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 

1st National Habitat Assessment Workshop

Moving Towards a National Habitat Science Program

Hosted by the Southeast Fisheries Science Center, Southeast Regional Office, and 

Office of Science and Technology

St. Petersburg, FL

May 17–20, 2010

Edited by Kristan Blackhart

U.S. Department of Commerce

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

NOAA Technical Memorandum NMFS-F/SPO-112

November 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 

1st National Habitat Assessment Workshop

Moving Towards a National Habitat Science Program

Hosted by the Southeast Fisheries Science Center, Southeast Regional Office, and 

Office of Science and Technology

St. Petersburg, FL

May 17–20, 2010

Edited by Kristan Blackhart

November 2010 

NOAA Technical Memorandum NMFS-F/SPO-112

U.S. Department National Oceanic and National Marine

of Commerce Atmospheric Administration Fisheries Service

Gary Locke Jane Lubchenco, Ph.D. Eric C. Schwaab

Secretary of Commerce Administrator of NOAA Assistant Administrator for Fisheries
Copies of this document may be obtained by contacting:

Office of Science and Technology, F/ST

National Marine Fisheries Service, NOAA

1315 East West Highway

Silver Spring, MD 20910

An online version is available at http://www.st.nmfs.noaa.gov/

The mention of trade names or commercial firms does not imply endorsement by the National Marine Fisheries Service, 

NOAA.

This publication may be cited as:

Blackhart, 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.
iii

Executive Summary

Introduction Stephen K. Brown and William L. Michaels

11th National Stock Assessment Workshop

Theme Session Summaries: Improving Characterization of Scientific Uncertainty in Assessments to Improve 

Determination of Acceptable Biological Catch (ABC) William L. Michaels

Breakout Session 1 Summary: Protocols for ABC Recommendations in Data-poor Situations Jim Berkson, Todd 

Gedamke, and Staci Hudy

Breakout Session 2 Summary: Methods for Quantifying Uncertainty in Assessments, Including Proxies for 

Unmeasured Variance Components Chris Legault, Dana H. Hanselman, and Amy M. Schueller

Breakout Session 3 Summary: Evaluation of Performance for ABC Control Rules; Risk Analysis; Management 

Strategy Evaluation Richard D. Methot, Jr. and Jonathan J. Deroba

Breakout Session 4 Summary: Addressing Long-term Climate/Ecosystem Factors Affecting Stock Assessment 

and Habitat Anne B. Hollowed and Melissa A. Haltuch

Joint Session of the National Stock and Habitat Assessment Workshops

Joint Session Summary Stephen K. Brown and Kristan Blackhart

Breakout Session 1a: Using Habitat Information in Survey Design and Analysis, Groundfish/Coastal Pelagic/

HMS & Pelagic Groups Vincent G. Guida, Paul Spencer, and Mark Sramek

Breakout Session 1b: Using Habitat Information in Survey Design and Analysis, Diadromous/Estuarine 

Dependent/Reef & Untrawlable Groups John F. Walter, Stephen Ralston, and Terill Hollweg

Breakout Session 2a: Including Habitat-specific Life History Rates in Population Models, Groundfish/Reef & 

Untrawlable/Diadromous Groups Richard S. McBride, Eric Bjorkstedt, and David Dale

Breakout Session 2b: Including Habitat-specific Life History Rates in Population Models, Coastal Pelagic/

HMS & Pelagic/Estuarine Dependent Groups Jon Brodziak, Lawrence Rozas, and Joe Nohner

Breakout Session 3: Using Time Series of Habitat Information in Population Models (All Groups) Patricia 

Livingston, Kirsten Larsen, Rick A. Hart, Correigh Greene, David Rydene, and Lora Clarke

1st National Habitat Assessment Workshop

Session 1 Summary: Current Processes for Providing Habitat Science for Management Peter Colosi and Kristan 

Blackhart

Session 1 Breakout Group A: Evaluating Current Science Center, Regional Office, and Restoration Center 

Interactions Karen Abrams and Allison Candelmo

Session 1 Breakout Group B: Evaluating Current Science Center, Regional Office, and Restoration Center 

Interactions Michael Parke and Ronald L. Hill

Session 1 Breakout Group C: Evaluating Current Science Center, Regional Office, and Restoration Center 

Interactions Mike Sigler and Ben Laws

Session 1 Breakout Group D: Evaluating Current Science Center, Regional Office, and Restoration Center 

Interactions Susan-Marie Stedman and Terill Hollweg

Session 2 Summary: Proposing Strategies for the Development of Habitat Science Capacity and the 

Incorporation of Habitat Science into Management Thomas Noji and Kirsten Larsen

Contents

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Session 2 Breakout Group A: Evaluating Strategies for the Development of Habitat Science Capacity and the 

Incorporation of Habitat Science into Management Karen Abrams and Allison Candelmo

Session 2 Breakout Group B: Evaluating Strategies for the Development of Habitat Science Capacity and the 

Incorporation of Habitat Science into Management John P. Manderson and Terra Lederhouse

Session 2 Breakout Group C: Evaluating Strategies for the Development of Habitat Science Capacity and the 

Incorporation of Habitat Science into Management Mike Sigler and Ben Laws

Session 2 Breakout Group D: Evaluating Strategies for the Development of Habitat Science Capacity and the 

Incorporation of Habitat Science into Management Susan-Marie Stedman and Terill Hollweg

Session 3 Summary: Implementing Proposed Solutions Regionally Kristan Blackhart

Session 3 Breakout Summary: Northeast Region Thomas Noji, Peter Colosi, and Ben Laws

Session 3 Breakout Summary: Southeast Region Tom Minello, Pace Wilber, and Kirsten Larsen

Session 3 Breakout Summary: Alaska Region Mike Sigler, Jon Kurland, and Terra Lederhouse

Session 3 Breakout Summary: Northwest Region Michael Tehan, W. Waldo Wakefield, and Kristan Blackhart

Session 3 Breakout Summary: Southwest and Pacific Islands Regions Mary M. Yoklavich, Michael Parke, and Joe 

Nohner

List of Common Acronyms

Appendix 1: Steering Committees

Appendix 2: Meeting Agendas

National Stock Assessment Workshop

Joint Session of the National Stock and Habitat Assessment Workshops

National Habitat Assessment Workshops

Appendix 3: List of Participants

Appendix 4: Abstracts 

Keynote and Invited Speakers

Perspectives on current issues in fish stock assessments Richard D. Methot, Jr.

Identifying the role of habitat science in NMFS Ned Cyr

Developing and implementing the Habitat Assessment Improvement Plan Mary M. Yoklavich

Building and funding a National Habitat Science Program in NMFS Stephen K. Brown

Stock assessment 101: Getting to ABC Richard D. Methot, Jr.

Informing and improving stock assessments with marine habitat information Churchill B. Grimes, Stephen Ralston, 

John C. Field, Brian Wells, and Mary M. Yoklavich

Are we running out of fish? And where will they live? Steven A. Murawski

Confronting the ghosts of Christmases past: A new context for habitat assessments John Boreman

National Stock Assessment Workshop

Theme A: Understanding the Trade Off Between Simple and Complex Models

Simple spreadsheet: Population models and policy simulations Linda Lombardi, C. Walters, M. Allen, and W.E. Pine

Determining yields for data-poor stocks using a DCAC-based stock reduction analysis of catch history E.J. 

Dick and Alec MacCall
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Theme B: Quantification of Uncertainty from Model Structure and Retrospective Patterns

Addressing cohort-strength related ageing error in fisheries stock assessment Owen Hamel and Ian J. Stewart

Modeling recruitment along the continuum from data-poor to data-rich Ian G. Taylor and Richard D. Methot, Jr.

Management strategy evaluation of a retrospective fix Chris Legault

Reconciling uncertain and conflicting trends in petrale sole abundance Melissa A. Haltuch, James D. Hastie, Allan 

Hicks, and Curt E. Whitmire

Theme C: Addressing Uncertainty Due to Key Parameters, Especially Natural Mortality

Estimating stock-recruitment steepness from life history information: A case study of North Pacific bluefin 

tuna, Thunnus orientalis Jon Brodziak, Marc Mangel, and Gerard DiNardo

Incorporating egg predation by haddock into a population model for Atlantic herring David E. Richardson, 

Jonathan A. Hare, and Harvey J. Walsh

An independent estimate of natural mortality for Atka mackerel using tagging data Susanne McDermott, James 

Ianelli, and Sandra A. Lowe

Do marine protected areas improve the ability to estimate biological parameters using an integrated stock 

assessment model? Thomas M. Garrison and André E. Punt

Theme D: Incorporating Statistical Uncertainty from Sampling Error

Specification of observation error variances Grant G. Thompson

A hierarchical model to estimate relative catchability at size Tim Miller

Mixture distribution models of Pacific rockfish schooling behavior James T. Thorson and Ian J. Stewart

Acoustical-optical surveys of coastal pelagic species, with emphasis on Pacific sardine, using improved 

allocation of effort, multifrequency acoustic methods, and a towed stereo camera system Juan P. Zwolinski, 

George R. Cutter, Jr., and David A. Demer

Trawl survey designs for reducing uncertainty in biomass estimates for patchily-distributed species Paul Spencer, 

Dana H. Hanselman, and Denise McKelvey

Theme E: Developing a Comprehensive Approach for Characterizing Uncertainty

Calculating the uncertainty in fishery assessment forecasts Richard D. Methot, Jr.

Some aspects of scientific uncertainty in west coast stock assessments Stephen Ralston, André E. Punt, and other 

members of the Pacific Fishery Management Council Scientific and Statistical Committee

Dominant sources of scientific uncertainty in recent Gulf of Mexico stock assessments—implications for ACLs 

Shannon L. Cass-Calay and Joseph Powers

Estimating scientific uncertainty in ABC control rules for Bering Sea Aleutian Islands (BSAI) crab stocks Jack 

Turnock, Robert Foy, Anne B. Hollowed, André E. Punt, Lou Rugolo, and Diana L. Stram

Incorporating uncertainty into ABC control rules for Bering Sea Aleutian Islands (BSAI) crab stocks Diana L. 

Stram, André E. Punt, Jack Turnock, Lou Rugolo, Robert Foy, and Anne B. Hollowed

Utilizing environmental information to reduce recruitment uncertainty in the Alaska sablefish stock 

assessment S. Kalei Shotwell, Dana H. Hanselman, and David G. Foley

The relationship between MSY fishing rates (FMSY) and productivity indices Jason M. Cope, Wesley S. Patrick, and 

Richard D. Methot, Jr.

Quantifying the trade off between precaution and yield in fishery reference points Deborah R. Hart

A review of harvest policies: Understanding the relative performance of control rules Jonathan J. Deroba and 

James R. Bence

Setting allowable biological catch for stocks with reliable catch data only Jim Berkson, Luiz Barbieri, Steve Cadrin, 

Shannon L. Cass-Calay, Andy Cooper, Paul Crone, Martin Dorn, Claudia Friess, Don Kobayashi, Thomas Miller, Wesley S. 

