Alaska 

Fisheries Science 

Center

National Marine 

Fisheries Service

U.S DEPARTMENT OF COMMERCE

AFSC PROCESSED REPORT 2017-05

doi:10.7289/V5/AFSC-PR-2017-05

Alaska Essential Fish Habitat Research Plan

A Research Plan for the National Marine Fisheries Service’s 

Alaska Fisheries Science Center and Alaska Regional Office

March 2017

This report does not constitute a publication and is for information only. 

All data herein are to be considered provisional.
This document should be cited as follows:

Sigler, M. F., M. P. Eagleton, T. E. Helser, J. V. Olson, J. L. Pirtle, C. N. Rooper, 

S. C. Simpson, and R. P. Stone. 2017. Alaska Essential Fish Habitat Research

Plan: A Research Plan for the National Marine Fisheries Service’s Alaska

Fisheries Science Center and Alaska Regional Office. AFSC Processed Rep.

2015-05, 22 p. Alaska Fish. Sci. Cent., NOAA, Natl. Mar. Fish. Serv., 7600 Sand

Point Way NE, Seattle WA 98115.

Available at http://www.afsc.noaa.gov/Publications/ProcRpt/PR2017-05.pdf

Reference in this document to trade names does not imply endorsement by the National 

Marine Fisheries Service, NOAA.
Alaska Essential Fish 

Habitat Research Plan

A Research Plan for the National Marine Fisheries Service’s

Alaska Fisheries Science Center and Alaska Regional Office

by

M. F. Sigler1

, M. P. Eagleton2, T. E. Helser1, J. V. Olson2, J. L. Pirtle2, C. N. Rooper1, 

S. C. Simpson2, and R. P. Stone1

1

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Alaska Fisheries Science Center

7600 Sand Point Way NE

Seattle WA 98115

2 National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Alaska Region

222 West 7th Ave.

Anchorage, AK 99513

March 2017

Contents

Introduction ......................................................................................................................................1 

Long-term Research Goals and 5-Year Research Objectives ..........................................................2 

Objective 1: Develop EFH Level 1 Maps ............................................................................2 

Objective 2: Raise EFH Level from Level 1 or Level 2 to Level 3 .....................................3 

Next 5-year EFH Plan (in ~2022) ....................................................................................................3 

Research Approach ..........................................................................................................................4 

Integrated Proposals .............................................................................................................4 

Modeling ..............................................................................................................................4 

Reporting New EFH Information ........................................................................................4 

Request for Proposals ......................................................................................................................5 

Plan Writing and Review .................................................................................................................6 

Citations ...........................................................................................................................................7 

Appendix 1. Definitions of EFH Levels ........................................................................................11 

Appendix 2. Core EFH Research Priorities ...................................................................................12 

Appendix 3. Example of Level 3 Mapping ....................................................................................14 

Appendix 4. Template for Proposals .............................................................................................20 

Appendix 5. Form for Annual Report of Project Status ................................................................22 

iii

Introduction

The Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA) mandates 

NOAA to identify habitats essential for managed species and conserve habitats from adverse 

effects on those habitats. These habitats are termed “Essential Fish Habitat” or EFH, and are 

defined as “those waters and substrate necessary to fish for spawning, breeding, feeding, or 

growth to maturity”. Further, the MSFCMA requires federal agencies to consult with the 

National Marine Fisheries Service (NMFS) when their actions may adversely affect EFH. These 

consultations occur for both fishing and non-fishing activities.1 The recently revised National 

Standard 1 guidelines add several provisions to facilitate the incorporation of ecosystem-based 

fisheries management into federal fisheries management. National Standard 2 of the MSFCMA 

requires NMFS to conserve and manage fishery resources based upon the best available 

scientific information. To meet these mandates, NOAA’s research must identify habitats that 

contribute most to the survival, growth, and productivity of managed fish species and determine 

science-based measures to best manage and conserve these habitats from adverse effects of 

human activities. 

The approach for identifying EFH is described in the NMFS EFH regulations (Appendix 1). The 

regulations require that, at a minimum, distributional data (level 1 information) be used in the 

identification of EFH. This level 1 information is based on presence/absence data of the species 

or life stages in specific habitats used. Where possible, data sets and information on habitatrelated densities of species (level 2), growth, reproduction and survival within habitats (level 3) 

and production rates by habitat (level 4) should be used to identify EFH. In Alaska, information 

for most commercial fish and crab species currently is level 1 or level 2, depending on the 

species and life stage, and no level 3 or level 4 information has been described. EFH research is 

conducted in part to elevate the EFH level for the studied species. While striving for level 4 

information, the current goal of this research plan is level 3 information (see research 

objective 2, listed below). 

Previous EFH Research Plans (AFSC 2006, Sigler et al. 2012) for Alaska have guided research 

to meet EFH mandates in Alaska since 2005. This document revises and supersedes these earlier 

plans, and similar to previous plans, is expected to guide the next several years of EFH research. 

