity, quality, and type of data available. 

• For most stocks, there is at least basic information on landed catch and the size frequency of the catch. However, for more than 40% of 

the 904 stocks listed in the 1999 Report to Congress on the Status of Fisheries of the United States (NMFS 1999a), there is no fi sheryindependent or fi shery-dependent index of abundance, which makes it extremely diffi cult to conduct a meaningful assessment. Other 

factors, such as the need to prioritize the stocks to be assessed, result in a total of about 60% of the stocks (545 stocks) lacking assessments 

suffi cient to evaluate stock status relative to overfi shing. On the other hand, although there are relatively few stocks with comprehensive 

input data, a total of 119 stocks are routinely assessed using state-of-the-art age or size structured models, some of which may also incorporate spatial and oceanographic eff ects. With a few exceptions, all of the high-valued, high-volume, or high-profi le species are routinely 

assessed, while most of the unassessed species contribute little or nothing to total landings. 

• Stock assessments conducted by NMFS are rarely, if ever, the product of a single individual, and peer review is an integral part of the process related to provision of scientifi c advice in support of fi sheries management that are carried out by fi sheries scientists from within and 

outside of NMFS. All fi ve Science Centers have systems in place for peer review of stock assessments.

• Th e most important programmatic needs vary by region, and even by species groups within regions. Overall, the two most important

needs are research vessel surveys designed to produce fi shery-independent indices of abundance and to collect related information on spatial and temporal distributions, associated species, habitat, and oceanographic variables; and observer programs that provide information 

on species composition, amounts of each species kept and discarded, and fi shing eff ort. 

• Assessment scientists are faced with many demands. Within a given year, an individual assessment scientist may be expected to: (i) participate in fi shery-independent surveys or other fi eld work, (ii) provide input and advice on sampling designs for research surveys and 

other fi shery-independent data collection activities, (iii) spend time on commercial or recreational fi shing vessels, (iv) provide input and 

advice on the development of data collection objectives and protocols for observer programs and other fi shery-dependent data collection 

activities, (v) conduct quality control or other preprocessing of data, (vi) conduct stock assessments, (vii) conduct research into stock assessment methods, (viii) present assessment results to peer review panels and constituent groups, (ix) participate on peer review panels, (x) 

participate in fi shery management plan development or evaluation teams, (xi) defends a stock assessment in a court of law, (xii) research 

and write scientifi c papers for primary publication, (xiii) attend colleagues’ seminars and off er critical review, (xiv) conduct formal, written peer reviews of articles submitted for publication in scientifi c journals, (xv) participate on committees to advance approaches to stock 

assessment and fi sheries management, (xvi) undertake training to stay abreast of new methodologies, (xvii) run courses or workshops to 

train others, (xviii) participate in national and international meetings and conferences to enhance professional development, and (xix) 

undertake a variable amount of administrative duties depending on supervisory level. With limited exceptions, there is insuffi cient scope 

for individual scientists to focus on just one or a few of these activities due to an overall shortage of assessment scientists. A survey of 

assessment scientists indicated that there is insuffi cient time to devote to important activities such as research to improve the basis for assessments, professional development, and interactions and cooperative research with national and international peers. Th e same is likely 

to be true for individuals involved in data collection, data processing, and data management.

Appendix 3: Executive Summary of the “Marine Fisheries 

Stock Assessment Improvement Plan” (NMFS, 2001)
84

• In fact, staffi ng needs associated with the production of stock assessments go well beyond stock assessment scientists per se, who represent 

only the “tip of the iceberg.” Far greater numbers of staff are needed for deployment in critical data collection activities, such as commercial or recreational catch and eff ort data, port sampling for biological data, observer programs, and fi shery-independent resource surveys. 

Additional staff are also required to process biological samples (e.g. to determine fi sh ages from hard structures, construct age-length keys, 

develop growth curves, construct maturity ogives, and possibly to identify and count eggs and larval fi sh from ichthyoplankton surveys, 

and to examine stomach contents), and to enter, audit, integrate, and preprocess data from the myriad of data collection activities. 

• Th e Task Force defi ned three Tiers of Assessment Excellence, which can be summarized as:

Tier 1−Improve stock assessments using existing data

(a) for core species, conduct assessments that are more comprehensive, more thorough, more timely, better quality-controlled, and better communicated; 

(b) for species of currently “unknown” status, mine 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 2−Elevate stock assessments to new national standards of excellence

(a) upgrade assessments for core species to at least Level 3 [the Task Force defi ned six levels at which assessments are conducted, ranging from 0 to 5; Level 3 assessments comprise analytical models in which ages or species are aggregated];

(b) conduct adequate baseline monitoring for all federally managed species (including rare species).

Tier 3−Next generation assessments

(a) assess all federally managed species or species groups at a minimum level of 3, and all core species at a level of 4 or 5 

[size, age or stage-structured models, possibly including spatial and seasonal considerations, species associations, and 

oceanographic eff ects];

(b) explicitly incorporate ecosystem considerations such as multispecies interactions and environmental eff ects, fi sheries 

oceanography, and spatial and seasonal analyses.

 

• A large part of the report specifi es region-by-region program and staffi ng requirements needed to meet the three Tiers of Assessment 

Excellence. Th ese are summarized in Table 8 of the report, which is reproduced here. 

• Among other things, the Task Force recommends that NMFS should aggressively pursue a course of action focusing on new budget and 

staffi ng initiatives to modernize its data collection and assessment capabilities. At the minimum, NMFS should attempt to bring stock 

assessment science to at least Tier 2, and should initiate dialog both within house and with the public to determine how far reaching and 

comprehensive Tier 3 should be. Th is will require hiring or contracting considerable numbers of additional qualifi ed staff for data collection, data processing, data management, stock assessments, and evaluations of alternative management strategies, to ensure adequate data 

and analyses on which to base conservation and management decisions, now and into the future. 

• It is also recommended that in order to develop more comprehensive and integrated future budget initiatives geared towards modernizing 

fi sheries assessments and management, NMFS should prepare an umbrella plan that integrates all relevant existing documents on these 

themes; for example, the current Stock Assessment Improvement Plan, the NOAA Fisheries Data Acquisition Plan (Appendix 3), the 

Current

Center In-house Contract Other Tier 1 Tier 2 Tier 1+2 Tier 3 All Tiers

NEFSC 123 49 16 18 43 61 25 86

SEFSC 71 30 46 14 42 56 39 95

SWFSC 80 15 26+ 27 60 87 66 153

NWFSC 18 33 59 13 74 87 39 126

AFSC 154 122 54 31 66 97 51 148

Summed FTEs 446 249 201 103 285 388 220 608

$$ (FTE x $150K) $15,450K $42,750K $58,200K $33,000K $91,200K

Table 8

Total Full-Time Equivalents (FTEs) required to meet the three Tiers of Assessment Excellence for each Science Center and all Centers combined. 

Estimated current FTEs include in-house staff, contractors such as observers, and “other,” which includes state government biologists, and employees 

or contractors associated with various regional, national, and international commissions. Numbers should be cumulated across tiers.
85

NMFS Strategic Plan for Fisheries Research (NMFS 2001b), the Proposed Implementation of a Fishing Vessel Registration and Fisheries 

Information Management System (Appendix 8), the NMFS Bycatch Plan (Appendix 9), the National Observer Program (Appendix 

10), the Social Sciences Plan (Appendix 11), the Advanced Technologies Working Group (Appendix 12), and relevant fi sheries oceanography initiatives (e.g. Appendix 13).

• In order to make substantial progress towards collecting the data needed to improve stock assessments, particularly next generation assessments, it is essential that NMFS continue to foster partnerships and cooperative research programs with other Federal agencies, state 

agencies, private foundations, universities, commercial and recreational fi shing organizations and individuals, environmental groups, and 

others with a vested interest in collecting similar types of data, although oft en for diff erent purposes. Programs involving cooperative 

research with the fi shing industry should continue to be developed and expanded as mechanisms for providing data relevant to improving 

the quality of stock assessments. 

SAIP Executive Summary References

NMFS. 1999a. Report to Congress on the status of fi sheries of the United States. National Marine Fisheries Service, Silver Spring, MD, 

104 p.

NMFS. 2001b. NMFS strategic plan for fi sheries research. National Marine Fisheries Service, Silver Spring, MD, 88 p.

NRC. 1998a. Improving fi sh stock assessments. National Academy Press, Washington, DC, 177 p. 

87

Th e FSSI is a Government Performance and Results Act level performance measure for the sustainability of 230 U.S. commercial and

recreational fi sh stocks or stock complexes. Th is stock index provides an overall indicator of the health of the nation’s most important commercial and recreational fi sheries. Th e FSSI tracks the outcome of increasing knowledge about the status of stocks, managing fi sh harvest 

rates, and building and maintaining fi sh stocks at productive levels. More information about FSSI scoring, as well as individual stock scores, 

overall FSSI scores, and summary changes are available on the NOAA Sustainable Fisheries website at http://www.nmfs.noaa.gov/sfa/statusoffi sheries/SOSmain.htm.

Th e FSSI is based on a set of 230 priority fi sh stocks and stock complexes selected for their importance to commercial and recreational 

fi sheries. Criteria for the selection of stocks for the FSSI included: 1) whether they were “major” stocks (i.e. annual landings greater than 

200,000 lb); 2) whether they were overfi shed or subject to overfi shing; 3) whether they had stock assessments scheduled in the near future; 

4) whether they had previously been identifi ed as important; and 5) other factors deemed important by the responsible Regional Offi ce as 

appropriate. Th ese stocks represent about 90% of all commercial and landings in the United States. 

Jurisdiction FMP Stock Name

Pacifi c Islands Fisheries Science Center

WPFMC Bottomfi sh and Seamount Groundfi sh Fisheries of the Western Pacifi c 

Region

American Samoa Bottomfi sh Multi-species Complex

Guam Bottomfi sh Multi-species Complex

Hancock Seamount Groundfi sh Complex

Hawaiian Archipelago Bottomfi sh Multi-species Complex

WPFMC Coral Reef Ecosystem of the Western Pacifi c Region Hawaiian Archipelago Coral Reef Ecosystem Multi-species Complex

Bigeye scad - Hawaiian Archipelago

Mackerel scad - Hawaiian Archipelago

WPFMC Pelagic Fisheries of the Western Pacifi c Region Albacore - South Pacifi c

Indo-Pacifi c blue marlin - Pacifi c

Kawakawa - Tropical Pacifi c

Opah - Pacifi c

Shortbill spearfi sh - Pacifi c

Skipjack tuna - Central Western Pacifi c

Striped marlin - Central Western Pacifi c

Wahoo - Pacifi c

Yellowfi n tuna - Central Western Pacifi c

Alaska Fisheries Science Center

NPFMC Bering Sea / Aleutian Islands King and Tanner Crabs Blue king crab - Pribilof Islands

Blue king crab - Saint Matthews Island

Golden king crab - Aleutian Islands

Red king crab - Bristol Bay

Red king crab - Norton Sound

Red king crab - Pribilof Islands

Red king crab - Western Aleutian Islands

Snow crab - Bering Sea

Southern Tanner crab - Bering Sea

NPFMC Groundfi sh of the Bering Sea and Aleutian Islands Management Area Alaska plaice - Bering Sea / Aleutian Islands

Appendix 4: Summary of the Fish Stock Sustainability Index 

(FSSI) and List of FSSI Stocks
88

Jurisdiction FMP Stock Name

Alaska Fisheries Science Center (continued)

NPFMC Groundfi sh of the Bering Sea and Aleutian Islands Management Area 

(continued)

Atka mackerel - Bering Sea / Aleutian Islands

Bering Sea / Aleutian Islands Arrowtooth Flounder Complex

Bering Sea / Aleutian Islands Flathead Sole Complex

Bering Sea / Aleutian Islands Rock Sole Complex

Greenland halibut - Bering Sea / Aleutian Islands

Northern rockfi sh - Bering Sea / Aleutian Islands

Pacifi c cod - Bering Sea / Aleutian Islands

Pacifi c ocean perch - Bering Sea / Aleutian Islands

Rougheye rockfi sh - Bering Sea / Aleutian Islands

Walleye pollock - Aleutian Islands

Walleye pollock - Eastern Bering Sea

Yellowfi n sole - Bering Sea / Aleutian Islands

NPFMC Groundfi sh of the Bering Sea and Aleutian Islands Management Area / 

Groundfi sh of the Gulf of Alaska

Sablefi sh - Eastern Bering Sea / Aleutian Islands / Gulf of Alaska

NPFMC Groundfi sh of the Gulf of Alaska Arrowtooth fl ounder - Gulf of Alaska

Flathead sole - Gulf of Alaska

Gulf of Alaska Deepwater Flatfi sh Complex

Gulf of Alaska Demersal Shelf Rockfi sh Complex

Gulf of Alaska Pelagic Shelf Rockfi sh Complex

Gulf of Alaska Thornyhead Rockfi sh Complex

Northern rockfi sh - Western / Central Gulf of Alaska

Pacifi c cod - Gulf of Alaska

Pacifi c ocean perch - Gulf of Alaska

Rex sole - Gulf of Alaska

Rougheye rockfi sh - Gulf of Alaska

Walleye pollock - Western / Central Gulf of Alaska

Northwest Fisheries Science Center

PFMC Pacifi c Coast Groundfi sh Arrowtooth fl ounder - Pacifi c Coast

Bank rockfi sh - California

Black rockfi sh - Northern Pacifi c Coast

Blackgill rockfi sh - Southern California

Blue rockfi sh - California

Bocaccio - Southern Pacifi c Coast

Brown rockfi sh - Pacifi c Coast

Cabezon - California

California scorpionfi sh - Southern California

Canary rockfi sh - Pacifi c Coast

Chilipepper - Southern Pacifi c Coast

Cowcod - Southern California

Darkblotched rockfi sh - Pacifi c Coast

Dover sole - Pacifi c Coast

English sole - Pacifi c Coast

Gopher rockfi sh - Northern California

Kelp greenling - Oregon

Lingcod - Pacifi c Coast
89

Jurisdiction FMP Stock Name

Northwest Fisheries Science Center (continued)

