Habitat Science is a Fundamental Element 

in an Ecosystem-Based Fisheries 

Management Framework: An Update to 

the Marine Fisheries Habitat Assessment 

Improvement Plan

The Habitat Assessment Improvement Plan Team:

Rebecca Peters, Anthony R. Marshak, Margaret M. (Peg) Brady, 

Stephen K. Brown, Kenric Osgood, Correigh Greene, Vincent Guida, 

Matthew Johnson, Todd Kellison, Robert McConnaughey, Tom Noji, 

Michael Parke, Chris Rooper, Waldo Wakefield, and Mary Yoklavich

U.S. Department of Commerce 

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

NOAA Technical Memorandum NMFS-F/SPO-181 

April 2018

Habitat Science is a Fundamental Element in an EcosystemBased Fisheries Management Framework: An Update to 

the Marine Fisheries Habitat Assessment Improvement 

Plan 

The Habitat Assessment Improvement Plan Team:

Rebecca Peters, Anthony R. Marshak, Margaret M. (Peg) Brady, Stephen K. Brown, Kenric 

Osgood, Correigh Greene, Vincent Guida, Matthew Johnson, Todd Kellison, Robert 

McConnaughey, Tom Noji, Michael Parke, Chris Rooper, Waldo Wakefield, and Mary 

Yoklavich 

NOAA Technical Memorandum NMFS-F/SPO-181 

April 2018

U.S. Department of Commerce 

Wilbur L. Ross, Jr., Secretary 

National Oceanic and Atmospheric Administration

RDML Tim Gallaudet, Ph.D., USN Ret., Acting NOAA Administrator

National Marine Fisheries Service

Chris Oliver, Assistant Administrator for Fisheries 
ii

Recommended citation:

Peters, R., A.R. Marshak, M.M. Brady, S.K. Brown, K. Osgood, C. Greene, V. Guida, M. 

Johnson, T. Kellison, R. McConnaughey, T. Noji, M. Parke, C. Rooper, W. Wakefield, and M. 

Yoklavich. 2018. Habitat Science is a Fundamental in an Ecosystem-Based Fisheries 

Management Framework: An Update to the Marine Fisheries Habitat Assessment Improvement 

Plan. U.S. Dept. of Commerce, NOAA. NOAA Technical Memorandum NMFS-F/SPO-181, 29 

p. 

Copies of this report may be obtained from: 

NOAA Fisheries Office of Science and Technology

National Oceanic and Atmospheric Administration 

1315 East-West Highway SSMC3, F/ST

Silver Spring, MD 20910 

Or online at:

http://spo.nmfs.noaa.gov/tech-memos/
iii

Table of Contents

Executive Summary........................................................................................................................iv 

Acknowledgements..........................................................................................................................v 

Overview..........................................................................................................................................1 

New Policies and Drivers.................................................................................................................1 

Habitat Science: Organizational Updates & Accomplishments........................................................3 

Habitat Science: Continued Gaps, Needs, and Next Steps................................................................5 

Moving Forward ..............................................................................................................................8 

Appendix A. Progress of the Nine 2010 HAIP Recommendations.................................................11 

Appendix B. Funded Habitat Science Projects from the NMFS Office of Science and Technology 

(OST) Habitat Information for Stock Assessments Internal Funding Allocation and from the NMFS 

Office of Habitat Conservation (OHC)...........................................................................................18 

Appendix C. Examination of Gaps/Needs for Carrying Out the 2010 HAIP Recommendations, and 

Approaches for Continued Progress...............................................................................................23 
iv

Executive Summary

The 2010 Marine Fisheries Habitat Assessment Improvement Plan (HAIP) was developed to 

guide the habitat science activities of the National Marine Fisheries Service (NMFS) and 

improve the availability of high-quality scientific information detailing the relationships among 

fishery species and their required habitats. A 2016 program review of the NMFS Office of 

Science and Technology ecosystem, climate, and habitat science program determined (i.e. action 

item 7.3.1) that an update of the 2010 HAIP was needed to identify accomplishments, 

information gaps, and needs in the context of new policies and research approaches in NMFS. Of 

particular relevance are recent efforts to implement Ecosystem-Based Fisheries Management 

(EBFM).

While overall progress in implementing the HAIP has been constrained by limited funding, 

efforts to address its key recommendations have led to an integrated national habitat science 

program, which has supported habitat research and advanced habitat conservation across the 

agency. Supported work under this program and the NMFS Habitat Information for Stock 

Assessments funding opportunity continues to increase understanding of the role that habitat 

plays in various life stages of managed species. As recommended in the HAIP, listings of stocks 

that would most benefit from habitat assessments have also been developed for each region to 

prioritize resources in addressing ongoing habitat-related uncertainties in stock assessments and 

in refining Essential Fish Habitat (EFH) descriptions.

Some success has been achieved with respect to habitat research across all NMFS Fisheries 

Science Centers; however, more efforts are needed to improve additional stock assessments, 

refine EFH designations, and to inform ongoing ecosystem-based fisheries management (EBFM) 

implementation. An internal review of the progress achieved since the HAIP was published 

identified a number of remaining gaps and emerging habitat science needs in the context of the 

2016 NMFS EBFM Policy and Road Map. 

Included within the document are a series of recommendations for filling identified post-HAIP 

habitat science gaps and needs as applied toward enhancing EBFM implementation and 

strategies to incorporate a broader habitat concentration into NMFS ecosystem science efforts.

As the agency transitions to EBFM, strengthened implementation requires ongoing identification 

of habitats that are most essential for sustaining living marine resources, and continued support 

for research to understand how these habitats directly contribute to fisheries productivity. This is 

especially necessary because habitat is a foundational component of ecosystem processes and a 

crucial component of EBFM. An integrated focus on the habitat aspects of ecosystem processes 

and their associated species will lead to a more coherent implementation of an ecosystem 

approach to management. It will also provide for the most scientifically sound conservation of 

our managed species, the ecosystems that support them, and the sustainability of our fisheries. 
v 

Acknowledgements

The authors thank the original Habitat Assessment Improvement Plan co-authors and all working 

group members past and present for their continued efforts to advance habitat science priorities 

for NOAA. We also thank Kara Meckley, Christopher Meaney, and Tauna Rankin from the

National Marine Fisheries Service Office of Habitat Conservation for their ongoing collaboration 

and support of NOAA habitat science efforts, and for their input on this technical memo. 

Additional thanks is expressed to Avi Litwack for his assistance in making this document fully 

compliant with Section 508 web publishing standards.

1 

Overview

Traditionally fisheries management in the United States, as directed by the Magnuson Stevens 

Fishery Conservation and Management Act (MSA), maintains stock levels by controlling fishing 

pressure on single-species fishery populations. More recently, NOAA’s National Marine 

Fisheries Service (NMFS) has made efforts to incorporate habitat, which the MSA explicitly 

cites as being essential to the long-term sustainability of recreational and commercial fisheries, 

into its assessments. As NMFS develops and attempts to implement ecosystem approaches to 

management, fundamental habitat information is needed to improve stock assessments and 

integrated ecosystem-based management efforts. In 2010, NMFS developed the Marine Fisheries 

Habitat Assessment Improvement Plan (HAIP) to guide the agency’s habitat science activities 

through a series of personnel and research investments that were needed to improve the 

availability of high-quality scientific information detailing the relationships among fishery 

species and their required habitats. Overall progress in implementing the HAIP has been 

constrained by limited funding for habitat science, though incremental improvements have been 

made through NMFS Office of Science and Technology (OST) initiatives. A program review of 

the OST ecosystem, climate, and habitat science program in 2016 determined (i.e. action item 

7.3.1) that an update of the 2010 HAIP was needed to identify accomplishments, information 

gaps, and needs in the context of new policies and research approaches in NMFS. It is clear that 

while some habitat research has been conducted across all NMFS Science Centers, more 

comprehensive habitat science efforts are needed to improve additional single-species stock 

assessments and to inform ecosystem-based fisheries management (EBFM) implementation. 

New Policies and Drivers

NMFS is moving forward in transitioning from single species fisheries management to a more 

holistic ecosystem approach through recommendations in the Ecosystem-Based Fisheries 

Management (EBFM) Policy,1

 Road Map,2 and forthcoming update to the NMFS Stock 

Assessment Improvement Plan (anticipated release in 2018). Moving toward holistic 

management requires identification of habitats that are most essential for sustaining living 

marine resources, their vulnerabilities, and understanding how these habitats support 

productivity.3

 This is necessary because habitat is a crucial component for EBFM (Figure 1). 

1 NMFS. 2016. Ecosystem-Based Fisheries Management Policy of the National Marine Fisheries Service, National Oceanic and 

Atmospheric Administration. Available: https://www.fisheries.noaa.gov/resource/document/ecosystem-based-fisheriesmanagement-policy. 2 NMFS. 2016. NMFS Ecosystem-Based Fisheries Management Road Map. Available: 

https://www.st.nmfs.noaa.gov/Assets/ecosystems/ebfm/EBFM_Road_Map_final.pdf. 3 Marshak, A.R. and Brown, S.K. 2017. Habitat science is an essential element of Ecosystem-Based Fisheries Management. 