Revisions of the EFH research plan (Sigler et al. 2012, this document) are timed to match 

required EFH 5-year reviews; the North Pacific Fishery Management Council (Council) and 

1 NOAA Fisheries recommends measures to conserve EFH resulting from fishing and non-fishing activities. EFH 

measures conserve sensitive habitats and features necessary to fish for spawning, breeding, feeding, or growth to 

maturity. For fishing activities (such as trawling and fixed gears), recommendations may include gear restrictions, 

time and area closures, and gear modifications. For non-fishing activities (such as oil and gas exploration and 

development, port and harbor expansions, mining, and roadway construction), recommendations may include 

measures such as in-water work timing windows, alternative site selection, onshore disposal of dredge spoils, and 

methods to avoid, remove and remediate impacts from accidental discharge of oil.
NMFS are required by EFH regulations to review the EFH components within each fishery 

management plan (FMP) every 5 years. The objectives of these reviews are to evaluate and 

synthesize new information on habitat, determine whether changes to the FMPs are warranted, 

and present this evaluation in a summary report to the Council. These reviews summarize the 

status of EFH research, which then provides a basis for determining future research directions 

(i.e., this revised research plan).

The 2015 EFH review demonstrated a large advance in EFH information, in particular by 

substantially refining EFH maps for fish and crab species (Fisheries Leadership and 

Sustainability Forum 2016). The refinement occurred through an analysis to determine the 

environmental influences on species distributions and used this information to refine the EFH 

maps. These maps provide EFH Level 2 information (habitat-related densities) for the adult life 

stage for many FMP species and EFH Level 1 information (habitat distribution) for the juvenile 

life stages of some FMP species. These maps also provide a solid foundation for the next 5 years 

of EFH research. 

Long-term Research Goals and 5-Year Research Objectives

A set of five long-term EFH research goals have guided EFH research in Alaska since 2005 

(Appendix 2). These long-term goals have been consistent since 2005 with only minor 

modifications. We will continue to use these five long-term EFH goals as broad guidelines for 

EFH research in this update of the EFH research plan. Briefly these are as follows: 1) 

characterize habitat utilization and productivity; 2) assess habitat sensitivity and recovery; 3) 

validate and improve fishing impacts model; 4) map the seafloor; and 5) assess coastal habitats 

facing development.

Here we describe specific EFH research objectives to be accomplished in the next 5 years; that 

is, by the next EFH update. These objectives are more focused than the five long-term research 

goals and describe specific tasks to accomplish in the next 5 years. There are two research 

objectives for the next 5 years: 

1. Develop EFH Level 1 information (distribution) for life stages and areas where missing. 

2. Raise EFH level from Level 1 or 2 (habitat-related densities) to Level 3 (habitat-related 

growth, reproduction, or survival rates). 

Objective 1: Develop EFH Level 1 Maps

Distribution information has not been fully developed for juvenile life stages of fish and crab 

species listed in the Gulf of Alaska, Bering Sea, and Aleutian Islands FMPs, as well as juvenile 

and adult life stages of fish and crab species listed in the Arctic FMP. The purpose of the first 

EFH research objective is to develop these maps where information is available for analysis, but 

2
this information has not yet been analyzed. One area with information available is settlement 

stage juveniles in the Gulf of Alaska, Bering Sea, and Aleutian Islands. Currently, many juvenile 

stage maps have been developed; this analysis would separate settlement and later stage 

juveniles (i.e., separate the juvenile stages based on length into early (settlement) and late 

juveniles, where practical (e.g., Pacific cod)).2 Likewise, information is available for early life 

stages and adults of fish and crab species in the northern Bering, Chukchi and Beaufort seas, but 

has not been analyzed. The goal is to analyze all of these data sets to develop EFH Level 1 maps. 

Objective 2: Raise EFH Level from Level 1 or Level 2 to Level 3

Habitat-related densities are available for the juvenile and adult life stages of most species listed 

in the Gulf of Alaska, Bering Sea, and Aleutian Islands FMPs. The next step is to incorporate 

habitat-related growth, survival, and reproductive rates into the EFH maps. In some cases, this 

incorporation also is possible for Level 1 species. There are two pathways for doing so. First, 

growth, survival, or reproductive rates are available for several species (Table 1). This 

information often was collected during laboratory studies (e.g., growth response to temperature 

of four gadid species [Laurel et al., 2016]). In these cases, analysis methods similar to those 

applied for the Level 1 and Level 2 maps could be applied to create Level 3 maps (Appendix 3). 

Second, additional laboratory and/or field studies could be conducted and this new information 

used to create Level 3 EFH maps. The performance objective for the number of species with 

Level 3 information examined through new studies after 5 years is 8-10 (assuming 2-3 years to 

conduct a study, 2-3 related species examined in each study and 1-2 studies conducted 

simultaneously). 