PFMC Pacifi c Coast Groundfi sh (continued) Longnose skate - Pacifi c Coast

Longspine thornyhead - Pacifi c Coast

Pacifi c cod - Pacifi c Coast

Pacifi c grenadier - Pacifi c Coast

Pacifi c hake - Pacifi c Coast

Pacifi c ocean perch - Pacifi c Coast

Pacifi c sanddab - Pacifi c Coast

Petrale sole - Pacifi c Coast

Rex sole - Pacifi c Coast

Rougheye rockfi sh - Pacifi c Coast

Sablefi sh - Pacifi c Coast

Sand sole - Pacifi c Coast

Shortbelly rockfi sh - Pacifi c Coast

Shortspine thornyhead - Pacifi c Coast

Spiny dogfi sh - Pacifi c Coast

Splitnose rockfi sh - Pacifi c Coast

Starry fl ounder - Pacifi c Coast

Vermilion rockfi sh - California

Widow rockfi sh - Pacifi c Coast

Yelloweye rockfi sh - Pacifi c Coast

Yellowtail rockfi sh - Northern Pacifi c Coast

Southwest Fisheries Science Center

PFMC Coastal Pelagic Species Jack mackerel - Pacifi c Coast

Northern anchovy - Northern Pacifi c Coast

Northern anchovy - Southern Pacifi c Coast

Opalescent inshore squid - Pacifi c Coast

Pacifi c chub mackerel - Pacifi c Coast

Pacifi c sardine - Pacifi c Coast

PFMC U.S. West Coast Fisheries for Highly Migratory Species Skipjack tuna - Eastern Tropical Pacifi c

Striped marlin - Eastern Tropical Pacifi c

Yellowfi n tuna - Eastern Tropical Pacifi c

Southwest Fisheries Science Center / Pacifi c Islands Fisheries Science Center

PFMC / WPFMC U.S. West Coast Fisheries for Highly Migratory Species / Pelagic 

Fisheries of the Western Pacifi c Region

Albacore - North Pacifi c

Bigeye tuna - Pacifi c

Blue shark - Pacifi c

Dolphinfi sh - Pacifi c

Pacifi c bluefi n tuna - Pacifi c

Swordfi sh - North Pacifi c

Southeast Fisheries Science Center

SAFMC / GMFMC Coastal Migratory Pelagic Resources of the Gulf of Mexico and South 

Atlantic

Cobia - Gulf of Mexico 

King mackerel - Gulf of Mexico

King mackerel - Southern Atlantic Coast
90

Jurisdiction FMP Stock Name

Southeast Fisheries Science Center (continued)

SAFMC / GMFMC Coastal Migratory Pelagic Resources of the Gulf of Mexico and South 

Atlantic (continued)

Little tunny - Gulf of Mexico

Spanish mackerel - Gulf of Mexico

Spanish mackerel - Southern Atlantic Coast

HMS Consolidated Atlantic Highly Migratory Species Albacore - North Atlantic

Atlantic Large Coastal Shark Complex

Atlantic sharpnose shark - Atlantic

Atlantic Small Coastal Shark Complex

Bigeye tuna - Atlantic

Blacknose shark - Atlantic

Blacktip shark - Gulf of Mexico

Blacktip shark - South Atlantic

Blue marlin - North Atlantic

Blue shark - Atlantic

Bluefi n tuna - Western Atlantic

Bonnethead - Atlantic

Dusky shark - Atlantic

Finetooth shark - Atlantic

Porbeagle - Atlantic

Sailfi sh - Western Atlantic

Sandbar shark - Atlantic

Shortfi n mako - Atlantic

Swordfi sh - North Atlantic

White marlin - North Atlantic

Yellowfi n tuna - Western Atlantic

SAFMC / GMFMC Dolphin and Wahoo Fishery of the Atlantic / Coastal Migratory Pelagic 

Resources of the Gulf of Mexico and South Atlantic

Dolphinfi sh - Southern Atlantic Coast / Gulf of Mexico

CFMC Queen Conch Resources of Puerto Rico and the U.S. Virgin Islands Queen conch - Caribbean

GMFMC Red Drum Fishery of the Gulf of Mexico Red drum - Gulf of Mexico

GMFMC Reef Fish Resources of the Gulf of Mexico Black grouper - Gulf of Mexico

Gag - Gulf of Mexico

Gray triggerfi sh - Gulf of Mexico

Greater amberjack - Gulf of Mexico

Hogfi sh - Gulf of Mexico

Nassau grouper - Gulf of Mexico

Red grouper - Gulf of Mexico

Red snapper - Gulf of Mexico

Snowy grouper - Gulf of Mexico

Vermilion snapper - Gulf of Mexico

Yellowedge grouper - Gulf of Mexico

CFMC Shallow Water Reef Fish Fishery of Puerto Rico and the U.S. Virgin 

Islands

Caribbean Grouper Unit 1

Caribbean Grouper Unit 2

Caribbean Grouper Unit 4

Caribbean Snapper Unit 1

Caribbean Snapper Unit 3

Caribbean Snapper Unit 4
91

Jurisdiction FMP Stock Name

Southeast Fisheries Science Center (continued)

GMFMC Shrimp Fishery of the Gulf of Mexico Brown shrimp - Gulf of Mexico

Pink shrimp - Gulf of Mexico

Royal red shrimp - Gulf of Mexico

White shrimp - Gulf of Mexico

SAFMC Shrimp Fishery of the South Atlantic Region Brown rock shrimp - Southern Atlantic Coast

Brown shrimp - Southern Atlantic Coast

Pink shrimp - Southern Atlantic Coast

White shrimp - Southern Atlantic Coast

SAFMC Snapper-Grouper Fishery of the South Atlantic Region Black grouper - Southern Atlantic Coast

Black sea bass - Southern Atlantic Coast

Gag - Southern Atlantic Coast

Gray triggerfi sh - Southern Atlantic Coast

Greater amberjack - Southern Atlantic Coast

Hogfi sh - Southern Atlantic Coast

Red grouper - Southern Atlantic Coast

Red porgy - Southern Atlantic Coast

Red snapper - Southern Atlantic Coast

Scamp - Southern Atlantic Coast

Snowy grouper - Southern Atlantic Coast

Speckled hind - Southern Atlantic Coast

Tilefi sh - Southern Atlantic Coast

Vermilion snapper - Southern Atlantic Coast

Warsaw grouper - Southern Atlantic Coast

White grunt - Southern Atlantic Coast

Wreckfi sh - Southern Atlantic Coast

SAFMC / GMFMC Snapper-Grouper Fishery of the South Atlantic Region / Reef Fish 

Resources of the Gulf of Mexico

Goliath grouper - Southern Atlantic Coast / Gulf of Mexico

Yellowtail snapper - Southern Atlantic Coast / Gulf of Mexico

CFMC Spiny Lobster Fishery of Puerto Rico and the U.S. Virgin Islands Caribbean spiny lobster - Caribbean

SAFMC / GMFMC Spiny Lobster in the Gulf of Mexico and South Atlantic Caribbean spiny lobster - Southern Atlantic Coast / Gulf of Mexico

GMFMC Stone Crab Fishery of the Gulf of Mexico Stone crabs (Menippe species) - Gulf of Mexico

Northeast Fisheries Science Center

NEFMC Atlantic Herring Atlantic herring - Northwestern Atlantic Coast

MAFMC Atlantic Mackerel, Squid and Butterfi sh Atlantic mackerel - Gulf of Maine / Cape Hatteras

Butterfi sh - Gulf of Maine / Cape Hatteras

Longfi n inshore squid - Georges Bank / Cape Hatteras

Northern shortfi n squid - Northwestern Atlantic Coast

NEFMC Atlantic Sea Scallop Sea scallop - Northwestern Atlantic Coast

MAFMC Atlantic Surfclam and Ocean Quahog Atlantic surfclam - Mid-Atlantic Coast

Ocean quahog - Atlantic Coast

MAFMC Bluefi sh Bluefi sh - Atlantic Coast

NEFMC Deep-Sea Red Crab Red deepsea crab - Northwestern Atlantic

NEFMC / MAFMC Monkfi sh Goosefi sh - Gulf of Maine / Northern Georges Bank

Goosefi sh - Southern Georges Bank / Mid-Atlantic

NEFMC Northeast Multispecies Acadian redfi sh - Gulf of Maine / Georges Bank
92

Jurisdiction FMP Stock Name

Northeast Fisheries Science Center (continued)

NEFMC Northeast Multispecies (continued) American plaice - Gulf of Maine / Georges Bank

Atlantic cod - Georges Bank

Atlantic cod - Gulf of Maine

Atlantic halibut - Northwestern Atlantic Coast

Haddock - Georges Bank

Haddock - Gulf of Maine

Ocean pout - Northwestern Atlantic Coast

Offshore hake - Northwestern Atlantic Coast

Pollock - Gulf of Maine / Georges Bank

Red hake - Gulf of Maine / Northern Georges Bank

Red hake - Southern Georges Bank / Mid-Atlantic

Silver hake - Gulf of Maine / Northern Georges Bank

Silver hake - Southern Georges Bank / Mid-Atlantic

White hake - Gulf of Maine / Georges Bank

Windowpane - Gulf of Maine / Georges Bank

Windowpane - Southern New England / Mid-Atlantic

Winter fl ounder - Georges Bank

Winter fl ounder - Gulf of Maine

Winter fl ounder - Southern New England / Mid-Atlantic

Witch fl ounder - Northwestern Atlantic Coast

Yellowtail fl ounder - Cape Cod / Gulf of Maine

Yellowtail fl ounder - Georges Bank

Yellowtail fl ounder - Southern New England / Mid-Atlantic

NEFMC Northeast Skate Complex Barndoor skate - Georges Bank / Southern New England

Clearnose skate - Southern New England / Mid-Atlantic

Little skate - Georges Bank / Southern New England

Rosette skate - Southern New England / Mid-Atlantic

Smooth skate - Gulf of Maine

Thorny skate - Gulf of Maine

Winter skate - Georges Bank / Southern New England

NEFMC / MAFMC Spiny Dogfi sh Spiny dogfi sh - Atlantic Coast

MAFMC Summer Flounder, Scup and Black Sea Bass Black sea bass - Mid-Atlantic Coast

Scup - Atlantic Coast

Summer fl ounder - Mid-Atlantic Coast

MAFMC Tilefi sh Tilefi sh - Mid-Atlantic Coast
93

Th ere are over 40 Liquefi ed Natural Gas (LNG) processing facilities proposed or in operation in North America, and about half of these 

are located in the northern Gulf of Mexico (GOM). LNG facilities are being built in response to an increased demand for imported natural 

gas. Th e process of converting LNG back into gas requires heat, and seven facilities in coastal waters of the northern GOM propose to use 

vaporization systems (mainly Open Rack Vaporization or ORVs) that obtain this heat from seawater. Cumulatively, these seven facilities are 

projected to use over 1 billion gallons of seawater per day to regasify LNG. Th e use of ORVs is mainly restricted to the GOM, is controversial, and is projected to have adverse ecosystem impacts. 

Th e controversy regarding potential fi shery and ecosystem impacts of LNG facilities has focused attention on the paucity of available scientifi c information needed to understand the eff ects of such facilities and highlighted the importance of basic scientifi c information on early 

life histories of fi shery species. Information available from ongoing NOAA research programs and from the scientifi c literature suggests that 

the operation of LNG facilities will have adverse impacts on habitats and organisms, including direct mortality of planktonic organisms in 

entrained water, limited mortality of organisms from impingement on intake screens, discharge of cooled water into the area, and discharge 

of antifouling agents such as chlorine and chlorine byproducts. Attempts by the SEFSC to assess the magnitude of these impacts, however, 

have accentuated signifi cant gaps in our databases, programs, and understanding of coastal systems. Th is research plan was developed to 

identify information needs, prioritize the problems to be addressed, distinguish between research and monitoring questions, describe the 

research needed to address information defi ciencies, and integrate this information with ongoing research programs. 

Th is Gulf LNG Research Plan will be used to guide the eff orts and activities of the SEFSC’s research on LNG facility impacts in the northern Gulf of Mexico for the next 5 years (FY 2007-FY 2011). A major focus of the research plan is to obtain a better understanding of the 

temporal and spatial distribution of eggs and larvae of fi shery species in coastal waters by increasing sampling coverage of the SEAMAP program, analyzing samples for decapod crustacean larvae, understanding vertical distribution and diel migration, measuring extrusion through 

nets, improving our ability to identify eggs and various stages of larvae to species level, and exploring the utility of remote sensing as a means 

of estimating larval abundance. Other research areas to be emphasized include 1) determining the fate of entrained organisms, 2) measuring 

growth and natural mortality during early life stages of fi shery species, 3) examining the extent of impingement on intake structures and 

the role of larval swimming speed in avoiding impingement, 4) examining the role of water currents on facility impacts, 5) understanding 

socioeconomic impacts, 5) assessing cumulative impacts of multiple facilities, and 6) modeling ecosystem of impacts. Th e Research Plan 

focuses on the early life history of fi shery species and their role in coastal ecosystems. Th e program will integrate new research with existing research programs and with expected monitoring information from licensed LNG facilities. Over the 5-year period, the program will 

require about $5 M per year (total $25 M) and a minimum of seven FTEs. Th e results of this research program will greatly benefi t resource 

managers within NOAA and within other management and licensing agencies.