Fisheries 42(6): 300-300.
2 

Figure 1: Hierarchical approaches to marine resource management, with each level showing the critical 

components for a given management strategy. 

One type of habitat research that has generated information called for in the HAIP has been the 

internally funded research from the NMFS Habitat Information for Stock Assessments (HISA) 

opportunity. These studies generate the type of data needed to complement mathematical 

modeling and move EBFM into practice. The data gained from HISA-funded studies increases 

our understanding of how habitat influences the abundances of managed species, underpins 

ecological linkages, and drives marine-ecosystem dynamics. Expansion of these data collection 

efforts and other fundamental habitat research can strengthen NOAA’s ability to move toward 

holistic assessments of living marine resources, and improve design and analysis of fisheryindependent surveys. Additionally, it can allow for reduced uncertainty in stock assessments, 

enhanced essential fish habitat (EFH) designations, and provide fundamental information needed 

for accurate ecosystem models.3 Even though past HAIP recommendations focused mostly on 

increasing habitat information for single species, many of the accomplishments for each 

recommendation can support EBFM because of the fundamental nature of the attributes. Future 

HAIP work should be integrated with other ecosystem science as NMFS moves toward 

implementing EBFM in consideration of available resources and emerging priorities, as detailed 

in the Moving Forward section of this document. 
3 

Habitat Science: Organizational Updates & Accomplishments

The HAIP included recommendations and a framework to improve habitat science by identifying 

gaps, recommending steps to improve habitat assessments, and creating an integrated national 

habitat science program. Below are the three foremost sets of accomplishments since 2010 that 

encompass multiple recommendations outlined in the 2010 HAIP. Detailed updates of NMFS 

habitat science accomplishments in context with the nine HAIP recommendations are compiled 

in Appendix A. Improved frameworks within NMFS and across NOAA that enhance 

coordination and communication of habitat science and conservation efforts, and allow greater 

leveraging potential to support and advocate for habitat research have additionally emerged postHAIP.

Accomplishments: 

1.) Identified Gaps and Funded Habitat Science Linked to NMFS Mandates

The HAIP identified data gaps in habitat science, particularly the lack of foundational habitat 

information on species-habitat relationships. To address these concerns, NMFS initiated the 

following actions: 

• Held two National Habitat Assessment Workshops (NHAWs 2010, 2012) that brought 

together scientists and mangers to identify major gaps in habitat science research;

• Created the Habitat Information for Stock Assessments (HISA) internal funding 

allocation to support short-term, small-scale projects focused on reducing habitat-related 

uncertainty in stock assessments. 

o Thirty-nine HISA funded projects (totaling $4.1 million) out of 141 submitted 

proposals have been funded since 2010, and range from studies that determined 

habitat use of single species to the development of tools that can inform ways to 

include habitat information into stock assessments or management. (See 

Appendix B for a description of HISA projects, and studies separately supported 

with NMFS Office of Habitat Conservation (OHC) discretionary funds for 

“Refine EFH” studies). 

Impact: The HISA-funded studies have increased our understanding of the role that habitat 

plays in various life stages of managed species. Continuation of these types of studies will fill 

major knowledge gaps on species-habitat dependencies, advance the incorporation of habitat data 

into stock assessment models, and enhance EBFM implementation.

2.) Habitat Assessment Prioritizations

Due to the high quantity of stocks to manage, the HAIP recommended identifying and 

prioritizing those stocks in each region4 that would most benefit from habitat assessments to 

 

4 NMFS Habitat Assessment Prioritization: http://www.st.nmfs.noaa.gov/ecosystems/habitat/prioritization/index
4 

address habitat-related uncertainties in their stock assessments, and provide higher-level 

information for characterizing their EFH. The following actions have taken place to prioritize 

resources for conducting habitat assessments of fishery species:

• Finalized habitat assessment prioritization listings for each of the regions (West Coast5, 

Northeast6, Alaska7, and Pacific Islands8) or produced draft preliminary listings 

(Southeast) of the relevant stocks under their jurisdictions. 

• These identified and prioritized stocks guided the NMFS HISA project selections during 

the FY17 and FY18 funding cycles, and will continue to guide future agency decisions. 

Impact: As NMFS shifts priorities toward EBFM, these listings will enhance its implementation 

by providing focus on stocks that require fundamental ecosystem information for improved 

management, and in applying a broader ecosystem focus toward EFH designations of prioritized 

species. These prioritizations are additionally included as milestones in the EBFM Road Map 

and forthcoming EBFM regional and headquarters implementation plans. 

3.)Improved Coordination and Collaboration between Habitat Science & Management: 

Since the publication of the HAIP, NOAA has: 

• Formed the National Habitat Leadership Team and developed the Habitat Enterprise 

Strategic Plan (2016-2020)9; 

• Advanced the National Fish Habitat Partnership (NFHP)10 - ”Status of Fish Habitats in 

the United States” five-year habitat assessment efforts, specifically in conducting its 

national coastal fish habitat assessments and contributing to regional marine habitat 

assessments;

 

5 Blackhart, K. 2014. Habitat assessment prioritization for West Coast stocks. Report of the Northwest and Southwest Regional 

Habitat Assessment Prioritization Working Groups. Internal Report, NMFS White Paper. Office of Science and Technology, 

NMFS, NOAA. Silver Spring, MD. 199p. 

https://www.st.nmfs.noaa.gov/Assets/ecosystems/habitat/pdf/Updated_WestCoast_HAP_Report.pdf

6 NMFS. 2015. Regional habitat assessment prioritization for northeastern stocks. Report of the Northeast Regional Habitat 

Assessment Prioritization Working Group. Internal report, NMFS White Paper. Office of Science and Technology, NMFS, 

NOAA. Silver Spring, MD. 31 p. https://www.st.nmfs.noaa.gov/Assets/ecosystems/habitat/pdf/regional-habitat-assessmentprioritization-for-northeastern-stocks.pdf 7 McConnaughey, R.A., K.E. Blackhart, M.P. Eagleton, and J. Marsh. 2017 Habitat assessment prioritization for Alaska stocks: 

Report of the Alaska Regional Habitat Assessment Prioritization Coordination Team. U.S. Dep. Commer., NOAA Tech. Memo. 

NMFS-AFSC-361, 102 p. https://www.afsc.noaa.gov/Publications/AFSC-TM/NOAA-TM-AFSC-361.pdf 8 Parke, M., H. Ma, R. Walker, I. Williams, R. Schroeder, B. Richards, and M. Sabater. 2018. Report of the Pacific 

Islands Habitat Assessment Prioritization Working Group. Internal report, NMFS White Paper. Office of Science 

and Technology, NMFS, NOAA. Silver Spring, MD. 31 p.

9 NMFS. 2016. NOAA Fisheries Habitat Enterprise Strategic Plan 2016-2020. 

https://repository.library.noaa.gov/view/noaa/14994 10 Crawford, S., Whelan, G., Infante, D.M., Blackhart, K., Daniel, W.M., Fuller, P.L., Birdsong, T., Wieferich, D.J., McCleesFuninan, R., Stedman, S.M., Herreman, K., and Ruhl, P. 2016. Through a Fish's Eye: The Status of Fish Habitats in the United

States 2015. National Fish Habitat Partnership. at url http://assessment.fishhabitat.org/
5 

• Created NOAA’s Habitat Conservation Team (NHCT), which guides cross-agency 

habitat conservation and science activities, tracks progress, and explores areas for new 

research;

• Developed the NOAA Habitat Blueprint11 from the NHCT, a three-pronged approach for 

NOAA to think and act strategically across programs in the agency and to partner with 

organizations toward improving habitat for fisheries, marine life, and coastal 

communities and in supporting habitat science; 

• Established the Council Coordination Committee (CCC) Habitat Working Group and 

held the National Essential Fish Habitat (EFH) Summit (May 2016);

• Established ten NOAA Habitat Focus Areas (HFAs)12; 

• Developed a National Habitat Policy13; and

• Formed the Habitat Science and Ecological Forecasting Technical Team, which used 

guidance outlined in the 2010 HAIP to develop the Habitat Science and Ecological 

Forecasting Roadmap14 that guides the agency on habitat science priorities over the next 

five years.

Impact: These actions have led to improved coordination and collaboration between the habitat 

science and management programs throughout NOAA. The formation of the NHCT and its 

Habitat Science and Ecological Forecasting Technical Team has additionally worked toward 

addressing habitat science data gaps at a NOAA-wide level, and encouraging further integration 

of habitat science efforts within and outside of the agency.

Habitat Science: Continued Gaps, Needs, and Next Steps

An internal review of the progress achieved since the release of the HAIP additionally identified 

a number of gaps and emerging habitat science needs. Recommendations were also provided on 

how to continue addressing the nine HAIP recommendations and these identified gaps/needs in 

the context of the EBFM policy/road map. A summary of the gaps/needs and corresponding 

recommendations follow: (Note: Appendix C provides a comparison of the 2010 HAIP 

recommendations, their progress to date, corresponding gaps/needs that continue, and 

recommendations for next steps). 