Next 5-year EFH Plan (in ~2022)

Another large advance for the 2016 EFH update was the revision of the fishing effects model. 

The revised fishing effects model includes much more sediment information (250,000 vs. 2,000 

sediment points) compared to the decade-old original model and adds recent recovery rate 

information. The revised fishing effects model provides estimates of the percent of EFH 

impacted by fishing based on Level 2 EFH information. A next step is to update the fishing 

effects model with Level 3 information. It is anticipated that sufficient Level 3 information will 

not become available until the 2022 EFH research plan revision. 

 

2 Use the presence only (MaxEnt) approach to analyze nearshore fish survey, ADFG small mesh survey, and small 

size fish from bottom trawl survey in combination.

3
Research Approach 

Integrated Proposals

To accomplish Objective 2, the primary research approach is to build integrated lab, field, and 

modeling studies, with the purpose of mapping, for example, the growth potential of the studied 

fish and crab species (Level 3 EFH). As for previous EFH research plans, studies that estimate 

functional relationships will be conducted (e.g., response of fish growth rate to a range of 

temperatures; Laurel et al. 2016). The difference for this research plan is that the functional 

response will be incorporated into a model and EFH Level 3 information mapped. The study 

components (lab and/or field components and the modeling) will be explicitly tied together, 

explained in the proposal, and then reported. Verification of EFH Level 3 maps should be 

conducted to confirm that results determined in the laboratory also occur in the field (sensu

Rooper et al. 2016 for confirmation of EFH Level 2 maps). The addition of verification also 

differs from the approach of most previous EFH research. The expectation is that the lab and/or 

field research, modeling, and if completed, verification, will be reported together in a peerreviewed publication. 

Modeling

Currently species distribution models exist for EFH Level 1 and Level 2 information. To date, 

the Level 1 models have been presence-only maximum entropy or MaxEnt models (Phillips et al. 

2006) and the Level 2 models have been based on generalized additive models (GAMs) 

predicting relative abundance (Wood 2006). These modeling approaches use different data sets, 

but both can be regional in scale and extended as Level 3 information is available (Appendix 3). 

These models are currently curated by Jodi Pirtle and Chris Rooper and we anticipate their roles 

will continue. They are constructing and parameterizing models and habitat metrics, as well as 

currently tracking life history stages and species where models can be developed or refined. 

These models can develop or refine EFH by constructing and parameterizing habitat metrics for 

a particular history life stage. For projects that collect new Level 3 information, project PIs will 

collaborate with the EFH model developers to incorporate project data into the regional models. 

PIs will be expected to consult with the modeler beforehand and describe the plan for 

incorporating data into the model in their proposal. 

Reporting New EFH Information 

The new EFH information will be integrated into the stock assessment process. Currently new 

habitat information is incorporated into the stock assessment process every 5 years with the EFH 

update. Going forward, this information will be provided to stock assessment authors as 

available through existing web locations. Most of the modeling is automated to the point that 

annual or biennial updates may become relatively simple. New models will be run as new data 

becomes available (including both the results of new field and lab studies as well as new density 

4
information and updated bathymetry (e.g., Zimmermann et al. 2013). In addition, the newly 

revamped Stock Profile and Ecosystem Considerations (SPEC) section of the Stock Assessment 

and Fishery Evaluation Reports (SAFE) allows for inclusion of EFH information in the stock 

assessment process (Shotwell et al. 2016). Relevant text descriptions and maps can be provided 

to the stock authors to be included within the SPEC framework. 

The EFH information for Alaska will be provided in three web locations: the EFH mapper

maintained by NOAA Fisheries Headquarters Office, the EFH maps archived by the Alaska 

Ocean Observing System (AOOS), and an Alaska Regional Office EFH web site which is the 

source web location for text and map descriptions and is maintained by Steve Lewis, NMFS 

Alaska Regional Office. 

Request for Proposals

1. The request for proposals (RFP) will call for 2- to 3-year integrated proposals, as well as 

1-year independent proposals (as before). Funding some 1-year proposals will maintain 

some flexibility in priority-setting (annual emphasis areas) and creativity from PIs. The 

integrated proposals can last no longer than 3 years.

2. The proportion of funds allocated to each proposal type will be two-thirds of the total for 

integrated proposals and one-third for independent proposals. For planning purposes, the 

amounts allocated to each category will assume $350,000 annually available for EFH 

projects, which is about the average amount spent the last few years. This new approach 

will have a staggered start for funding of integrated proposals: for FY 2018, one-third of 

funds will be allocated to integrated proposals, which will increase to two-thirds of funds 

for integrated proposals for FY 2019. In FY 2020, two-thirds of funds will support 

integrated proposals and one-third for independent proposals, anticipating that the third 

year of each integrated proposals will require only a small amount of funding (i.e., onethird of funding always will go toward individual proposals). Staggering the start will 

allow integrated proposal(s) to start each year, as seen in the following figure. 