Patrick, Sarah Pautzke, Stephen Ralston, and Michael Trianni

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Management uncertainty in the context of annual catch limits Mark Millikin and Galen Tromble

Joint Session of the National Stock and Habitat Assessment Workshops

Theme F: Incorporating Habitat Information into Stock Assessments

A framework for incorporating climate impacts on pelagic ocean habitats into stock assessments Anne B. 

Hollowed, Angie Greig, Libby Logerwell, and Chris Wilson

Incorporating the effects of an environmental regime shift in an assessment of Atlantic menhaden population 

dynamics John A. Quinlan, Amy M. Schueller, and Douglas S. Vaughan

Insights for stock assessment and empirical prerecruit indices from an environmentally forced individual-based 

model of early life history stages for west coast rockfishes Eric Bjorkstedt and Stephen Ralston

A habitat-specific approach for incorporating environmental variation into stock forecasting models Correigh 

Greene, Jason Hall, Eric Beamer, and George Pess

Integrating habitat change and population dynamics: Using the Shiraz framework to evaluate salmon recovery 

efforts Jeff Jorgensen

Can habitat-based densities predict stock status in a heavily fished Caribbean gastropod? Ronald L. Hill, Kevin 

McCarthy, and Richard S. Appeldoorn

Can we use habitat information to derive prior distributions for virgin biomass of deepwater groupers and 

tilefish? John F. Walter, Melissa Cook, Brian Linton, Linda Lombardi, and John A. Quinlan

Using statistical modeling and Ocean Observing Systems to identify fish habitat at broad scales: Potential 

applications for spatial planning, estimation of natural mortality, and reducing fisheries bycatch John P. 

Manderson, Josh Kohut, Laura Palamara, Steven Grey, and Matt Oliver

Theme G: Improving Calibration and Precision of Resource Surveys with Habitat Information

Incorporating satellite-derived environmental data with Gulf of Mexico pelagic longline observer data for the 

evaluation of bluefin tuna relative abundance and distribution patterns Craig Brown, Karina Ramìrez López, and 

John A. Quinlan

Expansion of Atlantic croaker (Micropogonias undulatus) larval habitat on the Northeast U.S. continental shelf 

Harvey J. Walsh, David E. Richardson, Jonathan A. Hare, and Katrin E. Marancik

Habitat-specific survey methods to improve assessments of rockfishes off California and Alaska Mary M. 

Yoklavich and Victoria O’Connell

Integrating benthic community structure data into a stratified random sampling design to improve reef fish 

abundance estimates in the Northwestern Hawaiian Islands Jason Helyer and Ivor D. Williams

Collaborative Optically-assisted Acoustical Survey Technique (COAST) for surveying the distributions, 

abundances, and lengths of demersal fishes, by species David A. Demer, John Butler, George R. Cutter, Jr., Kevin 

Stierhoff, Kyle Byers, David Murfin, Josiah Renfree, Scott Mau, and Thomas S. Sessions

Using mesohabitat information to improve abundance estimates for west coast groundfish: A test case at 

Heceta Bank, OR W. Waldo Wakefield, Julia E.R. Clemons, Ian J. Stewart, and Curt E. Whitmire

Modeling habitat relationships for rockfish to improve fishery-independent survey biomass estimates Chris 

Rooper, Michael Martin, and Paul Spencer

Advances in conducting spatially-explicit, fishery-independent, ecosystem-based reef fish and habitat 

assessments James A. Bohnsack and Benjamin Ruttenberg

Poster Session

Essential fish habitat three year strategic implementation plan: Priority habitats and data needs for improving 

EFH protection Karen Abrams, Terra Lederhouse, and Kara Meckley

Prioritizing data collection for assessments based on a cost-benefit analysis Kate I. Andrews and Linda Lombardi

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A spatially-explicit assessment of the adverse effects of fishing on benthic habitats in the Northeast United 

States: The Swept Area Seabed Impact model Michelle Bachman, Chad Demarest, Steve Eayrs, Jonathan Grabowski, 

Bradley Harris, Vincent Malkoski, David Packer, and David K. Stevenson

The value of habitat information at different life stages in refining white shrimp stock assessments in the Gulf of 

Mexico Ron Baker, Tom Minello, and Phil Levin

The Species Information System: Tracking the success of the Stock Assessment Improvement Plan Kristan 

Blackhart and Richard D. Methot, Jr.

The Advanced Sampling Technology Working Group’s recent efforts in improving NMFS’ stock and habitat 

assessment science Eric Breuer, Dezhang Chu, George R. Cutter, Jr., David A. Demer, Joseph Godlewski, Scott Ferguson, 

Brad Hanson, Michael Jech, Frank Parrish, Joseph E. Serafy, David Somerton, Charles H. Thompson, and Chris Wilson

R MAPS: R Mapping and Plotting Scripts for stock assessment Elizabeth Brooks and Chris Legault

Pilot habitat assessment of a mesohaline embayment of the Chesapeake Bay David Bruce, Jay Lazar, Steve 

Giordano, and Ward Slacum

On the road to extinction? Monitoring population trends of the endangered white abalone, Haliotis sorenseni 

John Butler, Kevin Stierhoff, and Melissa Neuman

The effect of contaminant exposure on the behavior and growth of young of the year bluefish, Pomatomus 

saltatrix Allison Candelmo, Ashok Deshpande, and Judith S. Weis

A mesohaline submerged aquatic vegetation survey of the U.S. Gulf of Mexico coast Jacoby Carter, Joy Merino, and 

Sergio Merino

The role of thermal habitat niche on mortality and recruitment in summer flounder, Paralichthys dentatus R. 

Christopher Chambers

Proposing a framework for integrating habitat science and management Louis A. Chiarella

AUV (autonomous underwater vehicle) for monitoring fish and their habitat on the U.S. west coast M. 

Elizabeth Clarke, Erica Fruh, Curt E. Whitmire, and Hanumant Singh

Interactive habitat database for the Pacific Coast Ocean Observing System (PaCOOS): An ecosystem 

observing tool for the California Current M. Elizabeth Clarke, Chris G. Romsos, Chris Goldfinger, Bob Gref, W. 

Waldo Wakefield, and Marlene Bellman

Estimating biomass from in situ counts of demersal fishes—the challenge in creating a random sample from 

data collected non-randomly Julia E.R. Clemons, W. Waldo Wakefield, Ian J. Stewart, and Curt E. Whitmire

Demographics by depth: Spatially-explicit densities and life history dynamics of hogfish (Lachnolaimus 

maximus) in the eastern Gulf of Mexico Angela B. Collins and Richard S. McBride

Integrated habitat restoration monitoring for program planning and project implementation Mathias J. Collins 

and Bryan DeAngelis

Estimating total spawning abundance from index area counts using a GIS-based habitat intrinsic potential 

model Thomas D. Cooney, Damon Holzer, and Rich Carmichael

Multifrequency biplanar interferometric imaging for ultra high resolution three-dimensional imaging of seabed 

habitat George R. Cutter, Jr. and David A. Demer

Under what circumstances, if any, do we need to post-stratify species/habitat data? Doug DeVries, Chris Gardner, 

Josh Brusher, and Gary Fitzhugh

The role of socio-economics in habitat conservation Peter E.T. Edwards

Identification and monitoring of dynamic habitat in the changing ocean David G. Foley

Mapping hard bottom reef fisheries habitat off northwest Florida—needs, methods, and status Chris Gardner, 

Doug DeVries, and David Naar

Growth variability of the splitnose rockfish (Sebastes diploproa) in the northeast Pacific Ocean: Pattern 

revisited Vladlena V. Gertseva, Jason M. Cope, and Sean E. Matson
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Mapping marine benthic habitats along the U.S. west coast: Current status, future plans and applications Chris 

Goldfinger, H. Gary Greene, Rikk G. Kvitek, Guy R. Cochrane, Samuel Y. Johnson, W. Waldo Wakefield, Mary M. Yoklavich, 

M. Elizabeth Clarke, and Crescent Moegling

Biotopes in a fisheries ‘habitat hot spot’: Investigating Georges Bank patch complexes in the larger context of 

habitat assessment Vincent G. Guida and Page C. Valentine

Patterns and processes underlying Pacific hake (Merluccius productus) migrations: Progress on developing 

forecast tools to predict distribution and density Melissa A. Haltuch, Carrie Holt, André E. Punt, and M. Elizabeth 

Clarke

Application of an adaptive acoustic/trawl survey to reduce uncertainty in rockfish biomass estimates Dana H. 

Hanselman, Paul Spencer, Denise McKelvey, and Michael Martin

Gulf of Mexico pink shrimp stock assessment model recalibration and model migration to Stock Synthesis Rick 

A. Hart and James M. Nance

Delay-difference, age-structured, and state-space models: Are hyphenated models useful for assessing stocks of 

orange roughy? Allan Hicks

Recent findings and accomplishments of NOAA’s Fisheries and the Environment (FATE) program Anne B. 

Hollowed, Steven Bograd, Elizabeth Brooks, Melissa A. Haltuch, Jonathan A. Hare, Roger Hewitt, Evan Howell, John Lamkin, 

Kenric Osgood, Jeffrey Polovina, and Michael J. Schirripa

The Deep Sea Coral Research and Technology Program: Assessing deep sea habitats Thomas F. Hourigan, M. 

Elizabeth Clarke, Andrew David, Dan Dorfman, Maile Sullivan, John Tomczuk, and Fan Tsao

Incorporating the negative impacts of chemical habitat quality into stock assessments John Incardona, Nathanial 

Scholz, and Tracy Collier

Adding ecological context to essential fish habitat models using groundtruthing technologies Steven Intelmann, 

Keith Smith, Bob McConnaughey, and Yuri Rzhanov

Can fishery policies for the U.S. west coast simultaneously sustain habitat, target species, and ecosystem health? 

Isaac Kaplan and Peter Horne

A multispecies bioeconomic model with biological and harvesting interactions using a surplus production 

model of stock dynamics Stephen Kasperski

Developing an essential fish habitat geodatabase, workflow, and data model Charles Keith

Assessment of geomorphological characteristics and reef fish utilization of reported reef fish aggregation sites 

in the Florida Keys, USA G.T. Kellison, A.C.R. Gleason, and J.C. Taylor

Multivariate models to predict distribution of structure-forming benthic invertebrates Lisa Krigsman, Mary M. 

Yoklavich, and Guy R. Cochrane

Successes and challenges in displaying essential fish habitat spatial data through the EFH Mapper Terra 

Lederhouse, Mike Onzay, Karen Abrams, and Kara Meckley

Predicting the distribution of anadromous fish in fresh water using habitat models Steve Lindley

Deciphering environmental patterns and effects from messy data Sandra A. Lowe and Jim N. Ianelli

The role of SEAMAP plankton surveys in monitoring the pelagic habitats of early life stages of fishes in the 

Gulf of Mexico Joanne Lyczkowski-Shultz, David S. Hanisko, Glenn Zapfe, Katrin E. Marancik, and Christina Schobernd

Large decline in resource species accompanied by a changing habitat in southern New England and New York 

since the mid 1980s Clyde L. MacKenzie, Jr.