Gaps and Emerging Habitat Science Needs: 

1. Increased collaboration and integration of NMFS habitat science with other NMFS 

internal funding opportunities (e.g., those addressing the Stock Assessment Improvement 

Plan, EBFM Road Map, and the Climate Science Strategy) is needed to support larger-

 

11 NOAA Habitat Blueprint: https://www.habitatblueprint.noaa.gov/ 12 NOAA Habitat Focus Areas: https://www.habitatblueprint.noaa.gov/habitat-focus-areas/ 13 NOAA National Habitat Policy: http://www.corporateservices.noaa.gov/ames/administrative_orders/chapter_216/NAO_216-

117.pdf

14 NOAA’s Habitat Science and Ecological Forecasting Technical Team’s Guidance Document: Support for NOAA’s Habitat 

Conservation Team and the Ecological Forecasting Roadmap. 2016. 

https://aamboceanservice.blob.core.windows.net/oceanservice-prod/ecoforecasting/HSEF-action-plan.pdf
6 

scale and longer-term projects toward incorporating habitat information into ecosystembased fisheries management decisions and enhancing NMFS climate science efforts.

Additionally, more funding is required to support continued collection of information on 

the distribution of benthic habitats, including habitat surveys and multibeam mapping 

during fishery-independent surveys. 

• Recommendation 1.1: Continue to work on future budget initiatives. 

• Recommendation 1.2: Integrate studies that focus on incorporating habitat and 

other ecosystem metrics into management decisions. Additionally, this 

information can be used to enhance Integrated Ecosystem Assessments (IEAs) 

and Ecosystem Status Reports. 

• Recommendation 1.3: Enhance and continue funding opportunities for work that 

focuses on collecting habitat data to improve stock assessment models, EFH and 

Habitat Areas of Particular Concern (HAPC) designations, and ecosystem 

information. Of particular need is fundamental habitat information for fishery 

species throughout their life histories, and understanding habitat distributions 

through mapping and use of acoustic-survey technologies. 

2. Habitats associated with regionally prioritized species need to be identified. Resources 

should be prioritized to investigate EFH requirements for the prioritized species, 

especially those that are habitat-limited. This information will need to be included into

their respective stock assessments. Additionally, resources should be allocated toward 

determining those habitats that are most important to multiple species of concern.

• Recommendation 2.1: Allocate resources using the regional prioritizations to 

improve habitat information for those species that would benefit most from 

increased habitat assessments.

• Recommendation 2.2: Regional science centers and offices should continue to 

examine regional priorities and identify where investments can be made using the 

prioritized lists in their region.

• Recommendation 2.3: Apply regional prioritizations to identify taxa and habitats 

that are most vulnerable to human and natural pressures, as part of broader 

ecosystem-level risk assessments.

• Recommendation 2.4: Prioritize geographic locations/habitats for future 

research. 

3. Funded projects need to continue to work toward incorporating habitat information into 

stock assessments and improving EFH information. Additionally, this information can be 

applied toward focusing on the broader role of habitats in ecosystems and in advancing 
7 

our understanding of the inshore-offshore connections for species that rely on nearshore 

habitats for various life stages. 

• Recommendations under gap 1 will also address this need.

4. Communication of the utility of the regional habitat assessment prioritization lists among 

scientists and managers should be improved to increase the use of these listings toward 

research and management. 

• Recommendations under gap 2 will also address this need.

5. A plan should be developed to provide guidance on how to better utilize new 

technologies (including multibeam echosounders and side scan sonar) to increase 

collection of habitat data on fishery-independent surveys. Recommendation 1.3, which 

addresses funding needs to support continued collection of habitat distribution 

information and multibeam mapping efforts is also applicable toward addressing this gap. 

• Recommendation 5.1: Recommendations from the 2017 workshop to 

improve the use of the ME70 multibeam echosounder aboard NOAA Fishery 

Science Vessels should be communicated to increase and improve habitat 

mapping. 

• Recommendation 5.2: Continue to develop ways to utilize new technologies 

to collect habitat information, working more closely with the NMFS 

Advanced Sampling Technologies Working Group, the NOAA Office of 

Coast Survey, the NOAA Office of Marine and Aviation Operations, and 

industrial partners. 

6. More engagement is needed among habitat managers in regional offices and fishery 

management councils, and fishery scientists in the fishery science centers with a focus on 

incorporating habitat science information into management decisions. 

• Recommendation 6.1: Encourage improved communication among scientists 

and managers, and additional collaboration with partners, like the United 

States Geological Survey (USGS), Bureau of Ocean Energy Management 

(BOEM), and the U.S. Army Corps of Engineers (ACOE), to leverage funds 

to increase collection of foundational habitat information. 

• Recommendation 6.2: Fund/expand fishery management council and fishery 

science center collaborative pilot projects to explore setting habitat objectives 

for fisheries management.

7. There has not been a NHAW since 2012, nor have initially recommended efforts to create 

regional NHAWs been carried out. 
8 

• Recommendation 7.1: Hold additional national and regional NHAWs to 

address ways to incorporate habitat into EBFM and strengthen communication 

and collaboration among habitat scientists, ecosystem modelers, and managers 

within and among regions. Additionally, efforts should be undertaken to 

increase collaboration with IEA meetings, National Stock Assessment 

Workshops, and the EBFM workgroup. This recommendation can also be 

applied toward the above need to engage habitat managers and fishery 

scientists.

• Recommendation 7.2: HAIP members should actively participate in 

development of regional implementation plans for EBFM and incorporate 

habitat science milestones into these plans. 

8. NMFS scientists should take advantage of existing graduate fellowship programs to 

mentor graduate students or post docs on habitat science related research. 

• Recommendation 8.1: NMFS scientists interested in mentoring graduate 

students or post docs on habitat science related work can mentor funded 

students from programs that focus on ecosystem science and modeling such 

as: NMFS Sea Grant Population and Ecosystem Dynamics Fellowships, 

National Research Council Research Associated Program, and NOAA Living 

Marine Resources Cooperative Science Centers.

9. Increased communication and broader application of funded habitat science efforts that 

provide fundamental ecological information on managed species, enhance stock 

assessments, and refine EFH designations remains necessary. Successful incorporation of 

this work into stock assessments and higher-level EFH data can serve as examples for 

other regions to conduct similar work and address habitat-related uncertainties.

• Recommendation 9.1: Hold workshops, briefings, etc. that improve 

communication and awareness among NMFS’ Offices of Science & 

Technology and Habitat Conservation with the aim to integrate habitat and

stock assessment information. Continue to brief NMFS leadership and NOAA 

wide committees on progress of habitat science and HAIP-related efforts 

across the agency.
9 

Moving Forward

Seven years after publication of the HAIP, more foundational habitat information and a greater 

understanding of the relationship between species and their habitats is still needed to strengthen 

fisheries science and management. The EBFM Policy and Road Map outline six guiding 

principles for the successful implementation of EBFM (Figure 2), with main habitat-centric 

principles being to “advance the understanding of ecosystem processes to improve foundational 

ecosystem science information” and “prioritize vulnerabilities and risks of ecosystems and their 

components.” 

Figure 2: Illustration of the interconnected and interdependent nature of the major EBFM guiding 

principles. Credit, the NOAA National Marine Fisheries Service Ecosystem-Based Fisheries Management 

Policy. http://www.nmfs.noaa.gov/op/pds/documents/01/01-120.pdf. 

Studies increasing foundational habitat information are crucial to advancing our understanding of 

ecosystem processes. Each of the past funded HISA and OHC “Refine EFH” studies has 

advanced our understanding of the role of habitat for species in their respective ecosystems. 

These collective investigations have led to improved estimates of abundance, greater 

understanding of climate-change vulnerabilities, and identification of habitat dependencies of 

managed fishery species. Additionally, these studies provide foundational information for 

continued efforts that examine the role of habitat in ecosystem responses to human and 

environmental pressures. 
10

For example, data from HISA-funded studies such as by Doerr and colleagues at the Southeast 

Fisheries Science Center (SEFSC)15 that document the effects of climate-mediated changes in 

habitat conditions on penaeid shrimp production supports an understanding of ecosystem-level 

consequences of black mangrove displacement of Gulf of Mexico salt marshes. Another study by 

Hollowed and colleagues at the Alaska Fisheries Science Center and University of Washington 

used statistical techniques to integrate data on species distribution and interactions, benthic 

structure, and physical forcing mechanisms to define ecoregions in the eastern Bering Sea16. 

Other studies have increased information on the distribution of available potential habitat for the 

snapper-grouper complex, which not only expanded the sampling area for fisheries-independent 

surveys, but also provided foundational benthic characteristics information for the southeast 

Atlantic17 and the Gulf of Mexico18. These efforts can allow for more precise population 

estimates, refining of EFH, and improved management strategies for these important species. 