Year

2018 2019 2020 2021 2022

Project A

Project B

Project C

5
3. Retain tool of annual emphasis areas to maintain flexibility in research direction.

4. Each integrated proposal: 

a. Must provide deliverables for each year. These annual deliverables must be 

clearly stated in the proposal. 

b. Must demonstrate satisfactory progress each year to continue to receive funding. 

Progress will be described in annual status reports (as before). The HEPR Team 

will review these annual status reports to determine progress and to determine 

whether or not funding should continue. 

c. At the PIs choosing, integrated proposals may (but are not required to) describe 

what research would be completed if only one year of funding is available. For 

example, three integrated proposals may be submitted but funding sufficient only 

for one of the three. In this case, the other two could qualify for one-year funding. 

To also compete for one-year funding, briefly describe (one-page limit) the oneyear project.

Plan Writing and Review

The writing team consisted of Mike Sigler (HEPR), Chris Rooper (RACE), Tom Helser (REFM, 

HEPR team), Bob Stone (ABL), Matthew Eagleton (AKRO, EFH coordinator), John Olson 

(AKRO, fishing effects), Jodi Pirtle (AKRO), and Samantha Simpson (AKRO). Each division of 

the AFSC which has conducted EFH research was represented on the writing team as well as the 

Alaska Regional Office. Draft plans were reviewed by the HEPR Team in February 2017. The 

new approach for writing EFH proposals was presented to interested AFSC staff in February 

2017. Draft plans were communicated at the December 2016 Council meetings and the 

December 2016 AFSC Board of Directors meeting. 

The review was based on the group’s EFH research and stock assessment experience, the 2012 

EFH research plan and two recent documents: 1) the AFSC science plan, which identified a 

habitat-related research priority3

 (AFSC 2016); 2) the North Pacific Fishery Management 

Council and NOAA Fisheries Alaska Region 5-year EFH review (NPFMC 2016). During 2006-

2016, NOAA Fisheries spent about $5 M on 91 EFH projects in Alaska resulting in 74 scientific 

publications (NPFMC 2016). 

 

3 Forecast direct and indirect effects of climate change on fish, crab, and marine mammal species, their habitats, and the 

associated communities which rely on these resources.

6
Citations

AFSC. 2006. Essential Fish Habitat Research Implementation Plan for Alaska for FY 2007 – 

2011. U.S. Dep. Commer., NOAA, Alaska Fisheries Science Center. 13 p. 

http://www.afsc.noaa.gov/HEPR/docs/UpdatedEFHResearchImplementationPlan.pdf

AFSC. 2016. Alaska Fisheries Science Center, Strategic Science Plan. U.S. Dep. Commer., 

NOAA, Alaska Fisheries Science Center. 32 p. 

https://www.afsc.noaa.gov/GeneralInfo/FY17StrategicSciencePlan.pdf

Batten, S.D., and D.L. Mackas. 2009. Shortened duration of the annual Neocalanus plumchrus

biomass peak in the Northeast Pacific. Mar. Ecol. Prog. Ser. 393:189-198.

Black, B.A., M.E. Matta, T.E. Helser, and T.K. Wilderbuer. 2013. Otolith biochronologies as 

multidecadal indicators of body size anomalies in yellowfin sole (Limanda aspera). Fish. 

Oceanogr. 22:523-532. 

Boldt, J.L., and C.N. Rooper. 2009. Abundance, condition, and diet of juvenile Pacific ocean 

perch (Sebastes alutus) in the Aleutian Islands. Fish. Bull., U.S. 107:278-285. 

Conrath, C.L., and B.L. Knoth. 2013. Reproductive biology of Pacific ocean perch in the Gulf of 

Alaska. Mar. Coastal Fish. 5:21-27. 

Elliot, J.M., and L. Persson. 1978. The estimation of daily rates of food consumption for fish. J. 

Anim. Ecol, 47:997-991. 

Farley, E.V., R.A. Heintz, A.G. Andrews, and T.P. Hurst. 2016. Size, diet, and condition of 

age-0 Pacific cod (Gadus macrocephalus) during warm and cool climate states in the 

eastern Bering Sea. Deep-sea Res. II 134:247-254. 

Fisheries Leadership and Sustainability Forum. 2016. Regional EFH Profile: North Pacific. 

National Essential Fish Habitat Summit, 2016. 4 p. 

https://www.fisheriesforum.org/HigherLogic/System/DownloadDocumentFile.ashx?Doc

umentFileKey=31200d36-c404-33d5-e057-ef468d6bcc6e

Harvey, C.J., 2005. Effects of El Niño events on energy demand and egg production of rockfish 

(Scorpaenidae: Sebastes): a Bioenergetics approach. Fish. Bull., U.S. 103:71-83. 