A Coastal and Marine Ecological Classification Standard (CMECS) G.F. Mayer, R.J.Allee, G. Cicchetti, M.A. 

Finkbeiner, K.I. Goodin, L.R. Handley, C.J. Madden, C.S. Moses, and J. Soule

Mapping environmental variables to produce essential fish habitat models Bob McConnaughey, Steve Syrjala, 

Cynthia Yeung, and Keith Smith

Using acoustics to characterize sediments for essential fish habitat models Bob McConnaughey, Lloyd Huff, Cynthia 

Yeung, Steve Syrjala, Steven Intelmann, and Meghan McGovern
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Science support needs for east coast diadromous fish protection and restoration: Addressing management 

priorities Sean McDermott, Pace Wilber, Louis A. Chiarella, Prescott Brownell, Jason Link, Kevin Friedland, Brian E. 

Smith, and Tim Sheehan

Determination of best scientific information available for acceptable biological catch and other fishery 

conservation and management measures William L. Michaels, Manoj Shivlani, and Stephen K. Brown

Merging abundance and habitat modeling: A predictive spatial approach Paula Moreno and Michael Mathews

Where should they spawn? An assessment of the oceanic habitat of larval brown shrimp using dynamic 

linkages between offshore waters and estuarine nursery grounds Redwood W. Nero, Doug S. Ko, and Ian McCoy

River response to dam removal: The Souhegan River and the Merrimack Village Dam, Merrimack, NH Adam J. 

Pearson, Noah P. Snyder, Mathias J. Collins, and David Santaniello

Ocean scale hypoxia-based habitat compression of Atlantic istiophorid billfishes Eric D. Prince, Jiangang Luo, 

C. Phillip Goodyear, John P. Hoolihan, Derke Snodgrass, Eric S. Orbesen, Joseph E. Serafy, Mauricio Ortiz, and Michael J. 

Schirripa

Benthic habitat assessment and mapping in the Pacific Islands region John Rooney, Jonathan Weiss, Emily Donham, 

Frances Lichowski, and Joyce Miller

Estimates of rockfish habitat utilization and biomass on an isolated rocky ridge using acoustics and stereo image 

analysis Chris Rooper, Jerry Hoff, and Alex DeRobertis

The effects of bottom fishing on the benthic macrofauna and demersal fish feeding habits of northern Georges 

Bank Brian E. Smith and Jeremy S. Collie

An assessment of coastal and nearshore fish habitat for the National Fish Habitat Action Plan Susan-Marie 

Stedman, David Moe Nelson, Patrick Polte, Correigh Greene, and Joe Nohner

Evaluating the habitat impacts of nonfishing human activities in Federal fishery management plans David K. 

Stevenson

Incorporating environmental factors affecting recruitment into the stock assessment for snow crab in the 

Bering Sea Cody Szuwalski and André E. Punt

Incorporating food web and habitat interactions in a forage fish stock assessment Howard Townsend

Science needs for coastal and marine spatial planning for offshore renewable energy siting Sue Tuxbury and Chris 

Boelke

Identifying pelagic habitat in Shelikof Strait and the Bering Sea using GIS-based tools for analysis and 

visualization Tiffany C. Vance, Sharon M. Mesick, Annette B. Dougherty, and Janet Duffy-Anderson

Hypoxia: An important component of benthic habitats for U.S. west coast groundfish stocks W. Waldo Wakefield, 

Aimee A. Keller, Victor Simon, Keith L. Bosley, Francis Chan, John A. Barth, Dezhang Chu, Stephen Pierce, and M. Elizabeth 

Clarke

Pelagic habitats and ecosystem considerations for salmon and other pelagics of the central coast of California 

Brian Wells

Identifying coral habitat areas that are potentially vulnerable to fishing interactions Curt E. Whitmire and M. 

Elizabeth Clarke

Catch composition in the NMFS west coast bottom trawl survey as a predictor of habitat complexity Curt E. 

Whitmire, M. Elizabeth Clarke, James D. Hastie, Beth Horness, and Aimee A. Keller

Multivariate bathymetry-derived landscape ecology model accurately predicts rockfish distribution in Cordell 

Bank National Marine Sanctuary, CA, USA Mary A. Young, Pat J. Iampietro, Rikk G. Kvitek, and Corey D. Garza

Appendix 5: Habitat Science and Management Questionnaire Summary

1

The theme of this year’s National Stock Assessment Workshop (NSAW) was “Improving characterization of scientific uncertainty in assessments for allowable biological catch.” 

This theme was developed by the NSAW Steering Committee (Appendix 1), which consisted of one representative 

from each of the regional Science Centers as well as a representative from the Office of Science and Technology. The 

main NSAW objective was the advancement of stock assessment methods to improve determination of the level of 

acceptable biological catch (ABC). The National Standard 

1 Guidelines lead to the need for improved assessment and 

forecasting methods so that ABC can be set with a known 

and acceptable probability of overfishing. Where feasible, 

these methods should take into account the effects of ecosystem and environmental factors on the fish stock. Where 

data-rich methods cannot be applied, suitable proxies need 

to be developed to provide guidance for fishing level recommendations. 

The workshop consisted of seminars, posters, and breakout 

Executive Summary

The 11th National Stock Assessment and 1st National Habitat Assessment Workshops were held May 17-20, 2010. The 

workshops were jointly hosted by the Southeast Fisheries Science Center in Miami, FL, the Southeast Regional Office in 

St. Petersburg, FL, and the Office of Science and Technology in Silver Spring, MD. Attendance at the workshops reached 

nearly 200 registered participants, and included participants from every Science Center, Regional Office, and regional Restoration Center, as well as several NMFS Headquarters Offices. Representatives from a few Fishery Management Councils, 

several nongovernmental organizations, and various academic institutions also attended. Overall the workshops were very 

well received and served as the basis for extensive discussions that led to a number of recommendations and will serve as the 

basis for improved communication and coordination moving forward. 

11th National Stock Assessment Workshop

NSAW Top Recommendations

 Continued improvements to data collection are 

needed. Priority should be given to improving survey design and data quality for data-poor stocks.

 Field research, including tagging and predation studies and closed area investigations, should be pursued 

to produce better estimates of natural mortality.

 Advanced sampling technologies and alternative 

survey designs should be used to improve estimates 

of survey biomass and reduce error related to heterogeneous habitat and patchy distributions.

 The trade offs and assumptions between simple and 

complex models should be carefully evaluated. 

 Annual catch targets should be used to address management uncertainty, especially in situations where 

in-season catch data are delayed or imprecise.

groups that addressed the overall theme as well as some identified sub-themes. NSAW presentations were held in five theme 

sessions:

1) Theme A—Understanding the trade off between simple and complex models;

2) Theme B—Quantification of uncertainty from model structure and retrospective patterns;

3) Theme C—Addressing uncertainty due to key parameters, especially natural mortality;

4) Theme D—Incorporating statistical uncertainty from sampling error; and

5) Theme E—Developing a comprehensive approach for characterizing uncertainty.

Breakout groups focused on four topics:

1) Protocols for ABC recommendations in data-poor situations (Facilitator: Jim Berkson);

2) Methods for quantifying uncertainty in assessments, including proxies for unmeasured variance components (Facilitator: Chris Legault);

3) Evaluation of performance for ABC control rules; risk analysis; management strategy evaluations (Facilitator: Richard 
2

Methot); and

4) Addressing long-term climate/ecosystem factors affecting stock assessment and habitat (Facilitators: Anne Hollowed 

and Melissa Haltuch).

Joint Session of the National Stock and Habitat Assessment Workshops

A Joint Session between participants of the National Stock 

and Habitat Assessment Workshops was held over 1.5 days 

to advance the integration of environmental variables and 

habitat information into stock assessments, improve communication and collaboration between NMFS stock and 

habitat assessment scientists, and identify potential pilot 

projects to integrate stock and habitat assessments. The 

overall theme of the Joint Session was “Incorporating habitat information in stock assessments.” The Joint Session was 

planned cooperatively by members of the Steering Committees for the NSAW and National Habitat Assessment 

Workshop. 

The Joint Session consisted of keynote lectures by Churchill 

Grimes and Steven Murawski, two theme sessions, and 

three breakout sessions. During the theme sessions, invited 

speakers delivered presentations on the topics “Incorporating habitat information into stock assessments” and “Improving calibration and precision of resource surveys with 

habitat information.” Breakout sessions focused on the following themes: 

1) Using habitat information in survey design and analyJoint Session Top Recommendations

 Habitat data should be integrated into resource 

survey sampling design where available to improve 

the precision and efficiency of surveys.

 NMFS should expand its capacity to collect habitat 

information and develop a comprehensive repository for existing and new habitat information. The 

highest priority to address is expanded habitat mapping and classification.

 Expanded collection of environmental data should 

occur during existing resource surveys, and development and implementation of advanced sampling 

technologies should continue.

 Cooperation and data sharing should be pursued 

and existing partnerships strengthened to make the 

best use of available habitat information.

 Encourage research to investigate the relationship 

between habitat change and key stock assessment 

factors.

sis;

2) Including habitat-specific life history rates in population models; and

3) Using time series of habitat information in population models.

The breakout sessions gave participants a chance to collaborate, discuss topics of mutual interest, and find common ground 

between the two disciplines. A number of recommendations resulted from the Joint Session and the breakout groups in 

particular, including some ideas for focused or pilot studies incorporating habitat information into survey design and population assessment efforts.

1st National Habitat Assessment Workshop

This marks the first ever national meeting of the habitat science community, including habitat scientists from the NMFS Science Centers, managers from Regional Offices, and restoration scientists and managers from the Restoration Centers. The 

1st National Habitat Assessment Workshop (NHAW) gave habitat scientists and managers the opportunity to address issues 

of mutual interest and lay the foundation necessary for improving cooperation and building a comprehensive habitat science 

program. The theme, “Moving toward a NMFS National Habitat Science Program,” provided the basis for discussions during the workshop. The objective of the first NHAW was to develop a cohesive national habitat science program and community within NMFS and establish approaches for implementing recommendations from the Habitat Assessment Improvement 

Plan (HAIP). The NHAW focused on ways to build and fund a habitat science program, aligning habitat assessments with 

management priorities, and identifying and refining habitat science products and tools for use by management. 
3

The workshop consisted of a keynote lecture by 

John Boreman and three sessions, each with overall 

group discussion and more focused breakout discussions. Session 1 focused on “Current processes 

for providing habitat science for management” and 

began with a panel discussion led by Peter Colosi. 