Without this type of work, information would still be lacking for many regions to move forward 

with a more holistic framework to examine multispecies interactions within habitats and 

ecosystem-level responses to emerging climate and anthropogenic factors. Continuing studies 

that improve benthic and oceanographic mapping, the relationships among these physical 

phenomenon and living marine resources, enhance EFH designations, and strengthen our 

understanding of habitat/species-productivity relationships produces the foundational ecosystem 

science that serves as the backbone of EBFM.

Accomplishing these tasks can be challenging in light of modest resources that are currently 

allocated for habitat science work. The continuation and advancement of this work is needed for 

NMFS to achieve its goal of working toward EBFM, especially given that foundational habitat 

information is a major currency with which to build comprehensive EBFM. Ongoing 

collaborations with University programs, external agencies and partners, and other NOAA Line 

Offices, along with executing the new recommendations in this HAIP update, will assist NMFS 

in its EBFM implementation efforts. An integrated focus on the habitat aspects of ecosystem 

processes and their associated species will lead to a more coherent implementation of an 

ecosystem approach to management, and provide for the most scientifically sound conservation 

of our managed species, the ecosystems that support them, and the sustainability of our fisheries.

 

15Doerr, J. and colleagues. 2016. Marshes to mangroves: examining growth and patterns of habitat use by penaeid shrimp in a 

changing marsh landscape to inform stock assessments. 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project16-030 16Baker, M.R. and A.B. Hollowed. 2014. Delineating ecological regions in marine systems: Integrating physical structure and 

community composition to inform spatial management in the eastern Bering Sea. Deep-Sea Research II. 109: 215-240. 

http://dx.doi.org/10.1016/j.dsr2.2014.03.001

17 Kellison, T. and colleagues. 2013. Predictive modeling of habitat distribution to support expansion of fishery-independent 

survey efforts: laying the groundwork to reduce uncertainty in stock assessments. 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project13-014 18 DeVries, D. and colleagues. 2013. Improving the identification of directed fishing effort when calculating CPUE using the 

relationship between habitat and reef fish abundance derived from fishery independent surveys. 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project13-013
11

Appendix A. Progress of the Nine 2010 HAIP Recommendations

1. NMFS and NOAA should develop new budget and staffing initiatives to fund habitat science 

that is directly linked to NMFS mandates. 

While defining EFH is an MSA mandate, there is no funding source dedicated to NMFS fisheries 

habitat science needs. But, FY2010-2018 funding (~$500 thousand per year) has supported 

short-term, small-scale habitat science studies that advance the goals of the HAIP. Each year 

resources have been put into the HISA internal funding allocation to support projects that focus 

on refining fishery-independent surveys and reducing habitat related uncertainty in stock 

assessments. Since 2010, 39 projects (totaling $4.1 million) have been funded, resulting in 

improved stock assessments, more precise definitions of EFH, better regional and inter-regional 

coordination, and a more efficient use of limited resources to support research. 

Additionally since 2010, the NMFS Office of Habitat Conservation (OHC) has provided over 

$5.6 million for research to support the identification, description, and conservation of essential 

fish habitat for federally managed fisheries. These funds include $4.7M distributed directly to 

Science Centers to support EFH research and $0.9M in discretionary funding for specific 

projects to support the data collection, assessment, and analyses necessary to complete required 

5-year reviews of EFH information in fishery management plans. Complementing this support, 

OHC has also provided over $12M in funding through the Deep-Sea Coral Research and 

Technology Program to generate information of immediate use to regional fishery management 

councils and other resource managers in conserving structurally complex habitats formed by 

deep-sea corals and sponges. However, overall funding has been limited for gathering 

information regarding the nearshore and offshore habitat associations of most fishery species, 

with knowledge gaps continuing. 

NMFS has developed budget initiatives toward creating a more fully and predictably funded 

habitat science program. In FYs 2016 and 2017, initiatives to support mission-driven applied 

science and the collection of foundational habitat science data were included in the annual 

President’s Budgets. Such requests have not ultimately been included in the congressional 

appropriations. However, efforts to advance their higher-level support toward future initiatives 

are ongoing.

2. NMFS should develop criteria to prioritize stocks and geographic locations that would 

benefit from habitat assessments. 

After development of the HAIP, the Habitat Assessment Prioritization Working Group was 

established to develop a nationally standardized set of criteria and process for prioritizing stocks 

that would benefit the most from habitat assessments in each region. This process allowed each 

region to create regional lists of stocks for habitat assessments based on two criteria:

• Stock Assessment Priorities: species whose stock assessments would benefit the most 

from habitat assessments;

• EFH Science Priorities: stocks that would benefit from habitat assessments to advance 

EFH designations. 
12

Each region has completed its prioritization process, with listings finalized and available online 

for the west coast (southwest and northwest), Northeast, Alaska, and Pacific Islands regions. The 

Southeast region has preliminary listings for its three subregions (Gulf of Mexico, South 

Atlantic, and Caribbean), and is working to finalize its prioritizations with final reports expected 

by FY2019. Additionally, for proposals submitted to the FY2017 and FY2018 HISA internal 

funding allocation, preference was given to project proposals that addressed prioritized species. 

Although there has been minimal progress and support for prioritizing geographic locations that 

are of key importance to fishery species and would benefit from targeted habitat assessments, 

there is a pilot project funded through OHC to develop a framework and conduct a habitat 

climate vulnerability assessment in the northeast. Additionally, through the NFHP in its 201019

and 201520 coastal and estuarine assessments, NMFS has worked toward characterizing 

conditions and vulnerabilities of inshore fish habitats. These efforts advance the need for 

geographic prioritizations for habitat assessments, especially as future NFHP assessments 

become more regionally focused at higher resolutions. Further work by NMFS, other agencies, 

and fishery management councils to identify priority inshore and offshore habitats of importance 

to coexisting species are also allowing for the identification of specific geographic locations 

within which assessments would be most valuable. As climate vulnerability assessments for 

regional habitats and their associated species continue to emerge, these efforts should also allow 

for improving the spatial and temporal resolutions needed to identify areas that would most 

benefit from priority habitat assessments.

3. 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.

As indicated above, 39 projects have been funded to date to support reduced habitat related 

uncertainty in stock assessments. They have been short-term, small-scale projects that have made 

incremental progress toward refining stock assessments. The full potential of these studies can be 

realized through larger-scale funding opportunities that would support continued study until their 

full incorporation into assessments. Although some funded studies have not yet been directly 

incorporated into stock assessments and management decisions, these projects have still 

increased understanding of the importance of habitat for many federally managed species, and 

provided results upon which future studies could build to allow for their incorporation into 

management decisions. Even with the limited budget, there are examples of HISA funded 

projects that have been applied toward improving stock assessments and management of 

federally managed species.

 

19National Fish Habitat Board. 2010. Through a Fish’s Eye: The Status of Fish Habitats in the United States 2010. Association of 

Fish and Wildlife Agencies, Washington, DC. 68p. Available at: http://www.habitat.noaa.gov/pdf/fishhabitatreport.pdf 20Crawford, S., Whelan, G., Infante, D.M., Blackhart, K., Daniel, W.M., Fuller, P.L., Birdsong, T., Wieferich, D.J., McCleesFuninan, R., Stedman, S.M., Herreman, K., and Ruhl, P. 2016. Through a Fish's Eye: The Status of Fish Habitats in the United 

States 2015. National Fish Habitat Partnership. http://assessment.fishhabitat.org/.
13

One such study that helped in improving the management of one federally managed species was 

work conducted at the Northeast Fisheries Science Center (NEFSC; funded in FYs 201221 and 

201422). This work enhanced the stock assessment for Atlantic Butterfish by calibrating survey 

data based on thermal habitat for use in its assessment models. These results also helped to 

determine which fishery-independent surveys had best sampled butterfish habitat and the 

appropriateness of their use in stock assessment models. Results from their work were useful in 

improving butterfish assessments; allowing the quota to undergo a seven-fold increase, from 3.2 

million pounds in 2014 to 22.5 million pounds in 201523. Other work by Shelton et al. (2014)24

integrated spatial habitat and fisheries effort data to improve estimates of west coast groundfish 

species. Their work also incorporated habitat variables into models to explore patterns of fish 

communities along the west coast, and results were incorporated into the California Current 

Integrated Ecosystem Assessment. Yet other funded studies improved catchability estimates of 

Alaska snow crab populations that led to an increase in overfishing limits by 64%25,26, 

investigated habitat-specific growth rates and productivity of juvenile penaeid shrimp species in 

the Gulf of Mexico27, and have addressed research gaps in foundational habitat information to 

improve understanding of the importance of habitat and development of fishery-independent 

studies28. 

4. NMFS should identify and prioritize data inadequacies for stocks and their respective 

habitats, as relevant to information gaps identified in the HAIP. 

Progress on this recommendation has been made in efforts described above under the second 

recommendation of the 2010 HAIP. 

5. NMFS should increase collection of habitat data on fishery-independent surveys and develop 

a plan for better utilizing new technologies (e.g. multibeam sonars) aboard the expanding 

NOAA fleet of Fishery Survey Vessels (FSVs). 