Appendix 5: Executive Summary of “A Research Plan−Assessing 

Ecosystem Impacts of Liquefied Natural Gas Processing Facilities 

on Marine Resources in the Gulf of Mexico” (SEFSC, 2006)

95

Th ere are many programs, both within and outside of NOAA, with goals and objectives related to marine habitat. A meaningful exchange 

of information is expected among these eff orts and HAIP-based initiatives.

Habitat-related Programs and Activities Within NOAA 

• Advanced Sampling Technology Working Group (ASTWG): ASTWG leads eff orts to improve the quality of living marine resource 

assessments through development, evaluation, and implementation of innovative sampling technology. ASTWG activities help NOAA 

meet increasing demands for accurate, precise, and timely information to protect, restore, and manage coastal and oceanic resources. Advanced sampling technologies include acoustic, optic, and tagging instrumentation and associated soft ware. ASTWG owns several pieces 

of sampling equipment that are available for NMFS-wide surveys, including a dual-frequency identifi cation sonar (DIDSON), a Fetch 

AUV, and an EK60 38-kHz deep-water transducer and transceiver. See http://www.st.nmfs.noaa.gov/st7/AdvancedSamplingTechnology.html. 

• Center for Operational Oceanographic Products and Services (CO-OPS): CO-OPS provides the national infrastructure, science, and 

technical expertise to monitor, assess, and distribute tide, current, water level, and other coastal oceanographic products and services. 

CO-OPS provides operationally sound observations and monitoring capabilities coupled with operational Nowcast Forecast modeling. 

CO-OPS developed and supports the NOAA Tides and Currents website, which provides a wide variety of coastal oceanographic data 

to the public. See http://tidesandcurrents.noaa.gov.

• Coastal and Marine Ecological Classifi cation Standard (CMECS): NOAA’s Coastal Services Center, in partnership with NatureServe, 

developed CMECS as a standard ecological classifi cation system that is intended to be universally applicable for coastal and marine systems and complementary to existing wetland and upland systems. CMECS framework accommodates physical, biological, and chemical 

information to describe a marine habitat type. CMECS structure is designed to support status and trend monitoring, policy development, 

restoration planning, ecological assessments, and fi sheries management at the local and national levels. CMECS uses three components 

(benthic cover, water column, and geoform) to describe diff erent aspects of the environment. See http://www.csc.noaa.gov/benthic/

cmecs/index.html. 

• Comparative Analysis of Marine Ecosystem Organization (CAMEO): CAMEO is implemented through a partnership between NMFS 

and the National Science Foundation’s Division of Ocean Sciences. Its purpose is to strengthen the scientifi c basis for an ecosystem approach to the stewardship of our ocean and living marine resources. Th e program supports research to understand complex dynamics 

controlling productivity, behavior, population connectivity, climate variability, and anthropogenic pressures associated with living marine resources and critical habitats. CAMEO research will employ the use of a diverse array of ecosystem models, comparative analyses 

of managed and unmanaged areas, and ecosystem-scale mapping that can form a basis for future forecasting and decision support. See 

http://cameo.noaa.gov/. 

• Deep-sea Coral Research and Technology Program (DSCRTP): DSCRTP has six goals: 1) to identify existing research on, and known

locations of, deep-sea corals; 2) to locate and map locations of deep-sea corals; 3) to monitor activity in locations where deep-sea corals 

are known or likely to occur, based on the best scientifi c information available, including methods using underwater or remote sensing 

technologies; 4) to conduct research on deep-sea corals and related species, and on survey methods; 5) to develop technologies or methods designed to assist fi shing industry participants in reducing interactions between fi shing gear and deep-sea corals; and 6) to prioritize 

program activities in areas where deep-sea corals occur, and in areas where scientifi c modeling or other methods predict deep-sea corals 

are likely to be present. See http://www.nmfs.noaa.gov/msa2007/deepseacorals.html. 

• Fisheries and the Environment (FATE): FATE’s mission is to provide information for eff ective management to mitigate ecological and 

social impacts of major shift s in productivity of LMR’s. Th e FATE program focuses on: 1) analysis of the response of fi sh and shellfi sh to 

environmental change; 2) development of ecosystem indicators; 3) incorporation of ecosystem indicators in stock assessments; and 4) 

construction of next generation forecasting models. FATE complements ongoing research activities of several mesoscale process oriented 

programs, including the North Pacifi c Research Board’s Bering Sea Integrated Ecosystem Research Program, the Alaska Fisheries Science 

Center’s Fisheries Oceanography Coordinated Investigations program, the U.S. Global Ecosystem Dynamics program (Georges Bank, 

Appendix 6: Habitat-related Programs and Activities
96

northern Gulf of Alaska, and the California Current), the Ocean Carrying Capacity study (Gulf of Alaska), and the California Cooperative Oceanic Fisheries Investigations program (southern California Bight). See http://fate.nmfs.noaa.gov/. 

• Fishery-independent Survey System (FINSS): FINSS is a national-level repository designed to provide trusted and integrated NMFS 

fi shery-independent survey data and associated metadata (including habitat and protected species surveys) through GIS visualization and 

online access to NMFS’ internal and external users. FINSS constitutes three inter-related databases: Historical Survey Inventory Database, Projected At-sea Fleet Requirement Database, and Incidental Protected Species Take Database; it is scheduled to be operational in 

2010. 

• Integrated Ocean and Coastal Mapping (IOCM): IOCM’s goals are to increase effi ciency, eliminate duplication, and enhance the use of 

mapping data sets that are collected for navigation, ocean exploration, coastal and living resource management, hazards preparedness, response and mitigation, habitat assessments, and ocean and coastal modeling eff orts. Some of IOCM’s current eff orts include the establishment of an IOCM Coordination Team and related work groups; development of an IOCM web site; support NOAA Joint Ocean and 

Coastal Mapping Centers of Excellence; gap analyses to assess needs for technology, training, and data management; and establishment 

of standards for improved use of mapping data.

• National Centers for Coastal Ocean Science (NCCOS): NCCOS conducts and supports research, monitoring, assessments, and technical assistance to meet NOAA’s coastal stewardship and management responsibilities. NCCOS focuses research on fi ve key ecosystem 

stressors: climate change, extreme natural events, pollution, invasive species, and land and resource use, directed specifi cally on coral reefs, 

in estuaries (including the National Estuarine Research Reserve System), National Marine Sanctuaries, and coastal ocean regions. Th e 

scientists within NCCOS conduct applied research and manage long-term research projects, which provide a link between laboratory 

research and coastal management. See http://coastalscience.noaa.gov/about/welcome.html.

• National Geodetic Survey (NGS): NGS is responsible for defi ning, managing, and providing public access to the National Spatial Reference System, a consistent national coordinate system that is the foundation for mapping and charting. NGS defi nes the National Shoreline, providing critical baseline data to manage coastal resources. An accurate, consistent, and up-to-date national shoreline can provide 

storm surge, coastal fl ooding, and pollution trajectory modeling; land and marine geographic information systems; and environmental 

analysis and monitoring. NGS also maps the coastal zone and waterways of the U.S. and its possessions. See http://www.ngs.noaa.gov/. 

• National Marine Sanctuary Program: Th e focus of this Program is to recognize, understand, forecast, and respond to natural and humancaused environmental changes within U.S. Sanctuaries. Sanctuary site characterizations are developed on biodiversity, habitats, resources, 

ecological processes, eff ects of human activities, and socioeconomic information. Monitoring programs focus on the status and condition 

of marine life and habitats to detect trends within the sanctuaries. Th e National Marine Sanctuary Program is partnering with NCCOS 

to conduct research within sanctuary waters. See http://sanctuaries.noaa.gov/.

• National Oceanographic Data Center (NODC): NODC is a national repository and dissemination facility of publicly available global 

oceanographic data (extending back over 100 years) of the Earth’s changing environment. NODC maintains and updates a national ocean 

archive with environmental data acquired from domestic and foreign activities and produces products and research from these data, which 

help monitor global environmental changes. Th ese data include physical, biological and chemical measurements from coastal and deep 

ocean areas derived from in situ oceanographic observations, satellite remote sensing of the oceans, and ocean model simulations. Th e 

National Coastal Data Development Center (NCDDC) is a major component of NODC and provides a coordinated data management 

system and data discovery mechanism for atmospheric, oceanographic, and terrestrial physical sciences to facilitate sustained economic 

growth, scientifi cally sound environmental management, and public safety to the Nation and international community. NCDDC ensures 

that core data variables for an Integrated Ecosystem Assessment (IEA) are available to scientists in common usage formats via a web-based 

portal providing timely access to integrated observations data, information, products, and model analyses. See http://www.nodc.noaa.

gov/ and http://www.ncddc.noaa.gov/. 

• NMFS Offi ce of Science and Technology Enterprise Data Management: F/ST is leading an eff ort to develop an Enterprise Data Management system for NMFS, with emphasis on standardized metadata collection, management, and distribution.

• NOAA Coastal Services Center (CSC): Th e CSC works with various branches of NOAA and other Federal agencies to bring information, services, and technology to the nation’s coastal resource managers. Data sources include: imagery; land cover; elevation data from 

LIDAR (light detection and ranging) or IfSAR (interferometric synthetic aperture radar); shallow benthic habitats primarily from aerial 

photography or multispectral imagery; NOAA Composite Shoreline; and NOAA Shoreline Data. See http://www.csc.noaa.gov/. 
97

• Offi ce of Oceanic and Atmospheric Research (OAR): OAR cooperates with its research partners to explore and investigate ocean habitats 

and resources, and to look for changes in the oceans due to natural and human activities. OAR is actively engaged in technology development to improve marine measurement and monitoring capabilities, integrated ocean mapping, habitat monitoring and modeling, and 

ecological observations and forecasting. OAR strives to build a stronger economy through marine products and businesses, such as biotechnology and sustainable aquaculture. OAR administers NOAA research laboratories (i.e. Pacifi c Marine Environmental Laboratory, 

Atlantic Oceanographic and Meteorological Laboratory), the National Sea Grant Program, the Offi ce of Exploration and Research, and 

the cooperative research institutes.

• Offi ce of Coast Survey: Coast Survey is responsible for acquiring hydrographic data in support of NOAA’s nautical charting program and 

producing and maintaining a suite of over 1,000 nautical charts that cover the coastal waters of the United States, the Great Lakes, and 

some U.S. territories. Th e Coast Survey Development Laboratory develops and improves cartographic, hydrographic, and oceanographic 

systems, helping to provide products and services in support safe and effi cient navigation and the utilization and protection of the coast. 

Coast Survey also off ers an expanded variety of products derived from chart data that are GIS user-friendly for the nonnavigational user 

group. Th ese data are important for many applications besides charting, such as coastal zone management, modeling of tides and currents, 

predicting hazardous algal blooms, responding to disasters, and assisting in fi sheries research and monitoring. See http://www.nauticalcharts.noaa.gov/. 

• Offi ce of Ocean and Coastal Resource Management (OCRM): OCRM provides national leadership, strategic direction and guidance to 

state and territory coastal programs and estuarine research reserves. Th e Offi ce oversees six major programs: the National Coastal Zone 

Management Program; the Coral Reef Conservation Program; the National Estuarine Research Reserve System; the Coastal and Estuarine Land Conservation Program; the National Marine Protected Areas Center; and the Coastal Nonpoint Pollution Control Program.

OCRM also partners with the University of New Hampshire to form the Cooperative Institute for Coastal and Estuarine Environmental 

Technology, a leader in transforming science into practical, innovative tools that coastal resource managers need to address the challenges 

of development, rising sea levels, pollution, and habitat restoration. See http://coastalmanagement.noaa.gov/. 

• Offi ce of Ocean Exploration & Research (OER): OER supports NOAA and National objectives by exploring the Earth’s largely unknown oceans for the purpose of discovery and the advancement of knowledge. Built from the merger of NOAA’s Undersea Research 

Program and the Offi ce of Ocean Exploration, OER is poised to build on a rich legacy of undersea exploration, discovery, and research. 

Th e four core activities in OER’s mission are: 1) interdisciplinary exploration; 2) systematic research in four thematic areas (extreme and 

unique environments, ecosystems frontiers of the continental shelf, new resources from the sea, and ocean dynamics: episodic events to 

long-term changes); 3) underwater technology; and 4) education and outreach. In 2008, OER began operation of a dedicated exploration 

vessel, the Okeanos Explorer. See http://explore.noaa.gov/ and http://www.nurp.noaa.gov/index.htm. 

• Offi ce of Response and Restoration (OR&R): OR&R protects coastal and marine resources, mitigates threats, reduces harm, and restores 

ecological function. OR&R’s core activities include: 1) scientifi c support for oil and chemical spill response and damage assessments in 

coastal waters; 2) evaluating coastal contamination; 3) working with communities to address critical local and regional coastal challenges; 

and 4) restoring and monitoring coastal and estuarine habitat. OR&R participates in the NOAA’s Damage Assessment, Remediation, and 

Restoration Program (DARRP), a multioffi ce eff ort involving the Damage Assessment Center, Offi ce of General Council for Natural Resources, and Restoration Center. DARRP conducts studies to identify the extent of resource injuries, the best methods for restoring those 

resources, and the type and amount of restoration required; OR&R’s Assessment and Restoration Division is responsible for assessing 

the impact to NOAA trust resources from releases of oil and hazardous materials to achieve the goal of restoration. See http://response.

restoration.noaa.gov/ and http://www.darrp.noaa.gov/.

• Sea Grant: Sea Grant is a nationwide network of 32 university-based programs administered through NOAA. Th e National Sea Grant 

College Program engages this network of the nation’s top universities in conducting scientifi c research, education, training, and extension 

projects designed to foster science-based decisions about the use and conservation of our aquatic resources. Under the Ecosystems and 

Habitats Th eme, Sea Grant determines the impacts of coastal pollution and develops innovative approaches to protect these habitats from 

further degradation as well as to reverse the changes that have occurred. Sea Grant emphasizes the land-sea interface in determining the 

quality of coastal waters, and provides managers with the scientifi c and technological tools needed to address regional and local problems. 