7
Heintz, R.A., E.C. Siddon, E.V. Farley, and J.M. Napp. 2013. Correlation between recruitment 

and fall condition of age-0 pollock (Theragra chalcogramma) from the eastern Bering 

Sea under varying climate conditions. Deep-sea Res. II 94:150-156.

Hewett, S.W., and B.L. Johnson. 1992. Fish Bioenergetics Model 2: An upgrade of a generalized 

bioenergetics model of fish growth for microcomputers. University of Wisconsin Sea 

Grant Institute Technical Report. WIS-SG-91-250, 79 p. 

Laurel, B.J., M. Spencer, P. Iseri, and L.A. Copeman. 2016. Temperature-dependent growth and 

behavior of juvenile Arctic cod (Boreogadus saida) and co-occurring North Pacific 

gadids. Polar Biol. 38:1127. DOI 10.1007/s00300-015-1761-5. 

Matta, M.E., B.A. Black, and T.K. Wilderbuer. 2010. Climate-driven synchrony in otolith 

growth-increment chronologies for three Bering Sea flatfish species. Mar. Ecol. Progr. 

Ser. 413:137-145. 

Matta, M.E., and T.E. Helser. 2016. Otolith biochronologies reveal latitudinal differences in 

growth of Bering Sea yellowfin sole Limanda aspera. Polar Biol. 39:2427-2439. 

Moss, J.H., M.F. Zaleski, and R.A. Heintz. 2016. Distribution, diet, and energetic condition of 

age-0 walleye pollock (Gadus chalcogrammus) and Pacific cod (Gadus macrocephalus) 

inhabiting the Gulf of Alaska. Deep-sea Res. II 132:146-153. 

North Pacific Fishery Management Council (NPFMC). 2016. 2016 Review of Essential Fish 

Habitat (EFH) in the North Pacific Fishery Management Council’s Fishery Management 

Plans. Summary Report. North Pacific Fishery Management Council, 605 W 4th Ave, 

Anchorage, Alaska 99501. 

Phillips, S.J., R.P. Anderson, and R.E. Schapire. 2006. Maximum entropy modeling of species 

geographic distributions. Ecol. Model. 190:231-259. 

Rooper, C.N., and L.J. Haldorson. 2000. Consumption of Pacific herring (Clupea pallasi) eggs 

by greenling (Hexagrammidae) in Prince William Sound, Alaska. Fish. Bull., U.S. 

98:655-659. 

Rooper, C.N., J.L. Boldt, and M. Zimmermann. 2007. An assessment of juvenile Pacific ocean 

perch (Sebastes alutus) habitat use in a deepwater nursery. Estuar. Coastal Shelf Sci. 

75:371-380. 

8
Rooper, C.N., J.L. Boldt, S. Batten, and C. Gburski. 2012. Growth and production of Pacific 

ocean perch (Sebastes alutus) in nursery habitats of the Gulf of Alaska. Fish. Oceanogr. 

21:415-429. 

Rooper, C.N., M.F. Sigler, P. Goddard, P. Malecha, R. Towler, K. Williams, R. Wilborn, and 

M. Zimmermann. 2016. Validation and improvement of species distribution models for 

structure-forming invertebrates in the eastern Bering Sea with an independent survey. 

Mar. Ecol. Prog. Ser. 551:117-130. 

Shotwell, S.K., D.H. Hanselman, S. Zador, and K. Aydin. 2016. Stock-specific Profiles and 

Ecosystem Considerations (SPEC) for Alaska groundfish fishery management plans. 

Report to Joint Groundfish Plan Team, September 2016. 15 p. Available Alaska Fisheries 

Science Center, Auke Bay Laboratories, 17109 Point Lena Loop Road, Juneau, Alaska 

99801. 

Sigler, M.F., M.F. Cameron, M.P. Eagleton, C.H. Faunce, J. Heifetz, T.E. Helser, B.J. Laurel, 

M.R. Lindeberg, R.A. McConnaughey, C.H. Ryer, and T.K. Wilderbuer. 2012. Alaska 

Essential Fish Habitat Research Plan: A research plan for the National Marine Fisheries 

Service's Alaska Fisheries Science Center and Alaska Regional Office. AFSC Processed 

Rep. 2012-06, 21 p. Alaska Fish. Sci. Cent., NOAA, Natl. Mar. Fish. Serv., 17109 Pt. 

Lena Loop Road, Juneau, AK 99801. 

http://www.afsc.noaa.gov/HEPR/docs/Sigler_et_al_2012_Alaska_Essential_Fish_Habitat

_Research_Plan.pdf

Van der Sleen, P, M.P. Dzaugis, C. Gentry, W.P. Hall, V. Hamilton, T.E. Helser, M.E. Matta, 

C.A. Underwood, R. Zurcher, and B.A. Black. 2016. Long-term Bering Sea 

environmental variability revealed by a centennial-length biochronology of Pacific ocean 

perch (Sebastes alutus). Climate Res. 71:33-45. 10.3354/cr01425. 