 

21Manderson, J.P. and colleagues. 2012. Accounting for habitat-dependent observation error in bottom trawl survey indices for 

pelagic stocks using butterfish (Peprilus triacanthus) as a model. Available at: 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project12-010 22Hare, J. and colleagues. 2014. Physiological ecology and habitat suitability: Combining experiments and surveys to inform 

stock assessments. Available at: 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project14-020 23Adams C. F., Miller, T.J., Manderson, J.P., Richardson, D.E., and Smith, B.E. 2015. Butterfish 2014 stock 

assessment. US Department of Commerce, Northeast Fisheries Science Center Reference Document 15-06. 

Available at: http://www.nefsc.noaa.gov/publications. 24Shelton, A.O., Thorson, J.T., Ward, E.J., and Feist, B.E. 2014. Spatial semiparametric models improve estimates of species 

abundance and distribution. Canadian Journal of Fisheries and Aquatic Sciences 71(11):1655-1666. 25Turnock, B. and Rugolo, L.R. 2011. Stock assessment of eastern Bering Sea snow crab. In North Pacific Fishery Management 

Council. Stock Assessment and Fishery Evaluation Report for the king and tanner crab fisheries of the Bering Sea and Aleutian

Islands Regions. 124 p. 26Somerton, D.A., Weinberg, K.L., and Goodman, S.E. 2013. Catchability of snow crab (Chionoecetes opilio) by the eastern 

Bering Sea bottom trawl survey estimated using a catch comparison experiment. Canadian Journal of Fisheries and Aquatic 

Sciences 70(12): 1699-1708. 27Leo, J.P., Minello, T.J., Grant, W.E., and Wang, H.H. 2016. Simulating environmental effects on brown shrimp production in 

the northern Gulf of Mexico. Ecological Modelling 330: 24-40. 28NMFS Office of Science and Technology. Improving the Use of Habitat Information in Stock Assessments. 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/index
14

Since publication of the HAIP, improvements have been made to collect habitat data on fisheryindependent surveys with the use of new technologies like Underway CTD-Stereo Camera 

Systems, camera floats, and acoustic technologies. The collection of benthic substrate and 

oceanographic data during stock abundance surveys through these technological improvements 

allows for greater spatial and temporal data coverage in understanding species distributions 

based on habitat availability. Additionally, HISA funded projects have increased information on 

favorable substrate availability for reef fishes in the U.S. southeast Atlantic and Gulf of Mexico. 

For example, results from a study conducted at the SEFSC and National Centers for Coastal 

Ocean Science increased understanding of hardbottom substrate distribution in the southeast 

Atlantic and facilitated the filling of spatial gaps in the sole regional-scale fishery-independent 

survey targeting the snapper-grouper complex in the southeast29. Another funded study at the 

SEFSC in Panama City, used side-scan sonar to characterize substrate for reef fish in offshore

regions in the Gulf of Mexico, which then informed scientists on the best locations to drop video 

arrays for surveying reef fish30 to determine which substrates serve as prime habitat. Other 

studies have increased understanding of substrate preferences that influence distributions of west 

coast groundfish, and efforts improved past west coast surveys of sardine and hake (SaKe 

surveys) by incorporating multibeam scanning and 3D imaging sonar. These advances can lead 

to better habitat-stratified samplings during surveys and reduce uncertainty in abundance 

estimates.

Five of NOAA’s FSVs have a ME70 Scientific Multibeam Echosounder, which allows for 

collection of fish and bathymetric data. This technology is used during various surveying 

programs, including the Southeast Area Monitoring and Assessment Program. The SEFSC 

Pascagoula Reef Unit and Beaufort Southeast Fishery Independent Survey cruises have been 

using the ME70 for Gulf and Atlantic Reef fish surveys to identify reef habitat that can later be 

sampled with trap and camera gear, or to allow for identification of untrawlable habitats in 

Alaska. Even though this technology has been useful, over the years various issues have arisen 

when using the ME70 for seafloor mapping. Along with these issues, there is concern over 

managing different uses of the system among scientists and FSVs, especially when balancing its 

utility to enumerate fish populations or to characterize benthic substrates. To help overcome 

these issues, fisheries scientists and experts convened a workshop that brought together ME70 

users and specialists together to develop recommendations for more effective use of ME70s for 

seafloor mapping. This effort will allow the agency to make best use of underutilized existing 

technologies and apply them toward improving fundamental understanding of fish-habitat 

associations. Allowing more coordinated opportunities among NOAA and inter-agency interests 

to leverage ship time and collect co-located habitat data can also increase progress at potentially 

limited additional cost. 

6. NMFS habitat scientists should engage partners within and outside of NOAA to exchange 

information about programs and capabilities. Habitat data collection and management 

 

29Kellison, T. and colleagues. 2013. Predictive modeling of habitat distribution to support expansion of fishery-independent 

survey efforts: laying the groundwork to reduce uncertainty in stock assessments. 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project13-014 30DeVries, D. and colleagues. 2013. Improving the identification of directed fishing effort when calculating CPUE using the 

relationship between habitat and reef fish abundance derived from fishery independent surveys. 

https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project13-013
15

efforts should be coordinated, and data integration applications should be upgraded to 

improve accessibility and synthesis. 

Progress on part of this recommendation has been made through increased engagement within 

NMFS, and complemented by efforts mentioned below under the ninth recommendation of the 

HAIP to unite with other NOAA Line Offices in broadening the applicability of habitat science 

and assessments. Since the publication of the HAIP, the OST and OHC participate in regular 

meetings to discuss advancing habitat science for improving management. Detailed information 

on the increased partnership between the OST and OHC can be found described above in 

progress made toward the first recommendation of the HAIP. In addition, efforts to align more 

strongly with the Bureau of Ocean Energy Management (BOEM) in characterization of speciessubstrate associations and to enhance EFH descriptions are ongoing throughout the U.S. Greater 

Atlantic region,31 and joint spatial studies using a jointly funded EFH mapper32 are working to 

understand the impacts of dredging on EFH. Other efforts to collaborate with USGS and ACOE

in their habitat-related studies and priorities are ongoing, especially through broader engagement 

through the NHCT and the National Ocean Service. 

In the years following publication of the HAIP, there has been a renewed interest from the 

federal government in improving data availability for the public. NMFS has created InPort, 

which is an online metadata information system under which all datasets within the agency must 

be registered. This system stores metadata, explains the accessibility of the data, constraints on 

its use, and a contact person to acquire the data since the system does not store the raw data. All 

projects supported from the HISA funding allocation are expected to create records in this 

system.

7. NMFS should convene workshops to develop strategies to better incorporate habitat science 

and assessments into stock assessment and IEA approaches and products. 

Post publication of the HAIP, two NHAWs occurred in 201033 and 201234. These workshops 

included NMFS habitat and stock assessment scientists from the fishery science centers, habitat 

and fisheries managers from Headquarters and Regional Offices, and restoration scientists and 

managers. The first NHAW brought together scientists and managers to address mutual interests 

to create a foundation for cooperative work in building a comprehensive habitat science program. 

Discussions at this workshop focused on ways to form and fund a habitat science program, align 

habitat assessments with management priorities, and identify and refine habitat science products 

and tools for use by management. The second NHAW built upon the first workshop and helped 

form recommendations that would improve the quality of NMFS habitat science needed to 

 

31Hooker, B. 2015. Fishery physical habitat and epibenthic invertebrate baseline data collection. https://www.boem.gov/AT-13-

02/ 32NOAA Habitat Conservation. http://www.habitat.noaa.gov/protection/efh/efhmapper/ 33Blackhart, K. (ed.) 2010. Proceedings. 11th National Stock Assessment Workshop: Characterization of scientific uncertainty in 

assessments to improve determination of acceptable biological catches (ABCs); Joint Session of the National Stock and Habitat

Assessment Workshops: Incorporating habitat information in stock assessments; and 1st National Habitat Assessment Workshop: 

Moving towards a national habitat science program. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-F/SPO-112, 153 p. 

https://www.st.nmfs.noaa.gov/Assets/ecosystems/habitat/pdf/NSAW_NHAW_Proceedings_final.pdf

34Clarke, L.M. (ed.) 2013. Proceedings of the 2nd National Habitat Assessment Workshop: Habitat Science to Support NOAA’s 

Habitat Blueprint. U.S. Dept. of Commer., NOAA Technical Memorandum NMFS-F/SPO-132, 89 p. 

https://www.st.nmfs.noaa.gov/Assets/ecosystems/habitat/pdf/NHAWIIProceedings.pdf
16

improve stock assessments and EFH designations. During this workshop, knowledge gaps were 

identified, and one identified high priority knowledge gap was the lack of information on the 

quantitative link between inshore habitat and offshore fisheries production. Both of these 

workshops were essential to improving habitat science throughout the agency by providing an 

uncommon opportunity for habitat scientists, stock assessment scientists, and managers to gather 

and interact, moving toward improved communication among centers, councils, and regional 

offices. Additionally following the second NHAW, three pilot projects addressing this 

knowledge gap in the Pacific and Atlantic regions were supported: 

• North Atlantic Pilot Project: “Restoring Access to Diadromous Fish Habitat and 

Linkages to Forage Fish Biomass in the North Atlantic Large Marine Ecosystem” 

Wes Patrick (NMFS/OSF), Tom Miller (University of Maryland), and JP Walsh (East 

Carolina University) 

The goal of this project was to predict long-term biological and sociological benefits of 

restoring diadromous fish habitat. Recent progress in this work includes calculation of the 

historic ranges and abundances of American shad and river herring, which shows 

substantial declines from their pristine conditions as a loss of habitat quality and 

accessibility over time.