See http://www.seagrant.noaa.gov/. 

• U.S. Global Ocean Ecosystem Dynamics (GLOBEC): U.S. GLOBEC is a multidisciplinary research program supported by NMFS, NCCOS, and the National Science Foundation. Th e program has been designed by oceanographers, fi shery scientists, and marine ecologists 

to understand how climate change and variability will translate into changes in the structure and dynamics of marine ecosystems and in 

fi shery production. U.S. GLOBEC data are available at an allied web site in a standardized format through a distributed data management 
98

system. U.S. GLOBEC is a component of the U.S. Global Change Research Program and is linked to worldwide research on this topic

through the International GLOBEC Program. See http://www.usglobec.org/. 

• U.S. Integrated Ocean Observing System (IOOS): IOOS is a multidisciplinary system designed to enhance our ability to collect, deliver, 

and use ocean information. Th e goal is to provide continuous data on our open oceans, coastal waters, and Great Lakes in the formats, 

rates, and scales required by scientists, managers, businesses, governments, and the public to support research and inform decisions. IOOS 

is the U.S. contribution to the Global Ocean Observing System, which is designed to improve weather forecasts and climate predictions. 

IOOS represents a national partnership in which 17 Federal agencies and 11 Regional Associations share responsibility for the design, 

operation, and improvement of a national network of observations. See http://ioos.noaa.gov/ and http://www.ioc-goos.org.

Habitat-related Programs and Activities Outside of NOAA

U.S. Fish and Wildlife Service (USFWS) Programs and Activities

• Coastal Program: Th is Program aims to effi ciently achieve voluntary habitat conservation, through fi nancial and technical assistance, 

for the benefi t of USFWS Trust Species. Th e Coastal Program works to avoid species declines by enhancing the agency’s eff orts within 

the Nation’s coastal areas and securing funding for conservation, including habitat restoration eff orts. Th e Coastal Program integrates 

all USFWS activities in high priority coastal ecosystems to: 1) identify the most important natural resource problems and solutions; 2) 

infl uence the planning and decision-making processes of other agencies and organizations with the Service’s living resource capabilities; 

3) implement solutions on-the-ground in partnership with others; and 4) instill a stewardship ethic, and catalyze the public to help solve 

problems, change behaviors, and promote ecologically sound decisions. Th e Coastal Program provides incentives for voluntary protection 

of threatened, endangered and other species on private and public lands alike. See http://www.fws.gov/coastal. 

• National Fish Habitat Action Plan (NFHAP): NFHAP leverages Federal, state, and privately raised funds to build regional partnerships 

to address the most important fi sh habitat problems. Th e emphasis of NFHAP has been on inland, freshwater systems. Led by USFWS, 

partners include the several states, the USGS, the National Fish and Wildlife Foundation, fi shing and conservation organizations and industry, and, more recently, NMFS. Th e current NFHAP program took shape over the last several years, marked by the publication of the 

“Action Plan” in 2006 and the recent release of a draft report, “A Framework for Assessing the Nation’s Fish Habitat”. Th e fi rst NFHAP 

national assessment is scheduled for completion in 2010. See http://www.fi shhabitat.org/. 

• National Wetland Inventory: USFWS has developed a series of topical maps of wetlands habitats to be used for management, research, 

policy development, education and planning activities. Digital data can be viewed and downloaded through several methods. A Congressional mandate also requires USFWS to produce wetlands status and trends reports for the nation and to report to the Congress at 

periodic intervals. See http://www.fws.gov/wetlands/index.html. 

Non USFWS Habitat-related Programs, Activities, and Agencies 

• Census of Marine Life (COML): Th e COML is a global network of researchers in more than 80 nations engaged in a 10-year scientifi c 

initiative to assess and explain the diversity, distribution, and abundance of life in the oceans. Th e Census aims to: 1) make a comprehensive global list of all forms of life in the sea and catalog these species in an on-line encyclopedia; 2) produce maps of the territory or range 

of the species; 3) complete measures of abundance. Th e world’s fi rst comprehensive Census of Marine Life will be released in 2010. In 

addition to fi eld projects, COML also runs the Ocean Biogeographic Information System (OBIS) that provides expert geo-referenced 

data and spatial query tools for visualizing relationships among species and their environment. Integrating biological, physical, and chemical oceanographic data from numerous sources, OBIS provides tools to test hypotheses about marine biodiversity and assist research on 

marine ecosystems. OBIS currently contains more than 8.7 million geo-referenced, accurately identifi ed species records from more than 

70 databases that are readily and freely accessible via the internet and require no special soft ware to use. See http://www.coml.org. 

• Heinz Center’s State of the Nation’s Ecosystems Project: Th e Heinz Center is a nonprofi t, nonpartisan institution dedicated to improving 

the scientifi c and economic foundation for environmental policy through collaboration among industry, environmental organizations, 

academia, and government. Th e goal of the State of the Nation’s Ecosystems project is to provide a national perspective on the condition 

of the nation’s ecological assets. Experts have identifi ed key aspects of our Nation’s coasts and oceans, fresh waters, forests, farmlands, 

grasslands and shrub lands, and urban and suburban areas that should be tracked through time to provide a consistent and comprehensive 

view of trends in each of these ecosystems. See http://www.heinzctr.org/ecosystems/. 
99

• Marine Geoscience Data System (MGDS): MGDS provides access to data portals for the National Science Foundation-supported Ridge 

2000 and MARGINS programs, the Antarctic and Southern Ocean Data Synthesis, the Global Multi-resolution Topography Synthesis, 

and Seismic Refl ection Field Data Portal. Th ese portals provide free public access to a wide variety of primarily marine geoscience data 

collected during expeditions throughout the global oceans. MGDS is also host to the U.S. Antarctic Program Data Coordination Center; 

2) GeoMapApp, a data visualization and analysis tool; 3) the Global Multi-Resolution Topography, a continuously updated compilation 

of seafl oor bathymetry integrated with global land topography; and 4) the MGDS MediaBank, which contains high quality images, illustrations, animations and video clips. See http://www.marine-geo.org/. 

• Minerals Management Service Off shore Energy and Minerals Management Program (MMS-OEMM): MMS, a bureau in the U.S. Department of the Interior, manages the nation’s natural gas, oil and other mineral resources on the outer continental shelf. Th is includes 

alternative energy programs (i.e. wind, wave, or ocean current energy) as well as off shore oil and gas leasing in U.S. waters. MMS is responsible for conserving these resources and taking maximum steps to protect the environment. OEMM has an Environmental Division that 

provides environmental policy guidance, direction, and program oversight with respect to: preparing the 5-year leasing program; carrying 

out a national Environmental Studies Program; seeing that Congressionally provided grant assistance funds are appropriately distributed 

and used; evaluating the potential and actual environmental impacts associated with extraction of off shore energy and marine minerals; 

and ensuring that OEMM policies and industry practices conform to the Nation’s environmental policies and laws. Th e Off shore Program 

is comprised of three regions: Alaska, Gulf of Mexico, and the Pacifi c. See http://www.mms.gov/.

• Ocean Observatories Initiative (OOI): OOI is a division of the National Science Foundation’s (NSF) Ocean Sciences Program that focuses the science, technology, education, and outreach of an emerging network of ocean observing systems. OOI is the NSF’s contribution 

to IOOS. Th is science-driven eff ort will focus on discoveries resulting from new technologies, with sensors measuring physical, chemical, 

geological, and biological variables in the oceans. Greater knowledge of these variables is vital for improved detection and forecasting of 

environmental changes and their eff ects on biodiversity, coastal ecosystems, and climate. See http://www.oceanleadership.org.

• U.S. Geological Survey (USGS): Th e USGS operates a number of habitat-related programs. Th eir seafl oor mapping and benthic characterization work (http://walrus.wr.usgs.gov/pacmaps/index.html) produces maps and geologic information useful for marine resource 

management. Projects use water and sediment sampling, bottom video, sidescan sonar, and multibeam sonar data, and develop new 

methods of integrating and distributing data and benthic characterization and surfi cial geology maps. Th e usSeabed Project (http://walrus.wr.usgs.gov/usseabed/) provides information about seafl oor characteristics from the beach to the deep sea, and aims to improve the 

understanding of interactions between land and sea, the eff ects of river discharge and sea level changes, distributions of benthic fl ora and 

fauna, location and type of resources, potential consequences of human activities on the oceans, and other critical issues. See http://www.

usgs.gov/. 

Regional Habitat-related Programs and Activities

• Atlantic Coastal Cooperative Statistics Program (ACCSP): ACCSP is a cooperative state-Federal program to design, implement, and 

conduct marine fi sheries statistics data collection programs, and to integrate those data into a single data management system that will 

meet the needs of fi shery managers, scientists, and fi shermen.

• California Seafl oor Mapping Project (CSMP): Th e CSMP is a state-Federal mapping eff ort to create a comprehensive coastal and marine 

geologic and habitat base-map series for the entire California land/sea margin (mean high water out to three nautical miles). CSMP includes: ship-based, high-resolution sonar data collection for unmapped coast; data ground-truthing using video or physical sampling of 

the seafl oor; and production of multisheet folio map sets (1:24,000 scale) of bathymetry, geologic, and habitat interpretation. Partners 

include the California Ocean Protection Council, California Department of Fish and Game, USGS, NOAA’s NMFS and Coastal Services Center, and California State University Monterey Bay.

• Center for Coastal Margin Observation & Prediction (CMOP): CMOP is dedicated to researching the health of the ocean and impact of 

human activity in the Oregon and Washington coastal margins, where the Columbia River meets the Pacifi c Ocean. CMOP facilitates interdisciplinary research, technology development, education, and knowledge transfer in order to better understand the physical, chemical, 

and biological processes regulating river-to-ocean ecosystems. Th e center studies coastal margins (watersheds, estuaries, plume dynamics, 

nutrient fl uxes, tides, microbial communities, estuary turbidity maximum, and the ocean continental shelf ) and is currently developing 

models that will predict everything from algal blooms to salmon runs and improve the health of our rivers and oceans. Th e center is a 

multiinstitutional National Science Foundation Science and Technology Center; partners include several academic and industry partners. 

See http://www.stccmop.org. 
100

• Gulf of Maine Council on the Marine Environment: Th is is a U.S.-Canadian partnership of government and nongovernment organizations working to maintain and enhance environmental quality in the Gulf of Maine to allow for sustainable resource use by existing and 

future generations. Th e Council organizes conferences and workshops; off ers grants and recognition awards; conducts environmental 

monitoring; provides science translation to management; raises public awareness about the Gulf; and connects people, organizations, and 

information. Some of the Council’s specifi c projects include the Gulf of Maine Mapping Initiative, the Gulfwatch Monitoring Program, 

the Regional Habitat Monitoring Data System, and habitat restoration and Action Plan competitive grants programs. See http://www.

gulfofmaine.org/.

• Gulf of Mexico Alliance: Th is partnership among Alabama, Florida, Louisiana, Mississippi, and Texas has the goal to enhance the ecological and economic health of the Gulf of Mexico. Four of six priority issues for the Alliance are related to habitat: water quality; habitat 

conservation and restoration; ecosystem integration and assessment; and nutrients and nutrient impacts. Th e Alliance’s most recent action plan, released in 2009, sets a course to improve the health of coastal ecosystems and economies of the Gulf in ways that a single entity 

could not achieve. See http://gulfofmexicoalliance.org/welcome.html.

• Hawaiian Archipelago Marine Ecosystem Research Plan (HAMER): HAMER is a conceptual layout of a place-based, 10-year, ecosystem 

research initiative dedicated to understanding broad-scale archipelagic ecosystem processes. Th is collaboration among NMFS, the Hawaii 

Division of Aquatic Resources, the Papahānaumokuākea Marine National Monument, the University of Hawaii, U.S. Fish & Wildlife 

Service, and the Western Pacifi c FMC addresses priority areas of research in the region. HAMER’s objective is to have Hawaii serve as a 

large-scale archipelagic laboratory, comparing biophysical processes in the protected and nearly pristine Northwestern Hawaiian Islands 

to those of the heavily used main Hawaiian Islands. See http://www.pifsc.noaa.gov/tech/NOAA_Tech_Memo_PIFSC_14.pdf. 

• North Pacifi c Research Board (NPRB): Th e NPRB was created by Congress in 1997 to recommend marine research initiatives to the U.S. 

Secretary of Commerce; funds are used to conduct research on fi sheries or marine ecosystems of the North Pacifi c Ocean, Bering Sea, and 

Arctic Ocean. Th e NPRB has two major research initiatives, the Bering Sea Integrated Ecosystem Research Project (IERP) and the Gulf 

of Alaska IERP, with goals to determine eff ects of environmental and anthropogenic processes on dynamic linkages among trophic levels 

of fi sh and fi sheries, marine mammals and seabirds. See http://www.nprb.org. 

• Pacifi c Coast Marine Habitat Program: Th is program was developed and is maintained by Pacifi c States Marine Fisheries Commission. 

Th is public website provides access to geospatial data, much of which was compiled in support of the Pacifi c Coast Groundfi sh EFH 

Environmental Impact Statement (EIS). Th e site features interactive mapping tool to view various data layers, including access to detailed 

information about each of the 82 groundfi sh species, economics, and fi shing regulations in marine managed areas. See http://marinehabitat.psmfc.org/index.php.

• Southeast Area Monitoring and Assessment Program (SEAMAP): Th is cooperative program from the southeastern U.S. has goals to: 

collect long-term, standardized, fi sheries-independent data on the condition of regional LMR’s and their environment; plan and evaluate SEAMAP-sponsored activities; operate the SEAMAP Information System for effi cient management and timely dissemination of 

fi sheries-independent data and information; identify and describe existing non SEAMAP databases and activities that are of value in 

fi sheries-independent assessments of regional LMR’s; and coordinate and document SEAMAP activities, and disseminate programmatic

information.