Wood, S.N., 2006. Generalized Additive Models: An Introduction with R., Chapman and Hall: 

CRC Press, Boca Raton, FL.). 

Zimmermann, M., M.M. Prescott, and C.N. Rooper. 2013. Smooth sheet bathymetry of the 

Aleutian Islands. U.S. Dep. Commer. NOAA Tech. Memo. NMFS-AFSC-250, 43 p.

9
Table 1. -- Growth, survival, or reproductive rates are available for several species. EFH Level 3 

maps can be created from this information. This table lists some examples. 

Species name Source

Arctic cod, saffron cod, Pacific cod, walleye 

pollock (growth)

Laurel et al. 2016

Yellowfin sole, northern rock sole, Alaska 

plaice (growth)

Matta et al. 2010, Black et al. 2013, Matta and 

Helser 2016

Pacific ocean perch (growth, bioenergetics) Rooper et al. 2012, Van der Sleen et al. 2016

Rockfish (maturity) Conrath et al. 2013

Many species (bioenergetics) Heintz et al. 2013, Farley et al. 2016, Moss 

et al. 2016 

10
Appendix 1. Definitions of EFH Levels

 

See 50 CFR § 600.815 (2002), Contents of Fishery Management Plans, 67 FR 2376 

https://alaskafisheries.noaa.gov/sites/default/files/finalrules/efhfr.pdf

Level Definition Information necessary to describe and identify EFH

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.

2 Habitatrelated 

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 efficiency of sampling methods is often affected by habitat 

characteristics, strict quality assurance criteria should be used to ensure 

that density estimates are comparable among methods and habitats. 

Density data should reflect 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 fish densities in this manner, 

temporal changes in habitat availability and utilization should be 

considered.

3 Growth, 

reproduction, 

or survival 

rates within 

habitats are 

available

At this level, data are available on habitat-related growth, reproduction, 

and/or survival by life stage. The habitats contributing the most to 

productivity should be those that support the highest growth, 

reproduction, and survival of the species (or life stage).

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 fish production 

consistent with a sustainable fishery and the managed species’ 

contribution to a healthy ecosystem. 

11
Appendix 2. Core EFH Research Priorities

EFH Research Priorities

A set of five core EFH research goals have guided EFH research in Alaska since 2005 (AFSC 

2006, Sigler et al. 2012). These core goals have been consistent since 2005 with only minor 

modifications. We will continue to use these five core EFH goals as broad guidelines for EFH 

research in this current update of the EFH research plan. These priorities support objectives of 

the AFSC Strategic Science Plan (AFSC 2016), including Theme 2 (Understand and forecast 

effects of climate change on marine ecosystems) and foci 2.5 (Forecast direct and indirect effects 

of climate change on fish, crab, and marine mammal species, their habitats, and the associated 

communities which rely on these resources). The five EFH research priorities are as follows:

Characterize Habitat Utilization and Productivity; Increase the Level of 

Information Available to Describe and Identify EFH; Apply Information 

from EFH Studies at Regional Scales – This priority focuses on understanding the 

relationship between habitat type, patterns of use by species, and differences between habitats

in productivity of managed species. Our approach is to support integrated research projects that 

combine measurements of habitat characteristics, habitat utilization, and habitat productivity in 

one study, and also combine laboratory experiments, controlled field manipulations, and field 

observations. Our approach also includes conducting studies that support refining the 

description and identification of EFH in FMPs. 

Assess Sensitivity, Impact, and Recovery of Disturbed Benthic Habitat – 

Habitat-forming biota such as corals and sponges often are sensitive to human activity and may 

take many years to recover from disturbance. Some managed fish and shellfish species use this 

habitat for protection and camouflage. Estimates of habitat impacts, sensitivity, and recovery, 

in both areal extent and temporal rates, are necessary to understand the effects of human 

activities. Recovery rates are defined as the rate of change of impacted habitat back to 

undisturbed habitat following disturbance. Sensitivity is defined as the susceptibility of habitat 

to degradation. Habitat may be affected by fishing and studies of sensitivity to and recovery 

from these effects are a priority. In addition, coastal areas often are affected by non-fishing 

impacts. Recovery and monitoring studies of impacted coastal areas, such as marine ports, are 

needed to determine if these sites have returned to their pre-utilization state following facility 

closure or development. Recovery rate studies remain as a high priority for habitat research.

Validate and Improve Habitat Impacts Model – A habitat impacts model has been 

used to estimate effects of fishing in Alaska, but the parameter estimates were not well 

resolved and had a high degree of uncertainty. Model validation remains a priority because 

the habitat impacts model played a key role in evaluating the effects of fishing and deciding 

12
on measures to conserve and protect habitat areas from fishing gear impacts (i.e., closure 

areas).