• Mid-Atlantic Pilot Project: “Parameterizing the Relationship Between Inshore Habitat 

Quantity and Quality and Summer Flounder Production” 

Howard Townsend (NMFS/OHC/NCBO), Tom Ihde (NMFS/OHC/NCBO), David 

Stevenson (NMFS/GARFO), and John Manderson (NMFS/NEFSC) 

The goal of this project was to provide habitat managers with methods to quantify the 

cumulative impacts of inshore habitat loss and degradation on the survival and production 

of juvenile summer flounder. Recent progress in this work includes using the Chesapeake 

Atlantis Model (CAM) and datasets compiled from the Atlantic States Marine Fisheries 

Commission Fish Habitat Program to demonstrate the strong impacts of salt marsh loss 

upon forage fish, broad-scale impacts of habitat change on summer flounder, and 

ecosystem-wide implications of habitat dynamics.

• West Coast Pilot Project: “Pacific Marine and Estuarine Fish Habitat Partnership 

Nursery Assessment” 

PMEP Steering Committee and Assessment Team (Kristan Blackhart, Correigh Greene, 

Korie Schaefer, John Bragg et al.) 

The goal of this project was to identify key threats and limiting factors to juvenile fish, 

and describe the role of nearshore habitats to offshore stock recruitment. Recent progress 

in this work includes inventory and classification of west coast estuaries, a spatial 

framework to support modeling, and ongoing collection of fish abundance and habitat 

quality/quantity data. Additionally, west coast wide tier 1 and 2 assessments were 

conducted to obtain information about existing datasets on juvenile fish use of estuaries 

and estuarine habitats. Findings from these studies are being applied toward NOAA 

habitat protection efforts and in refining EFH for west coast species. 
17

All of these projects reinforce the importance of inshore habitat dynamics toward fish 

productivity and provide methods for quantifying the contributions of habitats toward these 

productivity estimates and toward enhancing ecosystem models. 

As IEAs are being updated, habitat has become an important component in many of these 

assessments. For example, IEA program sponsored work by Greene et al. (2013)35 developed 

ways to incorporate habitat indicators in the California Current IEA. This work helped to provide 

information on cross-habitat linkages toward ecosystem-based management approaches and 

refined habitat information on west coast region prioritized species. Additionally, the results of 

the previously referenced (see above, progress under the third HAIP Recommendation) 

HISA-funded work by Shelton et al. (2014) are being incorporated into the California Current 

IEA. These projects serve as examples for other regions to begin to work on including habitat 

indicators into their IEAs and ecosystem status reports.

More recently, in acknowledgement of the twentieth anniversary of the inclusion of EFH in the 

MSA, habitat scientists and managers from NMFS, along with members of the regional fishery 

management councils and other partners, participated in the National EFH Summit in May 

201636. Even though this summit was not a habitat science specific workshop, it brought 

scientists and managers together to discuss priority areas of habitat science that are needed in the 

future to help effectively identify and manage EFH for fisheries species. This three-day 

workshop broadened the discussion on EFH in the context of climate change, how EFH can 

support ecosystem-based management, addressed cumulative fishing and non-fishing impacts to 

EFH, and discussed mechanisms to continue funding high-priority science needs for effective 

EFH management.

8. NMFS should establish a habitat assessment fellowship program and provide funds to 

graduate students and post-doctoral associates of specific sub disciplines that would advance 

habitat modeling, evaluation, and assessment efforts.

For continuation and advancement of habitat science within NMFS, the agency must keep 

supporting the funding of graduate and post-graduate students whose research consists of habitat 

modeling, evaluation, and assessments to support the goals of the HAIP. Although a dedicated 

habitat assessment fellowship program has not been started since publication of the HAIP, many 

graduate students and post docs have conducted research in conjunction with NMFS scientists 

funded from the HISA program. However, these opportunities have remained limited given 

constrained resources to support habitat science. Since there are many applicable NOAA funded 

graduate fellowships available, NMFS must continue to support these programs and scientists 

with interest in conducting habitat studies who can mentor funded students in advancing habitat 

scientific research. Some of the programs that exist that focus on ecosystem science and 

modeling are the NMFS Sea Grant Population and Ecosystem Dynamics Fellowships and the 

National Research Council (NRC) Research Associate Program. Additionally, the NOAA Living 

 

35Greene et al. 2013. Selecting and Evaluating Indicators for Habitats within the California Current Large Marine Ecosystem. 

https://www.integratedecosystemassessment.noaa.gov/Assets/iea/california/Report/pdf/9.Habitat_2013.pdf

36Leaderhouse,T., T. Marshak, L. Latchford, R. Peters, and K. Latanich. 2017. Report from the National Essential Fish Habitat 

Summit. U.S. Dept. of Commerce, NOAA. NOAA Technical Memorfandum NMFS-OHC-3, 44p. 

http://spo.nmfs.noaa.gov/sites/default/files/TM-OHC3.pdf
18

Marine Resources Cooperative Science Centers37 provide scholarships, internships, and funding 

resources to train graduate students to conduct research of interest to NMFS. This program has 

four main research themes. One of those themes includes increasing our understanding on the 

relationship between habitats and marine populations. Habitat scientists in NMFS can continue 

to collaborate with these programs to work toward training future habitat scientists.

9. NMFS should unite with other NOAA Line Offices 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. 

Since 2010, there has been steadily increasing recognition within NOAA of the fundamental 

importance of habitat science and conservation. The NOAA-wide NHCT was formed to guide 

cross-line office and cross-agency habitat conservation and science activities, including the 

initiation of the NOAA Habitat Blueprint38. The NOAA Habitat Blueprint was created to provide 

a framework to strategically coordinate activities within NOAA and increase engagement with 

outside partners and resources to improve habitat for fisheries, marine life, and coastal 

communities39. The Blueprint developed a three-pronged framework, which consists of: 1) 

establishment of NOAA HFAs for long-term habitat science and conservation, 2) 

implementation of a systematic and strategic approach to habitat science to inform effective 

decision-making, and 3) strengthened policy and legislation to enhance NOAA’s ability to 

achieve meaningful habitat conservation. This framework led to the establishment of NOAA 

HFAs40, which are coastal regions around the United States where NOAA offices and their 

partners can effectively use their resources to conduct long-term habitat science and conservation 

efforts. There are now ten HFAs around the United States, within which NMFS and other NOAA 

Line Offices have provided support for habitat science efforts. After development of the NOAA 

Habitat Blueprint, NOAA developed the National Habitat Policy41, which established NOAAwide guideline for using the agency’s resources to its fullest extent possible in protecting, 

maintaining, and restoring habitats. 

Under the NHCT, a science sub-team was formed and summarized the priority habitat science 

needs for NOAA. At the same time, a framework was developed to coordinate ecological 

forecasting activities within NOAA and across other agencies. With recognition of the need of 

ecological forecasting to support habitat science, the Ecological Forecasting Roadmap was 

developed and included habitat as one of its four priorities. The Ecological Forecasting group has 

now merged with the habitat science sub-team to form the Habitat Science and Ecological 

Forecasting Technical Team. This team recently developed habitat science priority guidance to 

advance and promote habitat science across the agency42. 

 

37 NOAA Living Marine Resource Cooperative Science Center: https://www.umes.edu/LMRCSC/ 38 NOAA Habitat Blueprint: https://www.habitatblueprint.noaa.gov/ 39NOAA Habitat Blueprint Fact Sheet. http://www.habitat.noaa.gov/pdf/habitatblueprint6pfactsheet.pdf 40 NOAA Habitat Focus Areas: https://www.habitatblueprint.noaa.gov/habitat-focus-areas/ 41 NOAA National Habitat Policy: http://www.corporateservices.noaa.gov/ames/administrative_orders/chapter_216/NAO_216-

117.pdf

42NOAA’s Habitat Science and Ecological Forecasting Technical Team’s Guidance Document: Support for NOAA’s Habitat 

Conservation Team and the Ecological Forecasting Roadmap. 2016. 

https://aamboceanservice.blob.core.windows.net/oceanservice-prod/ecoforecasting/HSEF-action-plan.pdf
19

Appendix B. Funded Habitat Science Projects from the NMFS Office of 

Science and Technology (OST) Habitat Information for Stock Assessments

Internal Funding Allocation and from the NMFS Office of Habitat 

Conservation (OHC). 

Table 1. OST Habitat Information for Stock Assessments Funded Projects 2010-2018. 