• West Coast Governors’ Agreement on Ocean Health: Th is is a proactive collaboration by the Governors of California, Oregon and Washington to protect and manage the ocean and coastal resources along the entire west coast. Th e Agreement has set goals of clean coastal 

waters and beaches; healthy ocean and coastal habitats; eff ective ecosystem-based management; reduced impacts of off shore development; increased ocean awareness and literacy among the region’s citizens; expanded ocean and coastal scientifi c information, research, 

and monitoring; and sustainable economic development of coastal communities. Four immediate actions are to reinforce opposition

to oil and gas leasing, exploration and development; to secure funding to address the threat of nonpoint source pollution; to develop a 

Sea Grant Research Plan for the west coast in coordination with the National Sea Grant offi ce, academia, and other institutions; and to 

request the White House Council on Environmental Quality to facilitate the implementation of the U.S. Ocean Action Plan, to assist 

the three states in requesting and receiving technical assistance from Federal agencies to address issues of regional signifi cance. See http://

www.westcoastoceans.gov/.
101

Appendix 7: Region-Specific Habitat Science Programs and 

Staffing Needs to Achieve Tiers of Habitat Assessment 

Excellence

Th e Pacifi c Islands Fisheries Science Center (PIFSC)

Th e PIFSC’s area of responsibility includes a vast expanse (1.7 million square miles) of the western and Central Pacifi c Ocean supporting 

a wide range of habitats that include shallow reefs, islands, banks, deep slopes, seamounts, and the oceanic seascape. Th e region comprises 

two archipelagos (Hawaii and the Mariana Islands) and parts of four other archipelagos (Samoa, Line Islands, Phoenix Islands, and Marshall 

Islands), and includes some of the most remote and densely populated islands in the world separated by the international high seas. Th e 

fi sheries of the region are diverse, ranging from commercial oceanic longline fi shermen to individual fi shers on remote islands who sell their 

reef catches at local markets. Th e culturally diverse fi shing communities in this region are a unique challenge to data collection, research, 

and management. Regional management of the pelagic, insular, and seamount fi sheries is conducted by the Western Pacifi c Fishery Management Council (WPFMC), located in Honolulu, Hawaii. 

PIFSC Current Habitat Activities 

Th e PIFSC is responsible for 56 management unit species listed under the jurisdiction of the WPFMC. FMP’s include bottomfi shes/seamount groundfi shes, coral reef ecosystems, crustaceans, pelagics (highly migratory species), and precious corals. No dedicated habitat funds

exist for the PIFSC, so all current habitat research is conducted as a byproduct of other activities or the result of piecemeal, opportunistic 

funding from sources outside of NOAA. Some habitat research has been conducted for pelagic fi shes by relating fi shery catches and environmental data from satellite tagging studies to the horizontal and vertical stratifi cation in the oceanic seascape. Much of this work has been 

conducted in conjunction with funding to mitigate sea turtle bycatch, and from support of the Fisheries and Environment (FATE) program 

(see Appendix 6). In particular, remote sensing has been used eff ectively to assess oceanic habitats and monitor change.

Steep pinnacles that rise from abyssal depths of the Pacifi c plate to create islands, reefs, and banks form the insular habitat of the Pacifi c 

Islands. Although comprising the minority of habitat in the region (the rest is oceanic), the entire insular ecology is dependent on this small 

area and it is the most vulnerable to impact from anthropogenic eff ects of development. External funds from the Coral Reef Conservation 

Program and NOS have supported diver and tow-board imagery surveys of shallow-water coral reefs. Multibeam mapping of mid-water

depths (30-2,500 meters) has been extensive and, along with limited optical validation, has led to preliminary benthic characterizations 

for the Hawaiian Archipelago, American Samoa, Guam and the Northern Mariana Islands, and the Pacifi c Remote Island Areas. Cooperative eff orts with the University of Hawaii have provided almost complete depth and backscatter data for the deep slope areas of the main 

Hawaiian Islands. Th ese data have been used to inform the management of commercial bottomfi sh. No dedicated and dependable funding 

is available to systematically study the resources of the banks, slope, and subphotic zone. Th e habitat work conducted in these ecosystems 

has depended on addressing issues at the intersection with protected species or on making use of ephemeral sources of funds (e.g. National 

Undersea Research Program [NURP], Ocean Exploration [OE], Cooperative grants). It has not been possible to address NMFS long-term 

priorities to monitor habitat because all funding for habitat work comes from non NMFS sources.

Recent area closures by Presidential decree have formed National Marine Monuments in the Northwestern Hawaiian Islands, the U.S. Line 

and Phoenix Islands, the Northern Mariana Islands, and Rose Atoll, which protect both insular and pelagic habitat in the Pacifi c Islands 

Region. Th is introduces new challenges to management and stock assessment. Managed species in archipelagic situations where demersal 

fi shes move among open and close areas can compromise the assumptions made in current stock assessment models. Movement data and an 

understanding of the species habitat ecology rapidly become more relevant in support of stock assessment eff orts. With mounting requests 

for ecosystem evaluations that discern eff ects of fi shing from other sources of variability, there is a need for a systematic, dependable source 

of habitat data in the Pacifi c Islands Region. 

PIFSC Staffi ng Levels Required to Meet the Goals of the Tiers of Excellence

Th e PIFSC currently has 30 full-time scientists dedicated to habitat issues (Table A7-1). Twenty of those staff (67%) are supported with non 

NMFS funds (NOS support) that are slated for reduction to an undetermined level in 2010. Th is is a critical consideration for projections 

of habitat staff to meet the goals of the three Tiers of Excellence in the HAIP. If coral funding levels are maintained, the need for habitat 

staff could be moderate; if, however, the PIFSC loses NOS coral funding, the need for habitat staff will be much higher. Table A7-1 refl ects 
102

Activity Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

Collect habitat-related data 15 15 5 20 20 40

Process and convert raw habitat data into usable products 5 5 2 7 10 17

Produce habitat-specifi c assessments 5 2 5 7 7

Determine habitat-specifi c vital rates over time 20 20

Refi ne existing habitat-related survey methods/tools and develop new ones 2

Refi ne existing population models and develop new habitat-related ones 2

Incorporate habitat and ecosystem information into stock assessments at SAIP Tier 3 5 5

Refi ne existing habitat and ecosystem models and develop new ones 2 2 4 6

Develop improved habitat risk assessments 3 3

Communicate improved assessment results and conduct other follow-up work 1 0 1 1 1 2

Total 30 22 15 37 63 100

Table A7-1

Number of additional staff (full-time equivalents) required to meet the three Tiers of Excellence by type of activity for the Pacifi c Islands Fisheries 

Science Center. Number of current staff in each category is an estimate and/or composite developed from survey responses (e.g. 20 staff spending 

20% of their time on habitat activities would equate to four full-time staff). Estimated numbers of staff include permanent employees, contractors, 

and students. Grey cells indicate that an activity did not apply in a particular tier, according to the questionnaire. 

the number of staff needed in the event that the coral funds are not renewed. Th e order that activities within the three tiers are conducted 

depends on the specifi c context of the research, and circumstances could involve addressing aspects of the three tiers simultaneously.

Tier 1: Identify Habitats for All Life Stages

As discussed in the above section, staff projections for Tier 1 habitat assessments could range between and two and 22 full-time staff depending on the level of continued support from funds outside the Center. Th at uncertainty aside, Tier 1 should require a minimal increase 

in staff and a source of funds to conduct operations and improve sampling infrastructure. Th e initial focus would be on managed species, 

particularly early life stages that have not yet had their habitat described. Emphasis would be on ecosystems, which would set the groundwork to launch Tier 2 objectives. 

Tier 2: Assess Spatial Extent and Temporal Variability of Habitats 

Tier 2 will require a considerable increase in staff and more resources to understand the distribution and natural variability by habitat type 

for managed species and their ecosystem. Tier 2 will make greater use of technology to improve observational capability in between periodic 

assessments. Research in this tier would seek to understand seasonal and inter-annual aspects of habitat use by managed species and the 

wider community. Tier 2 fi ndings should greatly refi ne the current broad defi nitions of EFH and improve the designation of HAPC’s. 

Tier 3: Role of Habitats in Growth, Reproduction, and Survival by Life Stage

Successful completion of Tier 1 and Tier 2 will provide the basis for the type and extent of habitat research conducted in Tier 3. Th is 

research will be focused on ecosystem interactions and have greater attention to the role of inter-specifi c competition in the growth, reproduction and survival of marine resources. Th is research will involve experimental manipulations and other more resolved approaches not 

used in the earlier tiers. As the work in Tier 3 is dependent on knowing the fi ndings of the Tier 1 and Tier 2, detailed descriptions are not 

possible.

Th e Alaska Fisheries Science Center (AFSC)

Th e AFSC conducts scientifi c research in support of management goals of the Alaska Regional Offi ce (AKRO) and the North Pacifi c FMC, 

which manage the nation’s marine resources in a vast expanse (3.3 million square kilometers of the U.S. EEZ) of the North Pacifi c Ocean. 

Alaska’s physical immensity and high-latitude geography pose major challenges to conducting fi sheries research. Alaska contains more 

than 70% of the nation’s continental shelf habitat, 55,000 kilometers of shoreline, and a highly varied submarine bathymetry owing to the 

numerous geological and physical processes at work. Th e marine environment can be divided into three major geographical subregions−the 
103

Gulf of Alaska, the Bering Sea including the Aleutian Island Archipelago, and the Chukchi and Beaufort Seas in the Arctic. Th e fi rst two 

subregions support particularly rich fi sheries. Alaska thus has diverse and major fi sheries resources to manage that provide approximately 

60% of all U.S. fi sheries production.

Th e AFSC does not have a habitat assessment program per se, but scientists within several diff erent research programs study habitat as it 

relates to their specifi c program disciplines. Only a handful of dedicated full-time scientists are trained to conduct habitat ecological assessments, but others are oft en retooled to study habitat issues as they emerge and time allows. For example, stock assessment scientists now 

undertake an ecosystem considerations analysis as part of their yearly stock assessment duties. Ecosystem factors considered in these analyses 

include eff ects of fi shing and climate, changes in the physical environment, trends in predator and prey abundance, and the temporal and 

spatial distribution of fi sheries bycatch. While the resolution of ecosystem data are generally insuffi cient to warrant modifi cations to recommendations on acceptable biological catch, the process has set in motion the framework for a stronger link between ecosystem research and 

fi sheries management (i.e. EBFM). First attempts to include habitat data in fi sheries stock assessments include the use of bottom temperature and surface current patterns to predict early life history growth and recruitment for some species.

Provisions of the Magnuson-Stevens Fishery Conservation and Management Act of 1996 fueled the most comprehensive habitat assessments completed in Alaska to date by mandating the identifi cation of EFH and the eff ects of fi shing on marine habitats. Recent global interest in the conservation of deep-sea corals sparked a fl urry of habitat assessments in areas of high coral and sponge fi sheries bycatch. Findings 

from those studies helped establish new area closures including HAPC’s, and initiated more detailed follow-up studies of those habitats 

and the ecological benefi ts they provide. AFSC scientists also conduct research and assessments in nearshore habitats to support National 

Environmental Planning Act consultations and other Environmental Impact Statement (EIS) requirements of the AKRO, including a massive eff ort to map Alaska’s coastline habitat with Shorezone imagery (a mapping and classifi cation system that specializes in the collection 

and interpretation of low-altitude aerial imagery of the coastal environment). 

In 2006, a Habitat and Ecological Processes Program was established to facilitate Center-wide habitat assessment activities at the AFSC. 

Th e Program provides the opportunity for AFSC scientists to competitively attain funding for small (< $150K per year) projects outlined 

in designated research priorities. Funding is provided by the AKRO (Habitat Conservation Division) and research priorities address current issues of habitat management. Aside from this single source of dedicated habitat research funding, scientists are encouraged to submit 

requests for funding to outside sources such as the North Pacifi c Research Board, NURP, and OE.

Center-wide contribution to the completion of two major documents, the “Alaska Groundfi sh Fisheries – Final Programmatic Supplemental EIS” (NMFS, 2004) and the “EIS for EFH Identifi cation and Conservation in Alaska” (NMFS, 2005b), provided comprehensive 

inventories of EFH for most of Alaska’s 57 FMP stocks and stock complexes (which include multiple species) as well as the eff ects of the 

fi sheries on EFH. Additionally, Stock Assessment and Fishery Evaluation Reports are updated each year and summarize the best available 

scientifi c information on EFH for each stock. Scientists and managers from the Alaska Region recently inventoried habitat data sets and

encouraged collaborative use of these data (McConnaughey et al., 2009). Much of the framework is therefore already in place as we move 

toward EBFM and integrated habitat research. However, our scientists currently face new challenges with respect to the eff ects of climate 

change on habitat in Alaska. Th ese include the loss of sea ice, acidifi cation of marine waters, and concomitant shift s in the spatial distribution of species and habitat use, particularly in the northern seas (e.g. Chukchi and Beaufort Seas). While these changes are not unique to 

Alaska, the changes expected here may be extreme and serve as a sentinel on a global scale. To meet these challenges along with continued 

human competition for limited marine resources, habitat assessment scientists will need a clear vision of the task ahead and the ability to 

adopt innovative technologies to complete that task.

AFSC Current Habitat Activities

Th e AFSC conducts research to support the management of 60 stocks/stock complexes of fi sh and shellfi sh managed in four FMP’s−the 

Bering Sea and Aleutian Islands Groundfi sh FMP, the Bering Sea and Aleutian Islands King and Tanner Crab FMP, the Gulf of Alaska 

Groundfi sh FMP, and the Arctic FMP. Th e latter FMP was implemented in December 2009 and governs commercial fi shing for all stocks 

of fi nfi sh, shellfi sh, and other living marine resources in the Chukchi and Beaufort Seas, except those managed by other authorities (i.e. 