The second session also began with a panel discussion led by Thomas Noji on “Proposing strategies for 

the development of habitat science capacity and the 

incorporation of habitat science into management.” 

Discussions during the first and second sessions were 

guided by the results of a survey that was sent out to 

habitat scientists and managers in the Science Centers, Regional Offices, and Restoration Centers prior 

to the workshop. The survey (see Appendix 5) asked 

questions related to near- and long-term planning for 

habitat science and interactions between the science 

and management sides. The overall goal of the survey 

was to determine differences in perception between 

the regional entities and uncover potential unmet 

needs. The survey results provided material that led 

to some lively discussion. The third session was focused on “Implementing proposed solutions regionally” and a majority of time was spent in breakout 

groups separated by region, with the larger group 

coming back together at the end of the session to 

have a discussion about differences and similarities in 

regional approaches. 

Discussions during the NHAW sessions and breakout groups were quite productive and led to a number 

of recommendations and action items. Many of these 

related to improving communication and coordination between science and management, improving 

prioritization for habitat science, and implementing 

the recommendations of the HAIP. 

NHAW Top Recommendations

 Improved communication and coordination is needed between regional Science Centers, Regional Offices, Restoration Centers, and NMFS Headquarters. An important step 

would be implementing regular, formal meetings between 

regional habitat staff.

 Regional entities should establish defined processes to: 1) 

jointly identify habitat research priorities on a periodic 

basis; 2) align habitat research funding decisions with the 

identified priorities; and 3) maintain open lines of communication regarding research planning, research results, and 

evolving management information needs.

 At the regional level, science and management staff should 

work together to identify current funding streams and look 

for opportunities to align identified priorities with existing 

funding or redirect funding to better meet needs.

 Low cost steps should be taken in the near-term to promote development of long-term habitat science capacity.

 Habitat scientists should continue to be opportunistic with 

funding sources, but should also promote collaborations 

and increased efficiency.

 Regional entities should work together to support implementation of the Habitat Assessment Improvement Plan

(HAIP) by supporting development of national HAIP 

budget initiatives and by incorporating the HAIP into 

regional habitat research plans and developing regional 

HAIP implementation plans.

 NMFS’ Restoration Center should have an increased role 

in the regional habitat dialog.

5

Introduction

The 11th National Stock Assessment Workshop (NSAW) 

and the 1st National Habitat Assessment Workshop 

(NHAW) represent very significant milestones in the development and evolution of the science conducted by the 

National Marine Fisheries Service (NMFS). Both workshops had a strong emphasis on improving the agency’s ability to meet its fisheries management mandates. The NSAW 

continued in the tradition of focusing on topical technical 

issues involving scientific assessments of fisheries stocks. The 

topic for this NSAW was “Characterization of Scientific 

Uncertainty in Assessments to Improve Determination of 

Acceptable Biological Catches (ABCs)” while the NHAW 

focused on “Habitat Science in Support of Management”. 

Perhaps the most innovative and, hopefully precedent setting, aspect of these two workshops was the Joint Session 

to improve the communication and collaboration between 

stock assessment and habitat scientists. The Joint Session 

addressed two major topics: “Incorporating Habitat Information into Stock Assessments” and “Improving Calibration and Precision of Resource Surveys with Habitat Information”.

The workshops coincided with the publication of a new 

agency plan for habitat science, the Marine Fisheries Habitat Assessment Improvement Plan (HAIP). This document 

defines NMFS’ unique role in pursuing habitat science and 

in developing habitat assessments to enable the agency to 

more fully meet its mandates to sustain marine fisheries and 

associated habitats. For the first time, this plan establishes a 

framework to coordinate its diverse habitat research, monitoring, and assessments and to target support for improving 

habitat science through the budget process. The HAIP is 

patterned after the agency’s 2001 Marine Fisheries Stock Assessment Improvement Plan, which has provided the basis 

for substantial and steady growth in the agency’s stock assessment capabilities.

To end overfishing, the Magnuson-Stevens Fishery Conservation and Management Reauthorization Act of 2006 

added new requirements for annual catch limits (ACLs) 

and accountability measures. ACLs are required for those 

fisheries subject to overfishing in 2010, and for all fisheries 

by 2011. To accomplish this objective, National Standard 1 

guidelines require that each Fishery Management Council’s 

Scientific and Statistical Committee (SSC) provide their 

council with recommendations for ABCs. The NMFS 

Science Centers have a key responsibility in providing the 

best scientific information available for the ABC determinations, including sources of uncertainty. The November 

2009 report from the National SSC Workshop (available 

at www.fisherycouncils.org) addressed the importance of 

characterizing sources of uncertainty in stock assessments 

for ABC determination, and noted differences among the 

regional Science Centers in how uncertainty is characterized. For these reasons, the NSAW focused on characterization of uncertainty to improve stock assessments for the 

determination of ABCs.

The NSAW consisted of five theme sessions that addressed 

primary aspects of uncertainty in stock assessments: 1) Understanding the Trade Off between Simple and Complex 

Models; 2) Quantification of Uncertainty from Model 

Structure and Retrospective Patterns; 3) Addressing Uncertainty due to Key Parameters, Especially Natural Mortality; 

4) Incorporating Statistical Uncertainty from Sampling 

Error; and 5) Developing a Comprehensive Approach for 

Characterizing Uncertainty. Several posters and 24 selected oral presentations provided an overview of the current 

methods used to evaluate uncertainty in stock assessments. 

The NSAW included four breakout sessions to address 

technical issues and bottlenecks associated with deriving 

estimates of uncertainty. The stimulating exchange of ideas 

among regional scientists at the NSAW will foster collaborations to improve practices for characterizing sources of 

uncertainty in stock stocks for ABC determinations. 

The Joint Session brought the agency’s stock assessment 

and habitat scientists together to address high priority issues that concern both disciplines. This session is the first 

time that these two groups have come together to focus on 

their mutual interests at the national scale. The theme sessions were introduced by a series of presentations to provide 

context, an overview of the HAIP, and a keynote lecture, 

“Informing and Improving Stock Assessments with Marine 

Habitat Information,” by Dr. Churchill Grimes, Director of 

the Southwest Fisheries Science Center lab in Santa Cruz, 

California. The theme sessions consisted of detailed scientific presentations that provided a broad range of regional 

perspectives for different habitats and species groups. These 

were followed by a keynote lecture, “Are We Running out 

of Fish? And Where Will They Live?” from Dr. Steven Murawski, NMFS Director of Scientific Programs and Chief 

Science Advisor. Dr. Murawski also provided an up to date 

overview of the Deepwater Horizon oil spill in the Gulf of 
6

Mexico, an event of great concern to NOAA and to all the 

workshop participants. The Joint Session concluded with 

breakout groups designed to promote in-depth discussions 

among practitioners from the two disciplines, which were 

intended to stimulate development of new collaborations 

and plant the seeds for future project proposals.

The NHAW provided a forum for discussion and dialog 

between the agency’s habitat scientists and habitat managers, including managers from both the habitat protection 

and habitat restoration components. The purpose was to 

improve the scientific support of the agency’s habitat management programs. Although these groups have interacted 

in the past, the intent of the NHAW was to use the publication of the HAIP to provide a focus for more regular and 

systematic interactions and collaboration from this point 

on. A keynote lecture, “Confronting the Ghosts of Christmases Past: A New Context for Habitat Assessments,” was 

delivered by Dr. John Boreman, the recently retired Director of the NMFS Office of Science and Technology, and a 

key figure behind the initiation of the HAIP. The NHAW 

consisted of three sessions to assess current practices around 

the country, develop the long-term capacity for the Science Centers to meet management needs, and implement 

regional solutions. These sessions began with presentations 

that summarized the results of questionnaires, and included 

panel discussions and breakout groups. The breakout groups 

initially mixed together participants across regions, to promote sharing of ideas and experiences. The groups were 

then reconfigured on a region-by-region basis to promote 

dialog that could lead to improved interactions between the 

scientists and managers within each region. 

As the chairs of these workshops, we are confident that 

these collaborative workshops provided fora for NMFS’ 

scientists and managers to come together to discuss some 

of the agency’s most important scientific and managerial issues. The success of the workshops can be attributed to the 

insightful contributions of the participants and to the guidance and vision provided by our steering committees. We 

are also grateful for the efforts of Kirsten Larsen, Ben Laws, 

Kristan Blackhart, and Joe Nohner, who devoted considerable time to workshop organization and logistics, so that 

the vision could become reality. The challenge we now all 

share is to use the ideas generated in the workshops improve 

the determination of ABCs, promote a closer integration of 

stock assessment and habitat science, and enhance the scientific support provided to habitat managers. These advances 

will enable improved solutions to the problems of today and 

to the new problems that will undoubtedly emerge in the 

future, so that NMFS can make better decisions for conserving and making wise use of the Nation’s fisheries stocks 

and the habitats they depend on.

Stephen K. Brown

William L. Michaels

NMFS Office of Science and Technology

Silver Spring, Maryland

May 2010
7

11th National Stock Assessment Workshop

There are increasing demands to determine the major sources of uncertainty in stock assessments, particularly in understanding the uncertainties associated with establishing 

catch limit specifications. The over arching theme “Improving characterization of scientific uncertainty in assessments 

to improve determination of acceptable biological catch 

(ABC)” provides an opportunity to compare differences in 

pertinent methodologies utilized between the regional Science Centers and to discuss the best practices in characterizing sources of uncertainty.

Theme A: Understanding the Trade Off Between 

Simple and Complex Models

 Simple models with few parameters often appear to 

outperform more complex models by providing highly 

precise estimates, but only examine a limited amount 

of data and can underestimate the true uncertainty of 

the stock’s status because they may be more vulnerable 

to bias. Scientists have increasing demands to evaluate 

relevant information using more complex models, and 

these models utilize more parameters with many prior 

distributions that might produce less precise estimates. 

Given the tendency to develop more complex models, 

fishery scientists must carefully evaluate the trade offs 

and assumptions between simple and complex models.

 Recent developments in software and modeling tools 

provide more interactive evaluation of data quality, 

parameter estimation, and graphic visualization that can 

easily be utilized by advanced modelers, fishery analysts, 

and stakeholders.

Theme Session Summaries: Improving Characterization of Scientific Uncertainty in 

Assessments to Improve Determination of Acceptable Biological Catch (ABC)

Rapporteur: William L. Michaels (OST)

Theme B: Quantification of Uncertainty from Model 

Structure and Retrospective Patterns

 The accuracy and precision of parameter estimation is 

highly dependent on the quality of the data used by a 

model. Priority must remain focused on improving data 

collection with appropriate consideration of the modeling requirements and assumptions.

 Scientists must evaluate retrospective results to determine measurement error and bias to apply appropriate 

adjustments to improve parameter estimations, and the 

application of a bias adjustment will be dependent on the 

degree of data-richness.