Year Region Title Lead PI(s)

2010 SW Relating population abundance of groundfish 

species to habitats using predictive models 

and broad-scale seafloor maps

Mary Yoklavich

2010 SE Habitat Modeling of Atlantic Blue Marlin 

with SEAPODYM and Satellite Tags

Michael Schirripa

2010 SE/NE Incorporating sediment and hydrography data 

assessments for tilefish and lobster

John Quinlan

2011 NE Detecting an environmental gradient in 

maturity, spawning rates, and fecundity of 

inshore winter flounder stocks: does thermal 

habitat create spatial heterogeneity of life 

history parameters within stock boundaries?

Richard McBride

2011 SE Incorporating environmental and habitat 

characteristics into the brown shrimp stock 

assessment for the northern Gulf of Mexico

Thomas Minello

2011 NE Incorporating measures of habitat area into 

stock assessments: a case study with winter 

flounder and summer flounder

Jon Hare

2012 PI Estimation of habitat-stratified catch 

efficiency of fishery-independent reef fish 

survey methodologies to improve estimates 

of stock size

Gerard DiNardo

2012 SE Estimating habitat related variability in 

natural mortality of juvenile white shrimp for 

incorporation into stock assessment models

Lawrence Rozas

2012 NE/SE Accounting for habitat-dependent observation 

error in bottom trawl survey indices for 

pelagic stocks using butterfish (Peprilus 

triacanthus) as a model

John Manderson
20

Year Region Title Lead PI(s)

2012 SW Spatially Predictive Modelling and Mapping 

of Groundfish Species to Advance Stock and 

Habitat Assessments Relevant to SW Habitat 

Blueprint Regional Initiative

Mary Yoklavich

2012 AK Locating essential spawning grounds for red 

king crab

Chris Long

2012 AK Defining eco-regions and applying spatial 

analyses of species abundance, community 

dynamics and stock substructure to 

incorporate habitat in SSMs and MSMs

Anne Hollowed

2013 AK Identifying habitat use by male and female 

red king crabs during mating season

Chris Long

2013 AK Evaluating the use of acoustic bottom typing 

to inform bottom trawl survey catchability 

models for snow crab in the eastern Bering 

Sea

Robert McConnaughey

2013 AK Evaluating Smooth Sheet Bathymetry for 

Determining Trawlable and Untrawlable 

Habitats

Wayne Palsson

2013 NW Integrating spatial habitat and fisheries effort

data to improve abundance estimates of west 

coast groundfish 

Andrew Shelton

2013 SE Predictive modeling of habitat distribution to 

support expansion of fishery-independent 

survey efforts: laying the groundwork to 

reduce uncertainty in stock assessments

Todd Kellison

2013 SE Improving the identification of directed 

fishing effort when calculating CPUE using 

the relationship between habitat and reef fish 

abundance derived from fishery independent 

surveys

Doug DeVries

2014 SE Prioritizing spawning habitats in terms of 

their relative contribution to recruitment 

success

John Walter
21

Year Region Title Lead PI(s)

2014 SE Estimating habitat-specific variability in 

growth rates of juvenile penaeid shrimps for 

incorporation into stock assessment models

Lawrence Rozas

2014 NE Integrating Habitat Information into Stock 

Assessments to Maximize Precision: A Case 

Study Using Data from the Annual Sea 

Scallop Survey Provided by HabCamV4, an 

Integrated Habitat Mapping Camera and 

Acoustics System

Dvora Hart

2014 NE Physiological ecology and habitat suitability: 

combining experiments and surveys to inform 

stock assessments

Jon Hare

2014 SW Identifying essential spawning habitats for 

improving assessment and management of 

the market squid fishery off California.

Emmanis Dorval

2014 SW Habitat assessment for Pacific Sardine 

juveniles

Russ Vetter

2015 SE/SW Incorporating hypoxia-based habitat 

compression impacts into the stock 

assessment process for tropical pelagic 

billfish and tuna

Eric Prince 

2015 NW/AK/NE Distribution and application of a new 

geostatistical index standardization and 

habitat modeling tool for stock assessments 

and essential fish habitat designation in 

Alaska and Northwest Atlantic regions

Jim Thorson 

2015 AK Improving Stock Assessments for Rockfishes 

Using Habitat-referenced Acoustic Surveys in 

the Gulf of Alaska

Chris Wilson

2015 NW Using habitat-specific, spatial demographic 

information to improve stock assessments of 

groundfishes

Jameal Samhouri

2016 AK Seabed mapping to develop a habitat-based 

catchability function for the Bristol Bay red 

kind crab (Paralithodes camtschaticus) stock 

assessment

Robert McConnaughey
22

Year Region Title Lead PI(s)

2016 SW Kill ‘em or hide ‘em: where are all the old 

female rockfish?

Susan Sogard

2016 SE Marshes to mangroves: examining growth 

and patterns of habitat use by penaeid shrimp 

in a changing marsh landscape to inform 

stock assessments

Jennifer Doerr

2016 SW Combining high-resolution bathymetry and 

recreational catch rates to model the spatial 

distribution of biomass for reef-associated 

nearshore species

E.J. Dick

2017 AK/NW Detecting changes in life history traits and 

distribution shifts in eastern Bering Sea fishes 

in response to climate change

Chris Rooper, 

Jim Thorson 

2017 AK Evaluating the effects of habitat quality on 

YOY sablefish physiological condition to 

inform estimates of recruitment in the stock 

assessment 

Ron Heintz

2017 NE Use of a Lagrangian camera float in 

association with surveys to examine benthic 

habitats and 

associated fish: operational test to improving 

survey-based estimates of abundance

Harvey Walsh

2017 SE Evaluation of methods of incorporating 

oceanographic indicators into indices of 

abundance for stock assessment

Michael Schirippa

2018 AK Using habitat information to assess Pacific 

cod life history parameters for stock 

assessment

Grant Thompson

2018 AK Accounting for habitat variables to improve 

abundance indices in Alaska trawl surveys 

with an emphasis on results from averaging 

multiple modeling methodologies

Chris Rooper

2018 AK Seabed mapping to quantify untrawlable 

habitats and reduce bias in Gulf of Alaska 

stock assessments

Robert McConnaughey
23

Table 2. Projects Funded to Refine EFH by NMFS OHC, 2010-2015. 

Year Region Title PI(s)

2010 PI Understanding key habitats of commercial demersal 

fishes – the Deep Seven Bottomfish complex in 

Hawaii

Alan Everson

2010 NE Use of state fisheries independent survey data to 

refine EFH in estuaries and nearshore coastal waters

Lou Chiarella

2011 SE Life history summaries and creation of the 

EcoSpecies Database to provide web-enabled 

information to support SAFMC habitat management 

and SEDAR

Pace Wilber

2011-12 NW/SW Summarize data in support of a 5-year review of EFH 

for Pacific Coast groundfish 

John Stadler,

Bryant Chesney, 

Waldo Wakefield

2012 NE Conservation of DelMarVa reefs, black sea bass 

habitats at risk

David Stevenson,

Lou Chiarella

2012 AK Seasonal distribution and habitat use of managed fish 

species in Upper Cook Inlet, Alaska

Jeanne Hanson,

Matt Eagleton

2013 SE Fish habitat value – salt marsh flooding in TX and 

LA

Tom Minello

2013 SE Improve EFH maps for GMFMC managed species David Dale

2014 SE Revising SAFMC EFH and HAPC GIS data Pace Wilber

2014 AK Gulf of Alaska and Norton Sound bathymetry and 

substrate compilation

Matt Eagleton

2015 AK Effects of offshore marine mining activities on 

Norton Sound Red King crab

John Olson,

Robert Foy

2015 NW/SW Habitat Use Database for the California Current Waldo Wakefield,

Mary Yoklavich, 

Steve Copps, 

John Stadler
24

Appendix C: Examination of gaps/needs for carrying out the 2010 HAIP recommendations, and approaches 

for continued progress.

2010 HAIP Recommendation HAIP Progress to Date Gaps/Needs 2018 Recommendations

NMFS and NOAA should develop new 

budget and staffing initiatives to fund 

habitat science that is directly linked 

to NMFS mandates.

• Initiatives were included in the 

President’s Budgets (FYs 2016 & 

2017) to support mission-driven 

applied science and the 

collection of foundational 

habitat science data. Ultimately, 

these requests were not funded.

1a. Increased collaboration and 

integration of habitat science 

with internal funding 

opportunities (e.g., those 

addressing the Stock 

Assessment Improvement Plan, 

EBFM Road Map, and the

Climate Science Strategy) is 

needed to support longer-term 

projects toward incorporating 

habitat information into 

management decisions and 

enhancing NMFS climate 

science efforts. 

1b. Funding to support 

continued collection of 

information on the distribution 

of benthic habitats, including 

habitat surveys and multibeam 

mapping during fisheryindependent surveys.

1.1. Continue to work on future 

budget initiatives.

1.2. Integrate studies that focus 

on incorporating habitat and 

other ecosystem metrics into 

management decisions, 

Integrated Ecosystem 

Assessments (IEAs) and 

Ecosystem Status Reports. 