Pacifi c salmon and Pacifi c halibut). Th e AFSC is also responsible for stewardship of the habitat for these managed fi sh and crab species in 

Federal waters. An Alaska High Seas Salmon FMP also exists, but management authority of salmon stocks has been delegated to the State 

of Alaska by the NPFMC. While the AFSC currently has more than 40 positions dedicated to stock assessment (more than 150 positions 

if fi shery independent surveys and supporting functions and analyses are included), there are only about 17 full-time positions dedicated to 

study the habitat of those species (Table A7-2); two of these (12%) are temporary contractors. Th e AFSC has a long history of conducting 

habitat research and pioneered the use of submersibles to conduct deep-water habitat assessments, but few comprehensive habitat assessments have been conducted in Alaska and have generally been conducted in relatively small geographical areas of high interest. Examples 
104

include: 1) ongoing habitat-specifi c density stock assessments for yelloweye rockfi sh in the eastern Gulf of Alaska (conducted by Alaska 

Department of Fish and Game biologists); 2) an assessment of red tree coral thickets and associated communities in HAPCs in the eastern 

Gulf of Alaska; and 3) assessment of coral and sponge garden habitats in the central Aleutian Islands−all habitat variables for these studies 

were measured in situ via submersible observations. 

AFSC Staffi ng Levels Required to Meet the Goals of the Tiers of Excellence

Tier 1: Identify Habitat for All Life Stages

Th e AFSC would require a minimum of 17 additional full-time staff to conduct Tier 1 habitat assessments (Table A7-2). New staff will 

be necessary to inventory existing habitat data (surfi cial sediment, bathymetry, oceanographic parameters, presence of sedentary invertebrates), integrate with species presence/absence data, and identify habitat data gaps that would be prioritized for future collection. Habitat 

assessments would be initiated for high priority stocks or geographical areas (e.g. HAPC’s). 

Tier 2: Assess Spatial Extent and Temporal Variability of Habitats

Tier 2 assessments would require the addition of 16 staff and access to new resources to initiate studies on the temporal variability in habitat 

use for managed species, to conduct risk assessments for those habitats, and conduct spatially explicit surveys to determine habitat-specifi c 

biomass by life stage for those species. Tier 2 assessments will require the use of new advanced technologies to improve observational capability in between periodic assessments (monitoring). Use of these new technologies would require new staff with proper training. Research 

would seek to understand seasonal and inter-annual aspects of habitat use by managed species and the ecosystems they depend on. Tier 2 

fi ndings should greatly refi ne the current broad defi nitions of EFH by identifying core use areas and improve the designation of HAPC’s.

Tier 3: Role of Habitats in Growth, Reproduction, and Survival by Life Stage

Successful completion of Tier 1 and Tier 2 will provide the basis for designing studies necessary to complete Tier 3 habitat assessments. Tier 

3 research will focus on ecosystem-level studies that include multispecies interactions, habitat-specifi c life cycle models, and the determination of habitat-specifi c vital rates (growth, survival, and reproduction). Th ese types of studies will provide for the undertaking of IEA’s and 

ultimately EBFM for many of the 60 FMP stocks/stock complexes in Alaska. Th is research requires the development of novel scientifi c approaches, the use of state-of-the-art technologies to measure habitat-specifi c vital rates in the laboratory, and 36 additional staff (including 

at least ten trained animal physiologists).

Activity Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

Collect habitat-related data 12 5 7 12 8 20

Process and convert raw habitat data into usable products 3 3 3 6 3 9

Produce habitat-specifi c assessments 1 7 2 9 9

Determine habitat-specifi c vital rates over time 5 5

Refi ne existing habitat-related survey methods/tools and develop new ones 1

Refi ne existing population models and develop new habitat-related ones 0

Incorporate habitat and ecosystem information into stock assessments at SAIP Tier 3 10 10

Refi ne existing habitat and ecosystem models and develop new ones 4 4 5 9

Develop improved habitat risk assessments 3 3

Communicate improved assessment results and conduct other follow-up work 0 2 0 2 2 4

Total 17 17 16 33 36 69

Table A7-2

Number of additional full-time staff required to meet the three Tiers of Excellence by type of activity for the Alaska Fisheries Science Center. The 

number of staff in each category does not necessarily refl ect the absolute number of individuals involved in these activities, because some individuals may divide their time among several activities. Estimated numbers of staff include permanent employees, contractors, and students. Grey cells 

indicate that an activity did not apply in a particular tier, according to the questionnaire. 
105

Th e Northwest Fisheries Science Center (NWFSC)

Th e NWFSC provides scientifi c and technical support to NMFS as mandated by MSRA and ESA for management and conservation of 

the Northwest Region’s marine and anadromous resources. Th e NWFSC conducts research in cooperation with other Federal and state 

agencies and academic institutions within the California Current Large Marine Ecosystem (LME) and Puget Sound, which comprise approximately 800,000 square kilometers. Five divisions, Fishery Resource Analysis and Monitoring, Conservation Biology, Environmental 

Conservation, Fish Ecology, and Resource Enhancement and Utilization Technologies, conduct applied research to resolve problems that 

threaten marine resources or that deter their use. Four of the fi ve divisions conduct research on marine habitats of stocks that fall within 

three FMP’s of the PFMC (Pacifi c Coast Groundfi sh [over 90 species], Coastal Pelagics [nine species], and Pacifi c Coast Salmon [three 

species]). With climate change emerging as an important issue, the NWFSC is also investigating impacts of environmental variability and 

climate on ecosystem processes that support marine and anadromous resources.

Th e Fishery Resource Analysis and Monitoring division consists of multidisciplinary teams with expertise in fi shery biology and ecology, 

stock assessment, habitat studies, economics, mathematical modeling, statistics, computer science, and fi eld sampling techniques. Members 

of this program are stationed at the NWFSC facilities in Seattle, Washington and in Newport, Oregon, with some Groundfi sh Observer 

Program staff located in California. Th e Fishery Resource Analysis and Monitoring division coordinates assessments on FSSI groundfi sh 

stocks coastwide as well as conducts assessments on individual stocks. Staff scientists develop models for managing multispecies fi sheries; 

design programs to provide information on the extent and characteristics of bycatch in commercial fi sheries, as they look at methods to 

reduce fi sheries bycatch; characterize EFH for key groundfi sh species; investigate the design, feasibility, function, and value of MPA’s; and 

employ advanced technologies in ongoing and emerging programs (e.g. the use of AUV’s in untrawlable habitats).

Th e Conservation Biology division is responsible for characterizing the major components of biodiversity in living marine resources using 

the latest genetic and quantitative methods. It also has responsibility for identifying factors that pose risks to these components and the 

mechanisms that limit natural productivity. Th e Division’s multidisciplinary approach draws on expertise from a broad spectrum of scientifi c disciplines, including risk analysis, genetics, evolutionary biology, ecology, and population biology.

Th e Environmental Conservation division investigates the impacts on fi shery resources by anthropogenic and natural perturbations caused 

by habitat alteration, chemical contaminants, and harmful algal blooms. Results are used regionally and nationally to determine scientifi -

cally sound approaches for conserving living marine resources, restoring habitat productivity and function, assessing the impacts of toxic 

substances on the health and safety of fi shery resources, and responding to environmental emergencies from the release of toxic materials. 

Th e Division integrates laboratory assays and fi eld studies in coastal and marine habitats to determine quantitative relationships between 

toxic substances and impaired habitat function upon fi sh, shellfi sh, and marine mammals. 

Th e Fish Ecology division’s role is to understand the complex ecological linkages between commercially and recreationally important marine and anadromous fi shery resources of the Pacifi c Northwest and their habitats. Particular emphasis is placed on investigation of the 

myriad biotic and abiotic factors that control growth, distribution, and survival of important species and on the processes driving short- and 

long-term population fl uctuations. Division scientists conduct regular surveys of pelagic fi shes in coastal waters and use several analytical 

and statistical approaches to determine optimal habitats for managed species. In particular, juvenile salmon have been examined in relation 

to mesoscale oceanographic features (river plumes, fronts, eddies) and habitat prediction maps have been produced based on satellite and 

in situ sampling of broad-scale biophysical variables. Similar analyses have been done for coastal pelagics (anchovy, sardines, and herring), 

highly migratory species (albacore), and the juvenile pelagic phase of many demersal species. In addition to trawling, noninvasive techniques such as acoustics and LIDAR have been used to characterize fi ne-scale habitat utilization by pelagic species in relation to oceanographic variables.

Th e Science Center’s developing Ecosystem Science Program within the Conservation Biology Division has a set of research themes that 

are designed to inform large, system-scale assessments and management of living marine resources. Th is program will be organized around 

the general framework outlined by Integrated Ecosystem Assessments (IEA’s); encompassing qualitative and quantitative approaches to 

analyzing the dynamics of natural and human components of ecosystems. Included in the work of the program will be the development of 

analytical approaches to: 1) identify indicators of system function and thresholds associated with diff erent states; 2) estimate the risk status 

of key natural and human system indicators and collectively, the system’s status; 3) evaluate the individual and cumulative eff ectiveness of 

alternative sets of management strategies in changing indicator status; and 4) design and test monitoring and adaptive management approaches to evaluate how natural and human systems respond to strategies.

Th e NWFSC has maintained an ongoing seafl oor mapping collaboration with Oregon State University’s Active Tectonics and Seafl oor 

Mapping Laboratory since 2001. Th e goal of this collaboration is to prioritize seafl oor-mapping eff orts in the area of the northern Califor-
106

nia Current. Th is mapping eff ort has been linked to similar eff orts off California with one result being the fi rst map of structural habitats 

for the entire California Current LME.

Th e NWFSC, working with one of its academic partners (Oregon State University), has developed the Pacifi c Coast Ocean Observing 

System West Coast Habitat Data Portal to integrate marine geological, geophysical, biological, fi sheries, and physical oceanographic data 

at many scales. Th is data portal provides direct access to data holdings through custom, interactive-view environments and supports datadiscovery tools as well as metadata harvest capabilities. Th is portal can operate as a decision support tool for research and management 

activities such as research planning, MPA and hydrokinetic facility site selection, and IEA’s.

NWFSC Current Habitat Activities

Currently, about 40 full-time staff (of which 30% are contractors) conduct habitat-related research or provide habitat-related data and 

information used to support fi sheries research and management for Pacifi c Coast FSSI stocks and salmonids managed under the Pacifi c 

Coast Salmon Plan at the NWFSC (Table A7-3). Approximately one-third of these individuals are directly involved in habitat-related data 

collection. Other habitat-related activities include data processing and database management, production of habitat assessments, refi ning 

existing habitat-related survey methods and tools, and developing new ones.

NWFSC Staffi ng Levels Required to Meet the Goals of the Tiers of Excellence

Tier 1: Identify Habitats for All Life Stages 

To meet a level of Tier 1 habitat information, the NWFSC would need 20 additional staff (Table A7-3), which would primarily focus on 

using existing data to examine the status of the current habitat knowledge for Pacifi c Coast FSSI stocks and salmonids. Ten researchers will 

be needed to compile habitat-related data and process and convert raw habitat data into usable products. Th is initial Tier 1 step will require 

integration into database and GIS information systems. Th ree additional staff will initiate incorporation of existing habitat-related data into 

ongoing stock assessments. Lastly, two additional staff will develop a plan for producing Tier 2 and Tier 3 habitat assessments.

Tier 2: Assess Spatial Extent and Temporal Variability of Habitats

To meet a level of Tier 2 habitat information, the NWFSC would need 44 new positions, in addition to the 20 staff necessary to reach Tier 

1 (Table A7-3). Th e staff requirements for Tier 2 refl ect needs for groundfi shes and salmonids. Th e majority of new staff (30) would be 

focused on the collection of habitat data, including seafl oor mapping with NWFSC academic partners, and expanded biological surveys in 

both trawlable and untrawlable habitats using bioacoustics, ROV’s, and AUV’s. Th e increase would be suffi cient to produce habitat maps 

for the majority of FSSI and salmonid FMP stocks by life stage as well as accurate descriptions of annual and seasonal variability in fi sh 

Table A7-3

Number of additional full-time staff required to meet the three Tiers of Excellence by type of activity for the Northwest Fisheries Science Center. 

Number of staff in each category does not necessarily refl ect the absolute number of individuals involved in these activities, because some individuals may divide their time among several activities. Estimated numbers of staff include permanent employees, contractors, and students. Grey 

cells indicate that an activity did not apply in a particular tier, according to the questionnaire. 

Activity Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

Collect habitat-related data 15 4 20 24 11 35

Process and convert raw habitat data into usable products 6 6 10 16 8 24

Produce habitat-specifi c assessments 4 7 7 14 14

Determine habitat-specifi c vital rates over time 8 8

Refi ne existing habitat-related survey methods/tools and develop new ones 5

Refi ne existing population models and develop new habitat-related ones 5

Incorporate habitat and ecosystem information into stock assessments at SAIP Tier 3 5 5

Refi ne existing habitat and ecosystem models and develop new ones 5 5 5 10

Develop improved habitat risk assessments 4 4

Communicate improved assessment results and conduct other follow-up work 5 3 2 5 3 8

Total 40 20 44 64 44 108
107

habitat use. Another major diff erence in staffi ng between Tier 1 and Tier 2 is the addition of fi ve individuals to the NWFSC’s compliment 

of modelers to support the refi nement of existing habitat and ecosystem models and the development of new ones. Th e total number of staff 

needed to meet Tier 1 and Tier 2 criteria is 64−more than a doubling over current levels. 