 Retrospective bias often is affected by changes in the data 

sampling protocol or survey operations, hence requiring 

a calibration factor. Analysis of splitting the survey time 

provides an additional approach for the retrospective fix.

 When discrepancies occur between fisheries-independent and fisheries-dependent time series, this presents an 

opportunity to understand factors that can cause bias in 

the trends from either source of data.

Theme C: Addressing Uncertainty Due to Key Parameters, Especially Natural Mortality

 The spawning stock biomass and recruitment relationship in stock assessments will likely continue to have 

a high degree of uncertainty for most stocks because 

of limited recruitment information, particularly with 

regard to the effects of environmental changes.

NSAW Top Recommendations

 Continued improvements to data collection are needed. Priority should be given to improving survey design 

and data quality for data-poor stocks.

 Field research, including tagging and predation studies and closed area investigations, should be pursued to 

produce better estimates of natural mortality.

 Advanced sampling technologies and alternative survey designs should be used to improve estimates of survey biomass and reduce error related to heterogeneous habitat and patchy distributions.

 The trade offs and assumptions between simple and complex models should be carefully evaluated. 
8

 Natural mortality is a key parameter that is most often 

assumed as a constant. There are obvious shifts in population abundance associated with species interactions 

that suggest natural mortality is not constant, and field 

research such as tagging and predation studies should be 

supported to estimate this key parameter.

 Marine protected areas and temporary closure areas 

provide opportunities to investigate key parameters such 

as natural mortality, growth, and maturity rates.

Theme D: Incorporating Statistical Uncertainty 

from Sampling Error

 The specification of observation error variances can easily be subjected to violation in the pertinent assumptions, 

and it is better to model the process error.

 A common source of error occurs in the gear sampling 

operations, and gear catchability coefficients are often applied when there are changes in the sampling gear or vessel. However, significant error might occur between tows 

due to changes in distributional patterns, habitat, and environmental factors.

 Significant error in survey biomass estimates commonly 

occurs from spatial variance associated with heterogeneous habitat and distributional patchiness. Innovative 

technologies like hydroacoustics and alternative survey 

designs can improve estimates.

Theme E: Developing a Comprehensive Approach 

for Characterizing Uncertainty

 Estimation of the buffer between the overfishing limit 

(OFL) and ABC by stock is a requirement, and further 

collaboration between the regional Science Centers is 

necessary to determine the best practice for determining 

the alternative methods to estimate the probability (P*) 

that ABC exceeds the actual OFL. 

 The major sources of uncertainty appear to come from 

parameter estimation and model mis-specification. 

Parameter estimation can be quantified with standard 

methods of variance estimation, but model mis-specification remains a difficult statistical problem.

 Other important sources of uncertainty that are not 

easily estimated and often require improvements in data 

quality include measurement error, variability in overall 

stock productivity, and forecast error. Priority should be 

given to improving survey design and data quality for 

stock assessments that have limited data. Understanding 

the effects of environmental fluctuations on recruitment 

will have increasing importance in management of a 

fishery to attain the target catch.

 Further research is recommended to investigate the 

application of productivity indices and reference point 

proxies in data-limited situations for scaling ABC relative to OFL, and the ability to translate uncertainty in 

proxies into management advice.

 Further research is recommended to compare control 

rules that account for uncertainty in key population dynamic parameters, stock-recruitment relationships, and 

assessment model performance.

 In addition to scientific uncertainty, determination of 

management uncertainty is an important consideration 

in setting annual catch limits. The use of an annual catch 

target is recommended to address management uncertainty, especially with delayed or imprecise catch data 

within a fishing season.

Breakout Sessions

During the first afternoon of the National Stock Assessment 

Workshop (NSAW), attendees divided into concurrent 

breakout sessions to discuss four topics: 1) Protocols for 

ABC recommendations in data-poor situations [Facilitator: Jim Berkson]; 2) Methods for quantifying uncertainty 

in assessments, including proxies for unmeasured variance 

components [Facilitator: Chris Legault]; 3) Evaluation of 

performance for ABC control rules; risk analysis; management strategy evaluation [Facilitator: Richard Methot]; and 

4) Addressing long-term climate/ecosystem factors affecting stock assessment and habitat [Facilitators: Anne Hollowed and Melissa Haltuch]. The purpose of each opening 

breakout session was to define the objectives and goals, and 

develop a preliminary priority list of pertinent questions for 

attendees to keep in mind during the overall meeting.

The second round for each breakout session was held during the last day of the NSAW meeting with the goals to revisit the objectives, narrow the information and ideas gather 

during the NSAW meeting, and evaluate the priorities for 

short-term and long-term improvements in the science. 
9

NSAW Breakout Session 1: Protocols for ABC Recommendations in Data-poor 

Situations 

Facilitator: Jim Berkson (SEFSC)

Rapporteurs: Todd Gedamke (SEFSC) and Staci Hudy (Virginia Tech)

The breakout session began with discussions on what the 

objectives should be. In an attempt to identify a unique 

niche that had not yet been explored, the group reviewed 

previous meetings that had discussed the topic and the various working groups that had been or are working on aspects 

of the topic. These included the second National Scientific 

and Statistical Committee meeting which took place in St. 

Thomas, USVI in November 2009, and the Only Reliable 

Catch Stocks (ORCS) Working Group which originated as 

a result of that meeting. 

During the discussion of possible topics, it became very 

clear that the term data-poor did not mean the same thing 

to scientists from different regions. Many datasets categorized as data-poor on the west coast or Alaska would likely 

be qualified as data-rich in the South Atlantic or Caribbean. 

The group recognized that just as data-poor stocks had different meanings across regions, the methods used to make 

acceptable biological catch (ABC) recommendations for 

data-poor stocks would, by necessity, be different across regions, as a direct reflection of regional differences in data 

availability. 

The group recognized that despite the numerous meetings 

and working groups which have tackled the data-poor issue, none, to the best of the participants’ knowledge, had 

categorized what was meant by data-poor on a regional basis. This would be an important contribution, assuming this 

task could be completed during this breakout session. The 

group began to review the methods currently being used to 

calculate overfishing limits and ABCs by region, demonstrating that the methods employed are a direct reflection 

of data availability by region.

To evaluate what makes a stock data-poor, the group felt it 

necessary to do a brief overview of the data typically available for stocks that are assessed in each region. Stocks that 

qualify as data-poor are those that do not have those data 

available. 

With the goal of reviewing all of the regions, discussions began with the South Atlantic. The group reviewed the length 

of the time series of the commercial, recreational and fishery-independent data. The limitations tended to be availability of data earlier than the late 1980s, and the fact that 

approximately 15% of the stocks have assessments.

The Gulf of Mexico, in contrast, has longer time series, with 

data going back to the early 1980s. Twelve of 42 stocks have 

been assessed, accounting for approximately 29%.

Scientists on the Pacific coast have spent a good deal of time 

on reconstructing historical commercial catch records and 

encouraged this to be done in other regions. As a result of 

these efforts, there is a full time series of catch for many 

stocks, and 30% of the groundfish stocks have assessments.

This concluded the group’s work on the first afternoon of 

the breakout group. The goal on the final day of the breakout was to continue this categorization of what data-poor 

means by region. Unfortunately, there were far fewer participants for the breakout session on the last day and the group 

spent the reduced time reporting rather than in discussion. 

The group was still able to have a productive discussion 

on a wider range of topics on the second day. Discussion 

began with the many unique challenges that create the extreme version of data-poor in the U.S. Caribbean. This was 

an excellent opportunity for breakout participants to learn 

about the cultural, economic, and political factors that affect data collection, management, and enforcement in the 

region. There currently are no stocks in the U.S. Caribbean 

with approved assessments.

Participants mentioned how there is a great deal of confusion about the appropriate creation and application of stock 

Top Recommendations

 ‘Data-poor’ should be defined on a regional basis.

 Commercial catch records should be reconstructed where possible.

 There needs to be clearer national guidance as to the treatment of stocks in stock complexes.
10

complexes to the management process, and that this confusion can hurt the very stocks meant to be effectively managed under the revised Magnuson-Stevens Act. The group 

felt that there needs to be clearer national guidance as to the 

treatment of stocks in stock complexes.

Despite being unable to complete the group’s initial objective, participants ranked the following regions in terms of 

data availability in the following order: Caribbean < South 

Atlantic < Gulf of Mexico < Pacific < New England. Clearly, what qualifies as data-poor is not the same in each region 

and the methods used to calculate OFLs and ABCs will 

vary between regions. 

This session should be viewed as an initial attempt to define data-poor across regions, and the quantity and quality 

of information was constrained because of the limited time 

available to achieve the objectives of the breakout session. 

The information presented in this write-up should not be 

viewed as an official description of any region by any agency. 

This task should be taken up in a more comprehensive manner in the future.
11

NSAW Breakout Session 2: Methods for Quantifying Uncertainty in Assessments, 

Including Proxies for Unmeasured Variance Components 

Facilitator: Chris Legault (NEFSC)

Rapporteurs: Dana H. Hanselman (AFSC) and Amy M. Schueller (SEFSC)

During the opening breakout session on the first day, participants had a wide-ranging discussion that could be summarized into three key questions: 

1) What sources of uncertainty are worthwhile to 

quantify? 

2) What methods are appropriate for capturing 

uncertainty? 

3) Do we have the tools to think about ecosystem 

uncertainties? 

Discussions during the second phase of the breakout session focused on rules of thumb for different situations and 

minimum and maximum uncertainty bounds. Overall, the 

discussions were open and benefited from a wide range of 

experiences among the Science Centers. Although there are 

many different approaches to quantify uncertainty used in 

the different Science Centers, the opportunity to exchange 

ideas and learn from each other was valuable to all participants.

What Sources of Uncertainty Are Worthwhile to 

Quantify?

The group acknowledged that it is impossible to quantify 

all sources of uncertainty in a stock assessment. Even if this 

were possible, the resulting uncertainty would be so large 

that management advice would be useless. Thus, there has 

to be a pragmatic approach taken to address uncertainty in 

stock assessments. 

Of course, the opposite problem of estimating too little 

uncertainty in an assessment is also unacceptable, because 

it gives the impression that estimates are more precise than 

they actually are. This can occur in different ways. Simple 

models with few parameters can produce highly precise 

estimates, which may be highly biased. Conversely, highly 

complex models utilizing many prior distributions may inadvertently pin the estimates in a certain region of the solution space. 

To find the “Goldilocks” solution of the just right amount 

of uncertainty, the uncertainty associated with a given stock 

assessment should be set relative to other species with more 

or less data. This means that situations with more and better data should be more certain than an assessment with 

less informative data. Thus, an information-limited stock 

assessment should not produce highly precise estimates 

and may have the variance of key parameters increased after 

the assessment is completed to adjust for this relative rule. 