 

Map the Seafloor – Information characterizing fish habitat and utilization in Alaska is 

limited to coarse-scale depth and habitat information (e.g., nautical charts) and utilization 

information from AFSC surveys for the adult stage of commercially important species. Missing 

are fine-scale depth and habitat information, as well as juvenile stage information, especially 

nearshore. Seafloor mapping is costly and time-consuming. The research approach is to support 

low-cost mapping efforts with existing sampling platforms (e.g., trawl survey vessels, NOAA 

vessels) to reduce costs, as well as reanalysis of existing data.

Assess Coastal and Marine Habitats Facing Development – Characterization of 

coastal habitats susceptible to disturbance from non-fishing activities is a priority. These nonfishing activities include oil and gas development, logging, mining, urbanization, and 

contaminants. The research approach includes coastal habitat mapping (ShoreZone), as well as 

field surveys of a representative subset of the mapped habitats to measure fish and shellfish 

utilization. Priority coastal habitats for study are those utilized by managed fish and shellfish 

species and facing development pressure.

13
Appendix 3. Example of Level 3 Mapping

Growth Potential Estimated for Juvenile Pacific Ocean Perch in the 

Gulf of Alaska

Currently species distribution models exist for EFH Level 1 and Level 2 information (Fig. 1). To 

date, the Level 1 models have been presence-only maximum entropy or MaxEnt models (Phillips 

et al. 2006) and the Level 2 models have been based on generalized additive models (GAMs) 

predicting relative abundance (Wood 2006). These modeling approaches use different data sets, 

but both can be regional in scale and extended as Level 3 information is available and in possibly 

Level 4 information. 

Figure 1. -- Examples of maps of Levels 1, 2, 3, and 4 information. 

The mapping of growth potential for juvenile Pacific ocean perch (POP; Sebastes alutus) is an 

example of Level 3 information. Previous EFH research on juvenile POP in Alaska showed that 

this species is strongly associated with rocky habitats at depths from 85 to 245 m along mostly 

the continental shelf (Fig. 2). Deep-sea corals and sponges are often found in these nursery 

habitats. Densities of juvenile POP were predicted to be highest in the eastern and central Gulf of 

Alaska. 

Level 4: Productivity

Level 3: Growth/reproduction

Level 2: Abundance

Level 1: Presence

14
Figure 2. -- Predicted 4th root transformed catch-per-unit-of-effort of juvenile Pacific ocean 

perch (< 250 mm) in the Gulf of Alaska. The predictions were based on two-stage 

generalized additive models fit to bottom trawl survey catches from 1991 to 2014. 

Based on the predicted distribution of juvenile POP abundance, EFH for juvenile POP habitat 

was widely distributed around the Gulf of Alaska near the continental shelf break (Fig. 3). Many 

of the shallow banks on the shelf (such as Portlock Bank, Albatross Bank, and Sanak Bank) as 

well as most of the shelf in the eastern Gulf of Alaska were predicted to be important habitats for 

juvenile POP. 

15
Figure 3. -- Essential fish habitat map for juvenile Pacific ocean perch (< 250 mm) in the Gulf of 

Alaska based on predictions from two-stage generalized additive models fit to 

bottom trawl survey catches from 1991 to 2014. Percentages indicate quantiles of 

predicted abundance (i.e., 25% indicates the top 25% of predicted juvenile POP 

abundance occurs within this color shade). 

In 2012 a Wisconsin bioenergetics model (Hewett and Johnson 1992, Harvey 2005) was 

parameterized for juvenile POP (Rooper et al. 2012). The model used diet, energetics and growth 

data from field data and laboratory analyses collected during a series of EFH-funded studies in 

the eastern Aleutian Islands from 2003 to 2008 (Rooper et al. 2007, Boldt and Rooper 2009). 

This bioenergetics model predicted growth potential for juvenile POP given daily consumption 

(predicted from the field and laboratory data using a consumption model; Elliot and Persson 

1978, Rooper and Haldorson 2000). The bioenergetics model was driven by monthly mean 

temperatures derived from relationships between satellite-derived sea-surface temperature (SST) 

and bottom trawl survey data. The model also incorporated the duration of the growing season 

inferred from continuous plankton recorder data from the central Gulf of Alaska (Batten and 

Mackas 2009). The model was run for 1982-2010 and growth predicted by the bioenergetics 

model was found to accurately predict growth measured in the field in the 2003-2008 Aleutian 

Islands EFH projects. Full details of the bioenergetics model and growth predictions are found in 

Rooper et al. (2012). 