Tier 3: Role of Habitats in Growth, Reproduction, and Survival by Life Stage

To meet a level of Tier 3 habitat information, the NWFSC would need an additional 44 staff (Table A7-3). As with Tier 1 and Tier 2, nearly 

half of these additional staff would be dedicated to habitat-related data collection and processing habitat data into usable products. Eight 

new staff would be needed to determine habitat-specifi c vital rates (age-specifi c rates of growth, mortality, and reproduction) of species for 

use in stock assessment models and other applications. Tier 3 also requires the addition of staff to incorporate habitat and ecosystem information into stock assessments at the SAIP Tier 3 level, and to develop improved risk assessments (nine individuals). Further refi nement of 

existing and new habitat and ecosystem models will require fi ve additional staff over the fi ve necessary to reach Tier 2, resulting in an overall 

increase in the assessment and ecosystem modeling component to 10 individuals.

Th e total number of additional staff required to meet all Tiers of Excellence is 108, a 270% increase over the current 40 full-time staff conducting habitat-related research or providing habitat-related data and information.

Southwest Fisheries Science Center (SWFSC)

Th e SWFSC provides both scientifi c and technical information in support of the management goals of NMFS and the PFMC. SWFSC 

staff conducts scientifi c research in the freshwater and marine environments of California, as well as in parts of the Antarctic, Mexico, and 

open-ocean international waters. Some of this research is carried out in cooperation with the NWFSC as well as the State of California.

Th e Southwest Region is part of the California Current LME, and comprises fi ve general habitat categories: freshwater streams and rivers; 

bays and estuaries (e.g. mudfl ats, marshes, seagrass beds, deep channels); the coastal continental shelf extending from the intertidal (e.g. 

sandy beaches and rocky shores) to 200 meter depth (e.g. rock pinnacles and off shore banks); benthic habitats of the off shore continental 

slope from 200 to over 1,000 meter depth (e.g. extensive submarine canyons and seamounts); and the oceanic system of pelagic habitats 

dominated by the California Current. Th is region represents one of the major coastal upwelling areas of the world, which supports high 

densities of forage for diverse assemblages of marine species. Fisheries in this region also are diverse and include the use of commercial trawl 

nets, hook-and-line gear, purse seines, gillnets, and traps, as well as recreational hook-and-line gear from commercial passenger fi shing vessels, private skiff s, beach, and jetty, and spear fi shing.

Most, if not all, of California’s coastal ecosystem has been dramatically altered by intense, continuous recreational and commercial fi shing 

beginning at least as far back as the 1940’s and by increased population growth and coastal development. Th ese human-induced changes are 

superimposed on natural, but unpredictable, environmental variability caused by large-scale ocean climate phenomena. All of this makes it 

challenging to identify and understand changes in coastal habitats. Southwest salmon habitat, for example, contains the most anthropogenically-impacted rivers in the country, and yet they support over 80% of the Oregon-California Chinook salmon fi shery (averaging just over 

one-half million fi sh). Habitat restoration to date has proceeded in a piecemeal fashion that may have contributed to the major declines 

in the 2008-09 salmon fi sheries. Useful scientifi c advice on what would be the most eff ective habitat restoration activities is badly needed. 

Other current management challenges and concerns include damage to seafl oor habitats (including deep-sea coral and sponge communities) due to fi shing, eff ects of climate change (including the ecological, political, and economic consequences of northward shift s in fi sh distributions with increased ocean temperatures and the implications for trans-national and trans-state allocations), eff ects of marine protected 

area management, and invasive species (e.g. the recent invasion of jumbo squid in the California Current Ecosystem).

SWFSC Current Habitat Activities

Th e SWFSC currently has 33 full-time staff (of which about 45% are contractors supported from a variety of sources both within and external to NMFS) that conduct research on marine habitats of over 110 stocks and species being tracked within the FSSI and/or included 

in four FMPs (i.e. Coastal Pelagic, Pacifi c Coast Groundfi sh, Pacifi c Coast Salmon, and Highly Migratory) of the PFMC. Most of this effort is focused on collecting habitat data and processing and converting these data into usable products (Table A7-4). Over the last decade, 

SWFSC researchers also have been refi ning existing habitat survey methods and tools and developing new ones. SWFSC habitat research 

is designed to eff ectively respond to the MSRA mandates to characterize and protect EFH and to improve stock assessments, as well as to 

understand and predict the eff ects of climate and environmental change on fi sh populations and marine ecosystems at global to local scales. 

Th e goal is to provide sound scientifi c information for eff ective decision-making and ecosystem management.
108

Researchers at the SWFSC are working to predict biological responses of coastal species such as Pacifi c sardine, chub mackerel, northern 

anchovy, market squid, and krill to changing environmental conditions in the California Current pelagic ecosystem. Likewise, researchers 

are relating variation in biotic and abiotic factors of the ocean environment to population dynamics of Chinook and coho salmon, thereby 

revealing the importance of various aspects of pelagic habitats. Satellite and acoustic tags are being used to identify habitat use by salmonids 

(Chinook and steelhead trout) and to defi ne hot spots of adult aggregations; long-line surveys are being used to identify nursery areas for 

migratory species both in the California Current ecosystem (e.g. common thresher shark) and in international waters (e.g. North Pacifi c 

albacore tuna). SWFSC environmental data products (e.g. upwelling index; northern oscillation index) provide the oceanographic context 

for interpreting seasonal and long-term patterns in distribution, abundance, and complex behaviors of several species along the west coast 

and throughout the North Pacifi c. In addition, the west coast node of NOAA CoastWatch program is located at the SWFSC and provides 

timely and relevant satellite-derived environmental products. Many of these environmental data sets have been made readily accessible to 

other scientists, managers, educators, and the general public.

Other researchers at the SWFSC have been using a variety of survey tools and approaches to improve our assessments of demersal fi shes, 

macro-invertebrates (including deep-sea coral communities and endangered white abalone), and associated seafl oor habitats in relatively 

deep water off central and southern California. Habitat-specifi c distribution (EFH Level 1 data) and densities (EFH Level 2 data) of juvenile and adult life stages of a few of 90+ species in the Pacifi c Coast Groundfi sh FMP have been determined from nonextractive, visual 

surveys conducted with ROV’s, a manned submersible, scuba, laser line scan, and high-defi nition drop cameras, oft en coupled with acoustic 

surveys and seafl oor maps of the continental shelf and upper slope off California. Th ese methods have resulted in habitat-specifi c assemblage 

analyses on multiple spatial scales; a fi shery-independent stock assessment; characterization of distribution and potential ecological impacts 

of marine debris; and baseline monitoring of MPA’s. Some of these data and methods were used in the recent risk assessment and policy 

development for EFH of groundfi shes on the west coast, and are being used in the California-NOAA-USGS Seafl oor Mapping Program.

Th e sustained pursuit of marine fi sheries habitat research by the SWFSC has been possible oft en due to successful partnerships with our 

academic colleagues and with opportunistic funding from other NOAA offi ces (e.g. Sea Grant, NURP, OE, and NOS), USGS, state agencies, and private foundations. A comprehensive research program that is directly focused on the ecological value of marine habitats to fi shery 

stocks and on IEA’s will require additional NMFS funding.

SWFSC Staffi ng Levels Required to Meet the Goals of the Tiers of Excellence

Tier 1: Identify Habitats for All Life Stages

Moving to Tier 1 and assessing habitat associations for all life stages of FSSI and FMP stocks using existing data could be achieved with ten 

additional SWFSC staff members (Table A7-4). Six researchers and database managers will be needed to identify, collect, and integrate existing data sets of various environmental and biological variables over time and space, which are archived by several state, Federal, and interActivity Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

Collect habitat-related data 9 28 10 8 18

Process and convert raw habitat data into usable products 12 4 4 8 6 14

Produce habitat-specifi c assessments 0 2 4 6 6

Determine habitat-specifi c vital rates over time 6 6

Refi ne existing habitat-related survey methods/tools and develop new ones 7

Refi ne existing population models and develop new habitat-related ones 1

Incorporate habitat and ecosystem information into stock assessments at SAIP Tier 3 6 6

Refi ne existing habitat and ecosystem models and develop new ones 4 4 4 8

Develop improved habitat risk assessments 2 2

Communicate improved assessment results and conduct other follow-up work 4 2 2 4 2 6

Total 33 10 22 32 34 66

Table A7-4

Number of additional full-time staff required to meet the three Tiers of Excellence by type of activity for the Southwest Fisheries Science Center. 

Number of Staff in each category does not necessarily refl ect the absolute number of individuals involved in these activities, because some individuals may divide their time among several activities. Estimated numbers of staff include permanent employees, contractors, and students. Grey 

cells indicate that an activity did not apply in a particular tier, according to the questionnaire. 
109

national sources. Habitats for most of these stocks have not been assessed or have been inadequately assessed. Two additional staff members 

will be needed to produce more comprehensive assessments with the data at hand. Identifying gaps in knowledge and prioritizing habitats 

for further assessment will be a part of these eff orts. Two additional technical staff members will be necessary to organize and communicate 

results among staff scientists, managers, scientifi c community, and PFMC. 

Tier 2: Assess Spatial Extent and Temporal Variability of Habitats

Meeting the objectives of Tier 2 assessments (i.e. to produce habitat maps over the geographic range of all stocks and life stages and to 

determine their habitat-specifi c abundances) will require an estimated 22 new positions in addition to the 10 identifi ed in Tier 1 (Table 

A7-4). At least 12 more staff members will be needed to expand habitat-specifi c fi eld surveys, as well as to process and convert the raw data 

into usable products. SWFSC scientists are developing and using advanced technology survey methods and tools such as manned submersibles, ROV, AUV, multibeam acoustics, LIDAR, satellite and acoustic tracking, and airborne thermal videography to assess habitats and 

associated species on multiple spatial scales. Th ese methods will form the core for fi shery-independent data collection and monitoring in 

Tier 2. Four additional staff will be needed to conduct assessments from these fi ne-scale data collection eff orts. Th e analyses of data from 

these advanced technology surveys will lead to better understanding of the natural patterns of habitat variability over time and across space. 

Th ese patterns, along with associated population processes, will be used to refi ne existing habitat and ecosystem models and to develop 

new ones to predict habitat suitability for the various stocks and to improve stock assessments. Th ese models can also be used to investigate 

initial risk assessments, which will lead to identifi cation and prioritization of habitat and stock restoration, conservation, and preservation 

activities. Additional staff will also be needed to communicate improved assessments to PFMC and its advisory bodies, as well as to other 

constituents.

Tier 3: Role of Habitats in Growth, Reproduction, and Survival by Life Stage

Meeting the objectives of Tier 3 assessments will be especially challenging and will require a substantial increase in scientifi c eff ort (Table 

A7-4). Explicit incorporation of habitat and other ecosystem considerations into stock assessments will require the additional eff ort of 34 

new personnel and the interdisciplinary cooperation and facilitation among stock assessment scientists and habitat biologists and ecologists. Th is eff ort will require increases in habitat-related data collection and processing, determination of habitat-specifi c vital rates over 

time for the diff erent life stages of the stocks, and integrating of these data into population and ecosystem models.

A total of 66 full-time positions, in addition to the current 33 staff positions, will be required to reach the goals of all Tiers of Excellence for 

habitat research on FSSI and FMP stocks at the SWFSC. As noted elsewhere in this document, the tasks and objectives identifi ed in each 

of the three tiers are largely interrelated and will lead to improved stock assessments, risk assessments, and IEA’s.

Southeast Fisheries Science Center (SEFSC)

Th e SEFSC provides science to assist in managing 77 FSSI stocks and stock complexes that are distributed over a wide variety of habitats. 

Th e SEFSC is based in Miami, Florida with additional laboratories in Beaufort, North Carolina; Panama City, Florida; Pascagoula, Mississippi; and Galveston, Texas. Th ese laboratories and associated offi ces conduct multidisciplinary research to provide management information supporting three diff erent FMC’s (the South Atlantic FMC, Gulf of Mexico FMC, and Caribbean FMC) and International Commission for the Conservation of Atlantic Tunas through NOAA’s Highly Migratory Species program. Th e Southeast Region encompasses three 

LME’s−the Southeast Shelf, the Gulf of Mexico, and the Caribbean Sea. Fisheries in the Region are diverse and range from artisanal traps 

for fi sh and crustaceans on coral reefs to open ocean long-lines for highly migratory species and trawls that sweep the muddy bottom of the 

Gulf of Mexico for shrimp. Commercial bycatch and large recreational fi sheries contribute to allocation controversies.

Coastal bottom habitats in this Region include extensive mud and sand bottom, low relief carbonate-based hard bottom, sponge and shell 

banks, topographic highs, sea grass beds, and coral reefs. Pelagic habitats are characterized by major oceanographic currents (such as the Gulf 

Stream and the Loop Current), the Mississippi River plume, and extensive mats of fl oating Sargassum. Many fi shery species in the region 

occupy the waters over the continental shelf as adults but spend early life stages in estuarine nurseries. Th is ontogenetic linkage connects 

coastal ecosystems with inshore habitats that are oft en impacted or threatened by human development of the coast. Common estuarine 

habitats used by juvenile fi shery species include coastal wetlands, seagrass beds, oyster reefs, mangroves, and tidal mudfl ats; these habitats are 

highly productive and appear to be important in sustaining fi shery productivity. Th e coastal zone also is infl uenced by freshwater and nutrient inputs from numerous watersheds, including the Mississippi River drainage area covering 41% of the 48 contiguous United States.
110

Table A7-5

Number of additional full-time staff required to meet the three Tiers of Excellence by type of activity for the Southeast Fisheries Science Center. 

Number of staff in each category does not necessarily refl ect the absolute number of individuals involved in these activities, because some individuals may divide their time among several activities. Estimated numbers of staff include permanent employees, contractors, and students. Grey 

cells indicate that an activity did not apply in a particular tier, according to the questionnaire. 