This adjustment is meant to provide a catalyst for collecting better data to allow more appropriate estimation of uncertainty. However, it was recognized that there may be a 

perverse effect of decreasing data collection if the added uncertainty is too small. One approach suggested is to create a 

minimum level of uncertainty at each Center based on the 

“best” assessment and require all other assessments to have 

at least that amount of uncertainty. This approach could be 

extended by using an expert panel or Delphi method to assign additional uncertainty to each assessment based on the 

amount of information available for the assessment relative 

to other assessments in the region.

The use of proxies for maximum sustainable yield reference 

points was also discussed. There was some concern that the 

Top Recommendations

 Uncertainty associated with a given stock assessment should be set relative to other species with more or less 

data.

 A minimum uncertainty bound should be used. 10% is the lowest acceptable value, but regional metaanalyses should be conducted to determine appropriate minimum uncertainty levels on a regional basis. No 

maximum bounds on uncertainty are appropriate.

 An examination of fishery management performance and consequences of different cultures of risk acceptability (comparing regional approaches to quantify uncertainty and the resulting fishing mortality rates 

relative to their overfishing limits) should be conducted in five to ten years.
12

proxies themselves may be biased in some cases, but this was 

not a widely held view. Of more importance was the ability to translate uncertainty in the proxy reference points 

into management advice. There are a number of technical 

means of computing this uncertainty. Care must be taken 

to ensure that the assumptions made when computing this 

uncertainty match the assumptions made in the assessment 

to allow comparison between the stock assessment results 

and the reference points.

What Methods Are Appropriate for Capturing 

Uncertainty?

The group recognized the usual methods for quantifying 

uncertainty, including analytical, bootstrap, Markov chain 

Monte Carlo, and empirical (retrospective). Technical details of each approach were not discussed. Instead the group 

focused on the question of whether the changes to the Magnuson-Stevens Act (MSA) are causing a radical change in 

how uncertainty is quantified, or is it just recognizing approaches that have been using for a long time. The group 

agreed that the changes to MSA are formalizing what has 

always happened during assessments; using judgment to 

look at validity of models and formulations. The new requirements have the potential to create a formalized process 

for how to look at uncertainty of overfishing limits (OFLs) 

in a more transparent way and make it easier to diagnose 

problems. 

A quick summary from members of each Science Center 

demonstrated that there are different approaches used to 

quantify assessment uncertainty. The major difference is the 

use of an axis of uncertainty versus attempting to include 

all the uncertainty in a single model run. The axis of uncertainty is a small set of different model results that are chosen 

to demonstrate the uncertainty in the assessment by changing only one or two parameters or assumptions. This can 

then be used in a decision table framework to examine the 

risks associated with making a management decision based 

on one model result when another model result is assumed 

to be true. Model averaging is starting to be used in some 

regions as well, although there remain some technical questions regarding the associated reference points. 

Do We Have the Tools to Think About Ecosystem 

Uncertainties?

The group agreed that tools are available to begin approaching this level of complexity, as demonstrated by some of 

the talks at this meeting. However, the resulting level of 

uncertainty may become unmanageable when forecasting 

multiple interacting species. One step in this direction that 

was discussed was incorporating a habitat or environmental covariate in a stock assessment to explain some of the 

process error. For example, a measure of habitat change over 

time could inform the bounds on a process error variable. 

If the correspondence held over time, this could reduce the 

amount of unexplained process error remaining in the assessment. 

Independent of how ecosystem uncertainty is incorporated, 

this approach leads to dynamic reference points. This is different from just uncertainty in reference points, as the central tendency changes over time, as well as the spread, due 

to changes in the fishery and biology. Recognition of the 

dynamic nature of reference points may prevent setting unrealistically high or low targets and improve understanding 

of how stocks respond to different types of management.

When considering ecosystem uncertainties, it should be remembered that humans are part of the ecosystem. Changes 

in behavior by fishermen in response to regulations have the 

potential to significantly impact catch per unit effort time 

series as well as the accuracy of management strategy evaluations. Including economists and social scientists may improve the ability to include the effect of human behavior on 

the data used in stock assessments.

Rules of Thumb

The group agreed that preserving some sort of relative uncertainty among stocks that reflects the information richness in the assessments is important. Information-rich 

assessments should have less uncertainty than informationlimited assessments. A meta-analysis approach that incorporates both within- and among-assessment uncertainty 

over time, as presented by the Southwest Fisheries Science 

Center (SWFSC) at this meeting, would be a good place to 

start in each region when trying to scale the amount of uncertainty in assessments. Care should be taken to avoid creating perverse incentives to not improve assessments over 

time due to additional uncertainty that could limit catch 

as assessments move from information-limited to information-rich.

The reduction of catch as uncertainty increases was recognized as an important aspect of fishery management under 

the new guidelines. This buffer can be increased by either 

reducing the acceptable probability (P*) of exceeding the 

OFL, or increasing the uncertainty associated with the 
13

OFL. There were pros and cons for both approaches. As 

long as the end result is a reduction in catch with increased 

assessment uncertainty, the group agreed either approach 

could be used.

Communication among regions and between scientists 

and managers will be necessary during the coming years 

as the new guidelines are implemented. The new “rules of 

the road” have some new language that will have to be communicated in an understandable fashion. Scientists need to 

continue producing the best possible assessments, but also 

provide appropriate levels of uncertainty for use by managers. To prevent abuse of process or use of policies in bad 

faith (“gaming the system”), lines of communication will 

need to be kept open so that all decisions are made transparently and openly.

Minimum and Maximum Uncertainty Bounds

The group agreed that a minimum uncertainty bound 

should be used, meaning that an assessment that has less 

uncertainty in the OFL than some predetermined amount 

would have the uncertainty increased to that minimum 

level. There was not agreement as to the specific value of the 

bound. A minimum coefficient of variation (CV) of 10% 

was agreed to be a bare minimum, but probably too low for 

most situations. The SWFSC presented analyses indicating 

36% as the average for information-rich assessments, but 

cautioned that this type of meta-analysis should be conducted in each region. 

The group agreed there is no reason to set a maximum 

bound on uncertainty, because information-limited assessments can be highly uncertain. It is hoped that large uncertainty will translate into more precautionary management, 

and that this will provide an incentive to collect better data 

to improve the assessment. It was recognized that highly 

uncertain assessments present challenges for management, 

but limiting the amount of uncertainty was not thought to 

be an appropriate response.

Final Thought

The range of approaches used by the different regions presents an opportunity to make comparisons over time as they 

are implemented. An examination of how each approach 

was used and the resulting fishing mortality rates relative to 

their overfishing limits would provide an assessment of performance similar to the comparison between productivity 

and reference points presented at this meeting. It is recommended that this analysis be conducted in five to ten years 

as an examination of fishery management performance and 

consequences of different cultures of risk acceptability.
14

NSAW Breakout Session 3: Evaluation of Performance for ABC Control Rules; Risk 

Analysis; Management Strategy Evaluation 

Facilitator: Richard D. Methot, Jr. (OST)

Rapporteur: Jonathan J. Deroba (NEFSC)

Background

Acceptable biological catch (ABC) control rules are protocols for specifying the annual ABC according to the National Standard 1 Guidelines (NS1G). These control rules 

are expected to take into account the abundance of the fish 

stock, its maximum sustainable fishing rate, the degree of 

uncertainty in estimates of these factors, and may also include other relevant factors. The explicit requirement to 

take uncertainty into account is new with the 2009 update 

of the NS1G, but the expectation to take a precautionary 

approach has been in place since the 1998 NS1G. The ABC 

control rule requirement is coupled with the MagnusonStevens Reauthorization Act requirement that the Fishery 

Management Council’s (FMC’s) Scientific and Statistical 

Committee (SSC) be the entity that specifies the ABC, 

which then serves as the upper limit to the FMC’s specification of the annual catch limit (ACL). Each SSC and FMC 

is vigorously deliberating on these issues, and the topic has 

been a significant focus of the National SSC Workshops in 

2008 and 2009. The degree of buffer between the ABC and 

the overfishing limit (OFL) should be informed by a risk 

analysis that balances the certainty with which overfishing 

is prevented (with P* being the acceptable probability of 

overfishing, not to exceed 50%) against the degree to which 

fishing opportunity is restricted to achieve this protection. 

The degree of acceptable risk is an FMC decision, informed 

by scientific analysis of the trade off. The technical means to 

conduct this risk analysis is pushing the envelope for quantification of uncertainty in stock assessments and for evaluation of the expected performance of proposed control 

rules. This breakout group discussed the development of 

ABC control rules with the goal of highlighting issues that 

should be evaluated and factors that have been treated differently in draft approaches under regional development.

Five topics were identified as areas needing further evaluation:

1) How can the sensitivity of a P* approach to life history characteristics be evaluated?

2) What are good ways to communicate the trade off between Pr(overfishing), Pr(biomass OK), and benefits 

in short-term and medium-term projections? 

3) What are the relative merits of adjusting P* vs. adjusting the variance level when making adjustments for 

unmeasured factors?

4) What are good practices for designing a tiered system 

that transitions from fixed buffers for lower tiers to a 

P* based buffer for one or more upper tiers?

5) Is there a way to bring additional considerations 

(stock vulnerability, ecosystem considerations, 

socioeconomic factors) into the ABC control rule, or 

are these best left to the optimal yield (OY) considerations?

How Can the Sensitivity of a P* Approach to Life 

History Characteristics be Evaluated?

The most pertinent life history characteristics are the stock’s 

rate of natural mortality, the resilience (steepness) of its 

spawner-recruitment relationship, and the age offset between maturation and selection by the fishery. These factors 

have a major influence on the maximum sustainable fishing 

rate and the degree to which this rate must guard against 

Top Recommendations

 Additional studies are needed to investigate methods to evaluate the sensitivity of a probability approach to 

life history characteristics.

 Trade offs of various buffers and options (e.g. relative change in revenue under different options) should be 

communicated transparently to stakeholders.

 Additional considerations (stock vulnerability, ecosystem considerations, and socioeconomic factors) should 

not be included directly into the acceptable biological catch control rule; such considerations are more appropriately included in the optimum yield specification. Continued research on more inclusive approaches 

should be pursued.
15

allowing the stock to decline to low levels of abundance. 

The natural mortality rate also controls the number of age 

groups in the stock and thus its inertia against fluctuations 

caused by annual recruitment variability. These factors need 

to be taken into account when evaluating the expected 

performance of a control rule and the potential need to 

set lower P* values for stocks with certain combinations of 

these characteristics. The group made no overall recommendation on this topic but supported studies.

What Are Good Ways to Communicate the Trade 

Off Between Pr(overfishing), Pr(biomass OK), 

and Benefits in Short-term and Medium-term 

Projections?

The goal is to clearly evaluate and communicate the trade 

off between prevention of overfishing and attainment of a 

large OY. It seems advisable to present the OY in terms of 

monetary value to better account for socioeconomic factors and discount rates. A logical addition to the trade off 

analysis is the probability that the stock is approaching an 

overfished condition, especially in medium-term projections. The trade off between P* and OY is expected to be 

nonlinear, especially over a multiyear period. Multiyear 

analyses are advisable to incorporate the cumulative effects 

of time lags, large overages, and autocorrelated errors. In a 

one year projection, the trade off is nearly linear, but over 

longer time periods a small reduction in P* below 50% 

can reduce the chance of overfishing while sacrificing little 

yield because of the flat-top to the production relationship. 