One of the outputs of the juvenile POP bioenergetics model was a spatially explicit calculation of 

growth potential for the Gulf of Alaska. This model in combination with the maps produced in 

16
2015 (Fig. 4) can be used to estimate the growth potential in juvenile POP essential fish habitat 

(i.e., EFH Level 3). Averaged across all years (1987-2010), growth potential for juvenile POP in 

the Gulf of Alaska was highest in the eastern Gulf of Alaska (where water temperatures are 

generally higher in the summer) and lowest westward of Kodiak. This spatial pattern was 

consistent across most individual years (Fig. 5), but the temporal pattern across years was highly 

variable. For example, growth potential was almost uniformly higher in the 2002, 2003, and 

2008 across the entire Gulf of Alaska, while growth potential was uniformly low in 2001 and 

2009. The interannual variability is a combination of the interplay between the duration of the 

spring and summer zooplankton bloom and the water temperature during that bloom. For 

example, in 2005, there was an extremely short duration for the zooplankton bloom, yet water 

temperatures in the spring were the highest in the time series (Rooper et al. 2012). This resulted 

in about average growth potential for the year. In contrast, 2002 and 2003 had two of the longest 

durations of the zooplankton bloom and about average water temperatures, which resulted in 2 

years of very high growth potential across the Gulf of Alaska. 

The results presented here is a compilation of a variety of studies, with data and modeling from 

different areas and regions. As such, there are a number of sources of potential error. For 

example, the energetics values for POP were taken from only the far western Gulf of Alaska and 

were applied across the entire region. Predictions of EFH are based on data from the entire 

region, but there is some unexplained variability associated with the models of distribution. It is 

important that research on EFH provides adequate estimates of the error associated with 

predictions and seeks to address data gaps that may limit the regional application of study results. 

These analyses show an example of integrating field and laboratory studies to determine vital 

rates (in this case potential for growth) and distribution models and maps to elevate EFH to 

Level 3 information for a species. Mapping growth potential to EFH distribution shows habitats 

and regions that potentially have more value in terms of productivity and are thus potentially 

more essential as fish habitat. This type of exercise could be done for other groundfish species in 

Alaska where there is some information from the laboratory or field to link through a model, 

vital rates (growth, survival, fecundity, etc.) to variables that can be measured on a broad scale. 

The new generation of regional ocean models (ROMS) for the North Pacific can potentially 

provide large-scale variables to explore and model Level 3 EFH processes on a Large Marine 

Ecosystem scale. Ideally, these Level 3 EFH descriptions would provide estimates of associated 

error that can be used to gauge confidence in the results.

17
Figure 4. -- Map of predicted growth potential for juvenile Pacific ocean perch (< 250 mm) in 

the Gulf of Alaska within the boundaries of the defined EFH (Fig. 2). Growth 

potential (g/g body weight/day) was estimated using a bioenergetics model (Rooper 

et al. 2012) and averaged across 1987-2010. 

18
Figure 5. -- Map of summer predicted growth potential for juvenile Pacific ocean perch 

(< 250 mm) in the Gulf of Alaska within the boundaries of the defined EFH (Fig. 2). 

Growth potential (g/g body weight/day) was estimated using a bioenergetics model 

(Rooper et al. 2012) for 1987-2010. 

19
Appendix 4. Template for Proposals

Write complete proposals that provide sufficient information for the review panel to judge your 

proposal. 

Study duration (years) (circle one): 1 2 3 

If multi-year, you may (but are not required to) describe what research would be completed if 

only one year of funding is available. To also compete for one-year funding, briefly describe 

(one-page limit) the one-year project. Indicate (yes/no) whether you also are competing for oneyear funding. 

Title

Principal Investigators: 

Research Priority: 

Justification: 

Project Description: 

Required Resources: Provide details of, for example, travel, rent (charters), equipment, and 

supplies (fuel) 

Expected Products: List the milestones to be achieved each year, the products to be delivered 

upon completion, and when the milestones and products will be completed. Product descriptions 

should include the method of dissemination (e.g., refereed publication). 

References: 

Budget

Title

Object 

Class

Description Amount ($) 

1100 Direct Labor: Funds will not be approved for labor or 

benefits.

 

1150 Overtime and hazard pay 

1200 Benefits: Funds will not be approved for labor or 

benefits.

 

2100 Travel 

20
2200 Transportation 

2300 Rents (vessel charter) 

2400 Printing 

2500 Contracts: List name or type of contractor 

2600 Supplies and Materials: Itemize large items, group small 

stuff

 

3100 Equipment: Itemize large items, group small stuff 

4100 Grants 

 Total 

21
Appendix 5. Form for Annual Report of Project Status

Essential Fish Habitat Project Status Report

 

Reporting date: 

 

Project number: 

 

Title: 

 

PIs: 

 

Funding year: 

 

Funding amount: 

 

Status: Complete Incomplete, on schedule Incomplete, behind schedule 

 

Planned completion date if incomplete: 

 

Reporting: Have the project results been reported? If yes, state where the results were reported 

and attach an electronic copy of the report.

 

Results: What is the most important result of the study? 

22