Activity Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

Collect habitat-related data 21 4 21 24 10 34

Process and convert raw habitat data into usable products 10 13 10 23 10 33

Produce habitat-specifi c assessments 5 6 10 16 16

Determine habitat-specifi c vital rates over time 10 10

Refi ne existing habitat-related survey methods/tools and develop new ones 3

Refi ne existing population models and develop new habitat-related ones 4

Incorporate habitat and ecosystem information into stock assessments at SAIP Tier 3 10 10

Refi ne existing habitat and ecosystem models and develop new ones 10 10 5 15

Develop improved habitat risk assessments 5 5

Communicate improved assessment results and conduct other follow-up work 4 1 5 6 5 11

Total 47 24 55 79 55 134

SEFSC Current Habitat Activities

Th e large number of habitats in the oceanic and coastal regions of the Southeast Region, combined with the number of fi shery species, make 

habitat research a challenge. We have estimated that an equivalent of 47 full-time staff positions (Table A7-5) are currently working on habitat issues related to FSSI/FMP stocks in the SEFSC. Approximately 27% of these are contract employees, and funding for these positions 

comes from a wide variety of programmatic and reimbursable sources both internal and external to NMFS. Th e goals and objectives of this 

habitat research are widely variable, commensurate with the ephemeral nature of these funding sources. 

Current habitat research at the SEFSC addresses all three tiers of the HAIP. Maps of coral reef habitats, topographic highs, and other 

bottom types in coastal waters are being produced using sidescan and multibeam sonar in response to existing and emergent natural and 

anthropogenic stressors. Th e abundance and size composition of fi shery species is collected and associated with habitat characteristics in 

many of these research programs. Habitat associations are developed using traditional sampling and video surveys along with hydroacoustic 

survey techniques, acoustic and popup satellite tagging, DIDSON, and stereo-video cameras. Th e objectives of this habitat monitoring and 

research are to identify and defi ne habitats, to elucidate their roles in structuring and maintaining marine communities, to evaluate habitat 

associations and condition, and to develop science-based practices to conserve and restore critical habitats. Regional threats include habitat 

damage and change from fi shing, hurricanes and storms, climate change and sea level rise, coral bleaching, disease, and biological accumulation and uptake of toxins. More recent habitat issues involve potential threats from invasive species (e.g. lionfi sh), ocean acidifi cation, the 

placement of liquid natural gas (LNG) facilities (see Appendix 5), off shore aquaculture impacts, and eutrophication that can lead to harmful algal blooms, hypoxia, and extensive dead zones.

Estuarine habitats in the Southeast Region are highly susceptible to impacts from development and increasing populations along the coast. 

Th us, research on habitat associations of juvenile fi shery species in estuarine nurseries has been emphasized over the last 30 years. For 

example, some of the earliest studies on the value of seagrass beds were initiated at SEFSC laboratories along with extensive research on 

estuarine shrimp habitats. Much of this work has been focused on developing techniques to collect quantitative density estimates and to 

measure habitat-related growth and mortality. An important goal of this research is to link habitats with fi shery production, and a variety 

of modeling approaches have been developed to combine density, growth, and mortality estimates into measures of productivity. Because 

many estuarine habitats are being lost to coastal development, techniques to restore functional habitats are being examined. Most recently, 

fi shery production models have been used to develop construction cost: fi shery benefi t ratios for habitat restoration projects.

SEFSC staff engaged in fi shery independent resource surveys for stock assessments have not been considered as habitat research staff in our 

analyses, but these surveys provide critical information on the spatial distribution of harvested and early life history stages of FSSI stocks 

needed to produce habitat assessments. Th e Southeast Area Monitoring and Assessment Program (SEAMAP) is a cooperative state-Federal 

program for the systematic collection, management, and dissemination of fi shery-independent data in the southeastern United States. Currently, limited habitat information is collected in this program due to funding constraints; however, a recent SEAMAP 2006-2010 Manage-
111

ment Plan has proposed an expansion of this program to provide habitat information along with increased temporal and spatial coverage 

of sampling. Th e value of SEAMAP ichthyoplankton data was recently highlighted when NMFS assessed the potential impacts of off shore 

LNG processing facilities (Appendix 5).

An extensive body of research has been developed on habitat use and value in the Southeast Region, but much of this work has been funded 

by other state and Federal resource agencies working cooperatively with NOAA and universities. A strong coordinated eff ort is needed with 

a strategic plan to develop the dedicated research necessary to link habitat ecology and stock assessments using an ecosystem approach. Th is 

link is a critical requirement for EBFM.

SEFSC Staffi ng Levels Required to Meet the Goals of the Tiers of Excellence

We emphasize in the following discussion of staff requirements to reach the three Tiers of Excellence, as outlined in the HAIP, that these 

tasks should not be accomplished sequentially. For some species and life stages, we have information on habitat associations and also have 

measured habitat-related growth and mortality rates. Th ese research programs need to progress into ecosystem modeling and incorporation 

of habitat parameters into stock assessments. Examples of success in this regard are needed to prove that proposed approaches are realistically feasible.

Tier 1: Identify Habitats for All Life Stages

To reach Tier 1 and assess habitat associations for stocks using existing data, we estimate that an additional 24 full-time staff will be needed 

(Table A7-5). Two full-time staff (a data manager and GIS expert) at each of the fi ve laboratories would be tasked with collecting and organizing the available data on habitat and stock distributions and associations. We will build preliminary life tables for all FSSI stocks; these 

tables will identify life stages and describe available information on spatial and temporal distributions. Available information on growth, 

mortality, and reproduction rates also will be identifi ed in relation to habitats. A Center-based coordinator would oversee an additional 

staff member at each lab (a total of six new staff ) to begin developing habitat assessments for diff erent stocks. Gear specialists (four new 

staff ) and system modelers (three new staff ) will be used to plan approaches to collect new quantitative abundance data and use it in habitat 

assessments. A technical writer would be supported to assist in developing technical reports.

Tier 2: Assess Spatial Extent and Temporal Variability of Habitats

Tier 2 research and monitoring are needed to upgrade habitat assessments to a minimally acceptable level. Increased eff orts to collect 

habitat-related abundance data would be supported by 20 staff (an average of four per laboratory; Table A7-5). Th ey would support the 

expansion of fi shery independent resource surveys such as SEAMAP by increasing the geographic range of sampling and temporal coverage 

(particularly for early life history stages) and expanding the collection of associated data on habitat characteristics. A particular focus also 

will be placed on collecting abundance data for reef fi shes to better assess habitat associations. Th e collection of data on habitat distributions 

will be increased and supported by data managers and GIS specialists (fi ve new staff ). At each laboratory, staff will be added (a total of 30 

new staff ) to produce habitat assessments, refi ne and develop habitat-related survey methods and tools, refi ne and develop habitat-related 

population and ecosystem models, and communicate habitat assessment results to FMC’s and other constituents.

Tier 3: Role of Habitats in Growth, Reproduction, and Survival by Life Stage

Tier 3 research is most diffi cult to plan. Th is work involves the measurement of growth, mortality, and reproduction for diff erent life stages 

of FSSI stocks in relation to habitat characteristics and the incorporation of this information on vital rates into stock assessments and integrated ecosystem assessments. We are tentatively estimating an additional 55 staff will be needed to work on these problems, with their 

eff orts focused on the collection of habitat related vital rates and population and ecosystem modeling. We will improve our ability to age all 

species (including crustaceans) in diff erent life stages in order to measure vital rates. As noted above, some of this work should be conducted 

on a parallel track with Tier 1 and Tier 2 research.

Northeast Fisheries Science Center (NEFSC)

Th e NEFSC is responsible for the Northeast Shelf LME, which ranges from Maine to Cape Hatteras, North Carolina. Th e diversity of 

habitats ranges from fi ne clay substrates to cold-water corals. Further, the hydrography of the northeast is complex with major infl uxes from 

the warm Gulf Stream from the south as well as cold, oft en fresher, waters from the Scotian Shelf to the north. Th is ecosystem is heavily 

exploited and human activities include commercial and recreational fi shing, whale watching, navigation, aquaculture, military operations, 
112

Activity Current Tier 1 Tier 2 Tiers 1+2 Tier 3 All Tiers

Collect habitat-related data 25 0 4 4 15 19

Process and convert raw habitat data into usable products 10 3 3 6 7 13

Produce habitat-specifi c assessments 7 3 4 7 7

Determine habitat-specifi c vital rates over time 15 15

Refi ne existing habitat-related survey methods/tools and develop new ones 5

Refi ne existing population models and develop new habitat-related ones 4

Incorporate habitat and ecosystem information into stock assessments at SAIP Tier 3 5 5

Refi ne existing habitat and ecosystem models and develop new ones 3 3 5 8

Develop improved habitat risk assessments 5 5

Communicate improved assessment results and conduct other follow-up work 3 1 3 4 4 8

Total 54 7 17 24 56 80

Table A7-6

Number of additional full-time staff required to meet the three Tiers of Excellence by type of activity for the Northeast Fisheries Science Center. 

Number of staff in each category does not necessarily refl ect the absolute number of individuals involved in these activities, because some individuals may divide their time among several activities. Estimated numbers of staff include permanent employees, contractors, and students. Grey 

cells indicate that an activity did not apply in a particular tier, according to the questionnaire. 

pipeline and cable construction, wind and wave energy production, off shore oil and gas development, and mining of sand and gravel. 

Th e NEFSC supports two FMC’s (New England and Mid-Atlantic) as well as a consortium of state agencies. Th us, the diversity of habitats, 

as well as multiple regulatory clients, creates a signifi cant challenge and burden for NMFS scientists that provide much of the habitat data 

and advice to inform management decisions. 

NEFSC Current Habitat Activities

Currently the equivalent of about 54 full-time staff (of which about 15% are contractors) provides the habitat data and information used to 

support fi sheries management and research in the NEFSC (Table A7-6). Roughly two-thirds of these researchers collect habitat data and 

develop products (e.g. maps, tools, EFH source documents, advice). Th e rest of these positions are focused largely on habitat assessments, 

refi nement of methods, tools and models, and communications.

NEFSC Staffi ng Levels Required to Meet the Goals of the Tiers of Excellence

Tier 1: Identify habitats for all life stages

To meet a level of Tier 1 habitat information, the NEFSC would need an additional seven staff (Table A7-6). Th e main focus of their work 

would be on tool development and habitat assessment with a smaller enhancement of current communications activities. Th e addition of 

these seven positions would particularly facilitate habitat characterization and mapping, development of habitat indices with respect to fi sh 

stock status, and provision of information to support management actions such as MPA designation. Including current staff (i.e. 54), 61 

NEFSC habitat researchers are needed to meet Tier 1 criteria.

Tier 2: Assess Spatial Extent and Temporal Variability of Habitats

Advancing to Tier 2 habitat information, the NEFSC would need an additional 17 staff . Th ese new positions would particularly facilitate 

improved habitat characterization and mapping, further development of habitat indices with respect to fi sh stock status, improve existing 

models focused on ecosystem and habitat functionality including simulations run in the Atlantis model, energy fl ow modeling, etc., and 

improve our understanding of the eff ects of habitat condition on fi sh stocks and stock assessment. Th is would bring the total number of 

additional staff needed to meet Tier 1 and Tier 2 criteria to 24 (Table A7-6).
113

Tier 3: Role of Habitats in Growth, Reproduction, and Survival by Life Stage

To move from Tier 2 to Tier 3 habitat information, the NEFSC would need an additional 56 staff (Table A7-6). Over half of these positions 

would support data collection, tool development, and particularly the determination of habitat-specifi c vital rates. About 10 positions will 

be needed to incorporate habitat and ecosystem information into stock assessments at the SAIP Tier 3 level as well as to improve habitat 

risk assessments with respect to impacts on managed species. Th e addition of these 56 positions would particularly facilitate the determination of habitat-specifi c rates for reproduction, growth, survival and mortality, the refi nement of the natural mortality used in most stock 

assessment models, the provision of other rates that can be used directly by stock assessment experts, the improvement of survey designs and 

subsequent quality of trawl survey data, the development of regional FMP’s, and the implementation of IEA’s. Th is would bring the total 

number of additional staff needed to meet Tier 1, Tier 2, and Tier 3 criteria to 80. Th is is an increase of 148% over current levels (i.e. 54); 

134 total staff will be needed to fully support a habitat science program at the NEFSC.

115

Appendix 8: National Priorities (not in any particular order) for 

Habitat Science Identified in the Our Living Oceans Habitat 

Report (NMFS, In press) and in “NOAA’s Habitat Program: NMFS 

Strategic Plan 2009-2013” (NMFS, 2009c)

• Enhance biological sampling to characterize distributions and abundances of fi sh species for all life history stages.

• Characterize benthic habitats and quantify habitat use by fi shery species.

• Identify habitat properties that contribute most to survival, growth, and productivity of fi shery species.

• Determine habitat properties important in recruitment.

• Identify indicators of ecosystem health.

• Establish baseline conditions, conduct baseline assessments of current threats, and monitor trends in habitat condition. 

• Quantify the impacts of threats on coastal and marine habitats, including those from fi shing gear, point and nonpoint sources, harmful 

algal blooms, hypoxia, endocrine disrupting chemicals, and pathogens.

• Predict vulnerability of coastal and marine habitats to new threats.

• Predict the resiliency of habitats to recover from environmental disturbances.

• Evaluate harvest refugia concepts for selected areas and managed species.

• Develop capabilities to detect declining habitat health and strategies to mitigate factors that aff ect the health of coastal and marine 

habitats.

• Develop new methods and approaches for restoration of degraded habitats, and monitor and evaluate habitat restoration eff orts.

• Improve knowledge of ecosystem processes and services.

• Develop information on the economic value of habitats and functioning ecosystems for supporting fi shery and protected resources.

• Identify and estimate the socioeconomic impacts of habitat modifi cations.

• Communicate habitat science knowledge to fi shery management councils and other management agencies.

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service