However, achievement of very low P* can require great sacrifices in fishing opportunity, because of the inherent uncertainty of the system. Because the risk associated with P*

is a societal judgment, it need not be constant over time. 

Specification of a P* framework requires explicit criteria, 

but these criteria may be difficult to accomplish. The flexibility, or lack thereof, might be disagreeable. However, for 

a fishery management plan, any flexibility to change P* over 

time should be pre-analyzed and a framework described. 

One option might be to phase-in a reduction in P* over a 

specified time period, although never to exceed 50%, so the 

immediate reductions in fishing opportunity would be lessened. One approach that could help the public understand 

the effect of uncertainty would be to define a total range of 

buffer size so that the most certain assessments would never 

create a buffer that was smaller than some prespecified small 

level, and the most uncertain assessment or data-poor tier 

would never create a buffer size that was larger than another 

prespecified level. Between these two extremes, assessment 

uncertainty and acceptable risk would quantitatively adjust 

the size of the buffer.

The overall conclusion of the group is that the trade offs of 

various buffers and options (e.g. relative change in revenue 

under different options) needs to be transparently communicated. Stakeholders will appreciate this.

What Are the Relative Merits of Adjusting P*

vs. Adjusting the Variance Level When Making 

Adjustments for Unmeasured Factors? 

Estimates of uncertainty in assessment results are typically 

more uncertain than the assessments themselves. Because of 

this incomplete characterization of uncertainty, it is necessary to make adjustments in order to apply the P* method. 

Some SSCs are considering adding extra components of 

uncertainty before applying the P* calculations. Others are 

reducing the P* to account for the underestimate of uncertainty. While both methods can produce the same overall 

buffer size, the pros and cons of the two approaches has not 

been fully articulated or evaluated. A related issue is consideration of a minimum degree of uncertainty calculation 

before any application of the P* approach becomes reasonable. If the calculated uncertainty is very small, then even 

large adjustments to P* will have little effect on the size 

of the buffer between ABC and OFL. The alternative approach would use a fixed buffer size when uncertainty cannot be calculated well enough.

Because P* is considered to be a representation of a societal 

risk, some participants felt that it was inappropriate to adjust P* to account for the degree to which uncertainty has 

been calculated, which is a scientific factor. Adjusting variance may require consideration of a “control rule” relating 

the level of variance to buffer size. A good control rule and 

an open process will ensure scientists are not making management decisions. A “keep it simple” approach may perform nearly as well as proposed elaborate methods to adjust 

P* or variance options. The group concluded that it would 

be helpful to list and evaluate pros and cons of adjusting P* 

vs. adjusting variance.

What Are Good Practices for Designing a Tiered 

System that Transitions From Fixed Buffers for 

Lower Tiers to a P* Based Buffer for One or More 

Upper Tiers?

The need for a tiered approach is related to the current lack 

of a comprehensive modeling framework that incorporates 

all sources of uncertainty, including suitably defined prox-
16

ies/priors for unmeasured components. If there was such a 

comprehensive framework, it would always create a larger 

buffer as the information about stock abundance and productivity degraded. Tiered approaches should retain this 

basic feature, so lower tiers should create buffers that are at 

least as large as the buffers created by more data-rich tiers. 

This property of tiers creates an incentive to move ‘up’ in 

tier level. For situations in which the only information is 

average catch, an important initial consideration is whether 

this average catch represents an estimate of OFL. In this 

case, a large buffer could be required for a fishery that some 

might consider to be stable. On the other hand, directly 

identifying the recent average catch as ABC and not creating a buffer is contrary to the concept of creating at least a 

small buffer for even the better assessments. This dichotomy 

deserves further consideration.

The group concluded that the transition between tiers 

needs to be logical with regard to effect on buffer size. The 

transition between tiers is related to the concept of adjustment for unmeasured uncertainty and the development of a 

pros/cons statement with regard to approaches for accounting for unmeasured uncertainty could also address tiers.

Is There a Way to Bring Additional Considerations 

(Stock Vulnerability, Ecosystem Considerations, 

Socioeconomic Factors) into the ABC Control Rule, 

Or Are These Best Left to the OY Considerations?

In concept, a multispecies ecosystem model could calculate 

each species’ maximum sustainable yield (MSY) and OFL 

while taking species interactions into account. In this case, 

ecosystem considerations would be in the OFL and uncertainty in these calculations could be used in an ABC calculation. However, because stock scientists are not currently 

able to implement such multispecies approaches, it seems 

advisable to keep MSY/OFL as a single species concept and 

to take ecosystem considerations into account at the end in 

the OY specification. An example is situations in which the 

target harvest level of a productive stock is constrained by 

the bycatch of a less productive or protected stock.

Productivity and Susceptibility Assessments (PSAs), used 

to evaluate a stock’s vulnerability, could address less tangible factors that are not explicitly included in OFL/MSY 

calculations. From this perspective, it may be logical to use 

PSA as a consideration in setting the buffer between OFL 

and ABC. However, at least one important productivity 

factor, natural mortality, is in both the PSA calculation and 

in the FMSY calculation, so use of PSA in scaling the ABC 

buffer needs to avoid double consideration of such factors. 

The PSA analysis seems most useful for data-poor tiers that 

are not able to quantitatively calculate FMSY. PSA calculations are also useful for guiding the assembly of stocks into 

complexes.

While socioeconomic factors are certainly important considerations in deciding on the acceptable level of risk in the 

ABC control rule, it does not seem advisable to directly 

include socioeconomic considerations directly in the ABC 

control rule. A better approach would include the socioeconomic factors in a more comprehensive analysis designed to 

guide the setting of optimum yield. A subset of this analysis 

could still be used to guide the setting of ABC.

The group concluded that PSA and ecosystem considerations are not tangible enough to codify in a control rule, 

but still necessary to think about in terms of risk. Such considerations are more appropriate at the OY level. Continued research on more inclusive approaches is encouraged.
17

NSAW Breakout Session 4: Addressing Long-term Climate/Ecosystem Factors 

Affecting Stock Assessment and Habitat 

Facilitators: Anne B. Hollowed (AFSC) and Melissa A. Haltuch (NWFSC)

During the opening breakout session, participants discussed 

eight key outcomes that stemmed from a joint International 

Council for the Exploration of the Sea (ICES)/North Pacific Marine Science Organization (PICES)/Food and 

Agriculture Organization of the United Nations (FAO) 

symposium on the Effects of Climate Change on Fish and 

Fisheries held in Sendai, Japan in April 2010. 

1) Long-term ocean monitoring programs are needed to 

track and understand ecosystem and climate change 

as they occur.

2) Networks of shelf seas models have already been developed for many of the world’s large marine ecosystems (LMEs).

3) Three sources of uncertainty in global ocean models 

(GOMs) are under investigation: 1) parameter uncertainty; 2) structural uncertainty; and 3) scenario 

uncertainty. Parameter uncertainty is being addressed 

to some degree with sensitivity tests, structural uncertainly is being explored via comparison of different coupled phyical-biological models, and scenario 

uncertainty deals with greenhouse gas emissions; 

economics could be addressed using ensemble model 

sets.

4) There are five approaches to predicting the effects of 

climate change on fish and fisheries: a) conceptual 

predictions; b) inferences from laboratory studies; c) 

statistical downscaling from GOM the regional scale; 

d) dynamic downscaling to regional ocean models; 

and e) whole earth system models. Each has strengths 

and weaknesses.1

5) Fisheries oceanography and laboratory studies are 

critical to integrating biological and oceanographic 

models, evaluating species environmental tolerances 

and adaptation, and tracking species responses to 

long-term ecosystem and climate change as it occurs. 

6) Models that couple marine, social, and economic 

responses are needed to evaluate management strategies; however, few examples exist.

7) Food security and marine conservation issues have 

conflicting goals.

8) Two-way communication is needed with scientists 

and stakeholders to develop meaningful scenarios 

on human responses to the impact of ecosystem and 

climate change.

The group considered a series of trigger questions as a basis 

for discussions.

1) Regional shelf circulation models: Should NMFS 

and NOAA scientists adopt a standard modeling 

platform for regional circulation models (e.g. Regional Ocean Modeling System [ROMS])? Should 

NMFS and NOAA adopt the Intergovernmental 

Panel on Climate Change approach of encouraging multiple modeling groups? If multiple regional 

models are encouraged, how will regional couplings 

be accomplished?

1

Stock, C.A., M.A. Alexander, N.A. Bond, K. Brander, W.W.L. Cheung, 

E.N. Curchitser, T.L. Delworth, J.P. Dunne, S.M. Griffies, M.A. Haltuch, J.A. Hare, A.B. Hollowed, P. Lehodey, S.A. Levin, J.S. Link, K.A. 

Rose, R.R. Rykaczewski, J.L. Sarmiento, R.J. Stouffer, F.B. Schwing, G.A. 

Vecchi, F.E. Werner. In Review. On the use of IPCC-class models to assess the impact of climate on living marine resources. Progress in Oceanography.

Top Recommendations

 NMFS should develop technical guidelines for short- and long-term use of environmental and ecosystem 

information in stock assessments and stock projection models.

 NMFS should consider developing a modeling framework for projecting regional responses to climate 

change.

 Mechanisms for building greater dialog and research collaborations among climate scientists, oceanographers, and fisheries biologists are needed. A biennial National Climate and Fisheries Workshop may help 

resolve this issue.

 NMFS should inventory climate change research efforts within each large marine ecosystem and create an 

online database of the results.
18

2) Regional shelf ecosystem models: Should NMFS 

utilize the ecosystem models that have already been 

developed for NMFS regions (e.g. Atlantis (Fulton, 

Australia), European Regional Seas Ecosystem Model 

[ERSEM] via QuestFish (Holt, United Kingdom)) 

or should NMFS continue to encourage the development of regional ecosystem models internally? If 

multiple regional models are encouraged, what are 

the strengths and weaknesses of different modeling 

approaches?

3) Downscaling to stock assessments: How can 

NMFS work with climate-ocean modeling communities to bring relevant information into stock assessment advice?

4) What are the funding opportunities (e.g. Fisheries 

and the Environment [FATE], Ocean Acidification, 

Loss of Sea Ice [LOSI], or Comparative Analysis of 

Marine Ecosystem Organization [CAMEO]) that 

could be tapped to enhance ongoing activities?

5) What laboratory studies can be started to assess 

tolerances and bio-energetic responses of living 

marine resources?

6) What are the key gaps in funding opportunities?

7) How and when can (should) NMFS stock assessment scientists and Fishery Management Councils inform stakeholders of future demands for 

food?