1.3. Continue to fund carefully 

targeted work that focuses on 

collecting habitat data to improve 

stock assessment models, EFH 

and Habitat Areas of Particular 

Concern (HAPC) designations, and 

ecosystem information. Of 

particular need is fundamental 

habitat information for fishery 

species throughout their life 

histories, and understanding 

habitat distributions through 

mapping and use of acousticsurvey technologies.
25

2010 HAIP Recommendation HAIP Progress to Date Gaps/Needs 2018 Recommendations

NMFS should develop criteria to 

prioritize stocks and geographic 

locations that would benefit from 

habitat assessments.

• Habitat Assessment 

Prioritization Working Group 

(HAPWG) formed. 

• Nationally standardized set of 

criteria and process to prioritize 

stocks in each region that would 

benefit from habitat 

assessments to improve stock 

assessments and advance EFH 

information. 

• Each region has finalized or 

developed preliminary listings. 

• These listings are currently 

being used to inform the HISA 

internal funding allocation, and 

HISA studies have increased 

habitat information for 21 high 

and medium priority listed 

species.

2a. Habitats that are associated 

with regionally prioritized 

species have not been fully 

identified. 

2b. Resources should be 

prioritized to allow for 

investigation into the EFH 

requirements of these species, 

especially those that are 

habitat-limited, and the 

inclusion of this information in 

their stock assessments. 

2c. Resources should be 

allocated toward determining 

those habitats that are most 

important to multiple species of 

concern.

2.1. Allocate resources using the 

regional prioritization listings 

toward research for those species 

that would benefit most from 

habitat assessments. 

2.2. Fishery Science Centers and 

Regional offices should examine 

regional priorities and identify 

where investments can be made 

using the prioritized lists in each

region.

2.3. Prioritizations can be 

included as a component of a 

broader ecosystem-level risk 

assessment to identify taxa and 

habitats that are most vulnerable 

to human and natural pressures.

2.4. Prioritization lists should be 

examined to work toward 

prioritizing geographic 

locations/habitats. 

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.

• ~$500,000 each year has been 

made available for the Habitat 

Information for Stock 

Assessments internal funding 

allocation.

3a. Funded projects must

continue to work toward 

incorporating habitat 

information into stock 

assessments and improving EFH 

information. 

• See recommendations 1.1 – 1.3.
26

2010 HAIP Recommendation HAIP Progress to Date Gaps/Needs 2018 Recommendations

• To date 39 projects have been 

funded out of 141 submitted 

proposals.

3b. Information should be 

applied toward focusing on the 

broader role of habitat in 

ecosystems and in advancing 

understanding of inshoreoffshore connections for 

species during life stages.

NMFS should identify and prioritize 

data inadequacies for stocks and their 

respective habitats, as relevant to 

information gaps identified in the 

HAIP.

• Prioritization lists mentioned 

above also support this 

recommendation.

4. Communication of the utility 

of the regional habitat 

assessment prioritization lists 

among scientists and managers 

should be improved to increase 

the application of these listings

toward research and 

management. 

• See recommendations 2.1 – 2.4.

NMFS should increase collection of 

habitat data on fishery-independent 

surveys and develop a plan for better 

utilizing new technologies (e.g. 

multibeam sonars) aboard the 

expanding NOAA fleet of Fishery 

Survey Vessels (FSVs).

• Five of the FSVs have a ME70 

Scientific Multibeam 

Echosounder, which allows for 

collection of fishery and 

bathymetric data.

• Two HISA funded studies 

supported the increase of 

habitat data through new 

technologies (ME70 and side 

scan sonar). 

• In November 2017, a two-day 

workshop was held to bring user 

and experts of the ME70 

together to discuss ways to 

5a. A plan should be developed 

to provide guidance on how to 

better utilize new technologies 

(including multibeam 

echosounders and side scan 

sonar) to increase collection of 

habitat data on fisheryindependent surveys. 

5.1. Recommendations from the

2017 workshop to improve the 

use of ME70s aboard NOAA 

Fishery Science Vessels should be 

communicated to increase and 

improve habitat mapping.

5.2. Continue to develop ways to 

utilize new technologies to collect 

habitat information.

• See recommendation 1.3. 
27

2010 HAIP Recommendation HAIP Progress to Date Gaps/Needs 2018 Recommendations

improve the use of this 

technology for seafloor mapping. 

The workshop resulted in short, 

mid, and long-term 

recommendations of their more 

effective use. 

NMFS habitat scientists should 

engage partners within and outside of 

NOAA to exchange information about 

programs and capabilities. Habitat 

data collection and management 

efforts should be coordinated, and 

data integration applications should 

be upgraded to improve accessibility 

and synthesis.

• OST and OHC participate in 

regular meetings to advance 

habitat science toward

improving management.

• There have been efforts to 

work with the Bureau of Ocean 

Energy Management (BOEM) on 

characterizing species-substrate 

associations and to enhance 

species EFH descriptions.

• Through efforts with the NHCT 

and the National Ocean Service, 

collaboration has increased 

between NMFS and the U.S. 

Geological Survey (USGS) and 

U.S. Army Corps of Engineers 

(ACOE) in their habitat-related 

studies and priorities. 

• NMFS created InPort to 

provide an online metadata 

information system where all 

6. There needs to be more 

engagement between habitat 

managers in regional offices 

and fishery management 

councils, and fishery scientists 

to incorporate habitat science 

information into management 

decisions.

6.1. Collaborate with partners, 

like USGS, BOEM and ACOE, to 

leverage funds to increase 

collection of foundational habitat 

information. 

6.2. Fund/expand fishery 

management council and fishery 

science center collaborative pilot 

projects to explore setting habitat 

objectives for fishery 

management.

• See recommendation 7.1. 
28

2010 HAIP Recommendation HAIP Progress to Date Gaps/Needs 2018 Recommendations

datasets within the agency must 

be registered. 

NMFS should convene regional and 

national workshops to develop 

strategies to integrate habitat science 

and assessments, stock assessments, 

and IEA’s.

• NHAWs were held in 2010 and 

2012. These workshops focused 

forming and funding a habitat 

science program in NOAA and 

identified knowledge gaps in 

habitat science that needed to 

be filled to improve 

management of living marine 

resources.

• A National EFH Summit was 

held in May 2016 to bring 

together habitat scientists and 

managers from NMFS, regional 

management council 

representatives, and 

representatives from interested 

partners to discuss 

achievements and ways to 

improve designation of EFH.

7. There has not been a NHAW 

since 2012, nor have initially 

recommended efforts to create 

regional NHAWs been carried 

out.

7.1. Hold additional national and 

regional NHAWs to address ways 

to incorporate habitat into EBFM 

and strengthen communication 

and collaboration among habitat 

scientists and managers within 

and among regions. Additionally, 

efforts should be undertaken to 

increase collaboration with IEA 

meetings, National Stock 

Assessment Workshops, and the 

EBFM workgroup.

7.2. HAIP members should 

actively participate on regional 

implementation plans for EBFM 

and incorporate habitat science 

milestones into these 

implementation plans.

NMFS should establish a habitat

assessment fellowship program and 

provide funds to graduate students 

and post-doctoral associates of 

specific sub disciplines that would 

advance habitat modeling, 

evaluation, and assessment efforts.

• Graduate students and postdocs have conducted research in 

conjunction with NMFS scientists 

funded from the HISA program.

However, funding opportunities 

have been limited.

8. No habitat assessment 

fellowship program has started 

since publication of the HAIP, 

but NMFS scientists should take 

advantage of existing graduate 

fellowship programs to mentor

graduate students or post docs 

8.1. NMFS scientists interested in 

mentoring graduate students or 

post docs on habitat science 

related work should mentor 

funded students from current 

programs that focus on 

ecosystem science and modeling 

such as: NMFS Sea Grant 
29

2010 HAIP Recommendation HAIP Progress to Date Gaps/Needs 2018 Recommendations

on habitat science related 

research.

Population and Ecosystem

Dynamics Fellowships, National 

Research Council Research 

Associated Program, and NOAA 

Living Marine Resources 

Cooperative Science Centers.

NMFS should unite with other NOAA 

Line Offices 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.

• NHCT was formed to guide 

cross-agency habitat 

conservation and science 

activities, which led to the 

development of the NOAA 

Habitat Blueprint.

• Under the NHCT, there is a 

science sub-team, which has 

formed the Habitat Science and 

Ecological Forecasting Technical 

Team. This team developed 

habitat science priority guidance 

to advance and promote habitat 

science across the agency.

9. Increased communication 

and broader application of 

these types of habitat science 

studies remains necessary and 

can serve as examples for other 

regions to conduct similar work 

and address habitat-related 

uncertainties.

9.1. Hold workshops, briefings, 

etc. that improve communication 

and awareness among NMFS’ 

Offices of Science & Technology 

and Habitat Conservation with 

the aim to integrate habitat and 

stock assessment information. 

Continue to brief NMFS

leadership and NOAA wide 

committees on progress on the 

HAIP-related and habitat science 

efforts across the agency.