8) How and when can (should) NMFS facilitate 

communication with stakeholders to establish 

scenarios for human responses in the face of 

climate change?

Of this suite of discussion topics and key questions, the 

group elected to focus on questions 1, 4, and 7. Synthesis 

of the group discussion resulted in the following key group 

recommendations:

 NMFS should develop best practices for long- and shortterm use of environmental and ecosystem information in 

stock assessments and stock projection models. This guidance should clarify the requirements for tactical fisheries 

advice and longer-term strategic advice.

 NMFS should consider developing a modeling framework 

for projecting regional responses to climate change.

 When modeling ecosystem responses to climate change, 

proposed functional relationships should be vetted outside of the stock assessment process. 

◉ FATE provides funding for this type of vetting when 

the available data has already been collected. 

◉ New funding is needed to conduct the field or laboratory experiments that would provide time series to periodically monitor and verify functional relationships 

used in the stock assessment and stock projection models.

◉ Ecosystem models may reveal core processes that could 

be included in stock assessments or stock projection 

models. The FATE and CAMEO programs could provide funding for projects that explore the feasibility of 

utilizing ecosystem models to identify key processes or 

indicators that could be used in stock assessments.

 NMFS scientists need to consider the trade offs between 

model complexity and model mis-specification.

 Many off the shelf physical modeling tools are developed 

by experts outside of NMFS, therefore mechanisms for 

building greater dialog among climate scientists, oceanographers, and fisheries biologists are needed. A biennial 

National Climate and Fisheries Workshop (NCFW) of 

NOAA climatologists, oceanographers and fisheries scientists may help to resolve this issue. 

 Including long-term projections in annual stock assessments provides a method to evaluate the predictive skill 

of models. Over time, this will inform the public of the 

uncertainty in the predictions and to encourage collaboration in the development of strategy scenarios.

During the assembly of the breakout session, the group revisited the key questions and discussed what opportunities 

exist to enhance climate-fisheries research.

Regional Shelf Circulation Models

The group recommended that in the short term, NMFS 

and NOAA should encourage research collaborations between global ocean modelers, regional shelf seas modelers, and fisheries scientists through a biennial NCFW and 

through dedicated research. Short-term 2–3 year research 

projects could be funded by providing opportunity funds 

for competitive research. The group noted that the FATE 

program is well positioned to oversee the proposal review 

and selection of new projects focused on the effects of climate change on fish and fisheries. FATE has a long track 

record of funding interdisciplinary research projects designed to enhance the use of climate and ecosystem forcing 

on stock assessments and ecosystem assessments. Utilizing 

the current FATE leadership would minimize redundancy 

within NMFS, and would build on existing coordination 

groups, providing an efficient use of staff time. 

Statistical downscaling methods are well suited for appli-
19

cations in single species or multispecies stock assessments 

and single or multispecies management strategy evaluations 

(MSEs). It will be important for NMFS to have advisors on 

how to extract and utilize GOM data. Some Science Centers already have this facility because of the close proximity 

of oceanographic research institutions to Science Centers 

(e.g. the Alaska Fisheries Science Center [AFSC] and Pacific Marine Environmental Laboratory [PMEL]; the Southwest Fisheries Science Center and Environmental Research 

Division [ERD]; and the Southeast Fisheries Science Center [SEFSC] and Atlantic Oceanographic Meteorological 

Laboratory); however, other regions may need funding to 

build this capacity. The FATE program has funded collaborations of this sort between PMEL and ERD and between 

PMEL and AFSC.

As NMFS endeavors to embed models of fish and fisheries 

in dynamic regional ocean models, additional full-time staff 

will be needed. Members of the breakout group recognized 

that NMFS scientists are not trained climatologists, global 

ocean modelers, or earth systems modelers, so it would be 

useful to identify funds for permanent staff in either the 

new NOAA Climate Office or NMFS who would act as 

a liaison between NMFS and GOM modelers, and who 

would facilitate the coupling of climate models and ecosystem assessments or stock assessment models. 

At the current time NMFS is working with GOM outputs 

from modeling groups around the world. Members of the 

breakout group thought this practice was useful, because it 

allows analysts to address structural uncertainty in the forecasts. Until the global ocean modeling community settles 

on a common structure for models, NMFS scientists will 

need access to model output from models developed outside of the United States. PICES, ICES, and FAO currently provide funding for meetings and symposiums, and these 

forums provide a useful opportunity for scientific exchange. 

These international forums help to improve communication 

on this issue. The new Basin-scale Analysis, Synthesis, and 

Integration (BASIN) program in the Atlantic may also provide opportunities for international collaboration. However, financial incentives may be needed to entice global ocean 

modelers outside of the United States to collaborate with 

NMFS scientists on new research projects. 

At some point in the future NOAA climate modelers and 

NMFS scientists will probably settle on a modeling structure that includes upscaling information from regional 

shelves and downscaling to ROMS models that provide 

time and space scales relevant to ecosystem processes. When 

this occurs, the group recommends that long-term funding 

for permanent staff be identified to assist with the routine 

maintenance and operation of the model. 

Modeling Climate Effects on Fish and Fisheries

Multiple ecosystem models are up and running in U.S. regions integrating physics, nutrient/plankton/zooplankton, 

and fish (Atlantis, North Pacific Ecosystem Model for Understanding Regional Oceanography (NEMURO-Fish; 

individual-based models and fishing), Quest-fish (sizebased), or others). At the current time there is no clear preferred modeling structure. Members of the breakout group 

thought it would be premature for NMFS to adopt a standard modeling structure. NMFS should continue to encourage development of multiple types of ecosystem models with varying levels of complexity. Most NMFS Science 

Centers have recently hired ecosystem modelers. Therefore, 

the key ingredient that would advance the state of the art 

would be funding opportunities to develop and compare 

the performance of ecosystem modeling approaches. The 

CAMEO research program could serve as the vehicle for 

model comparisons and ecosystem comparisons. In addition, the biennial National Ecosystem Modeling Workshop 

will provide a forum for communication of modeling approaches within NMFS. Members of the breakout group 

noted that NMFS is partnering with international modeling groups. For example, the SEFSC plans to hold an Atlantis workshop in the near future.

Should NMFS and NOAA Scientists Work to Create 

a Linked Network of Shelf Ecosystem Models? 

Regional ocean circulation models have been developed, or 

are under development, in most of the U.S. LMEs. Biological couplings have been implemented for some regions of 

the United States. Members of the breakout group noted 

that if fish and shellfish are expected to shift their distributions in response to climate change, then the regional approach would be inadequate. Some method to link regional 

shelf models will be needed. Members of the breakout group 

made the following recommendations: 

 LME programs—NMFS should inventory the individual 

climate change research efforts within its LMEs by creating an online database containing metadata about the 

major climate related modeling and research projects 

within each LME. This inventory should be compiled 

on a web site to provide one source to access information 

from these types of models. The metadatabase should 
20

include an inventory of what’s available in terms of biophysical data outputs from climate models. Funds from 

the U.S. Integrated Ocean Observing System (IOOS) 

have supported the development of databases of this type 

and it may be possible to leverage the IOOS nodes to 

add information to existing databases.

 Link between oceanography—Fish and fisheries requires 

continued mechanistic process studies that integrate 

across multiple spatial scales. Field work is needed to 

groundtruth projected changes in habitat quantity, quality, and distribution, and to reduce uncertainty in model 

parameterization. There are only limited funds for this 

type of research; therefore, some expansion of NMFS’ 

process-oriented at-sea research capability is needed. The 

CAMEO program may be a vehicle for conducting studies to verify a mechanism. However, long-term seasonal 

monitoring of climate change related processes is needed 

to capture shifts in phenology, changes in behavioral 

responses or shifts in tolerances of marine fish. Programs 

like LOSI should provide funding for changes in the 

Arctic.

 Are ocean models good enough? Members of the breakout group recognized that there is a division between the 

daily spatial observations provided by satellite data and 

the Reynolds reanalysis of surface temperature, and the 

spatial data derived from ocean models. Ocean modelers should continually review the skill of their models 

relative to their ability to resolve observed features (e.g. 

fronts and eddies) and events.

 In the near-term, the stock assessment community will 

probably continue to work with ecosystem indicators. 

Therefore, efforts on how to extract ecosystem indicators from ecosystem models will continue to be a high 

priority.

◉ Circulation models can generate/explore hypotheses 

about impacts.

What Laboratory Studies Can Be Started to Assess 

Tolerances and Bio-energetic Responses of Living 

Marine Resources? 

Most of the projections currently published or under development assume that adaptation will not occur. Laboratory studies are needed to assess the tolerances of fish and 

shellfish to changes in temperature, pH, and oxygen levels. 

Synergistic impacts may further exacerbate the stress on 

fish. FATE and CAMEO do not currently fund fieldwork; 

therefore, there is a gap in NMFS’ capability to monitor, 

assess and project climate change impacts on marine ecosystems. One possible source of funding would be the 

Ocean Acidification program, in which laboratory projects are planned. If these projects could be expanded to 

include oxygen and temperature effects, this would be an 

efficient way to implement and fund this type of research. 

If laboratory research is initiated, NMFS stock assessment 

and ecosystem assessment modelers will need to identify 

methods to translate tolerances observed in laboratory 

studies to population levels in the field. 

What At-sea Experiments and Monitoring Could 

Be Started to Assess Tolerances and Bio-energetic 

Responses of Living Marine Resources? 

At-sea experiments and seasonal monitoring are needed 

to verify mechanisms observed in a laboratory setting or 

inferred from functional relationships used in models. 

Changes in survey design will probably be needed to monitor distribution shifts and changes in phenology. Field measurements and experiments are needed to inform stock assessment scientists and ecosystem scientists as to how the 

systems are changing relative to historical baselines. NMFS 

should strive to collect core life history rates for managed 

species across species’ ranges, particularly at the edges of 

their ranges. Spatial responses of fish and shellfish could be 

assessed by augmenting biophysical measurements during 

NOAA surveys with underway data collection (e.g. surface 

temperature, oxygen, pH, chlorophyll, and nutrients) and 

acoustics. Funding for this activity could be drawn from 

the stock assessment funding lines and IOOS. Range extensions would require new funding in the Arctic and perhaps 

the central Pacific. The LOSI program could provide funding for the Arctic. New programs will be needed to conduct 

field experiments to verify assumed behavioral responses to 

climate change. Temporary funding for this activity could 

be derived from CAMEO, while long-term monitoring of 

changes in predator-prey interactions and functional responses would require funding of programs like the Fisheries Interaction and Local Ecology program. 

How Can NMFS Facilitate Communication With 

Stakeholders to Establish Scenarios for Human 

Responses in the Face of Climate Change?

Members of the breakout group recommended that NMFS 

should engage the management and stakeholder communities in the discussion of scenarios for predicting climate 

effects on fish and shellfish. This could be accomplished 

through the Fishery Management Council review process 

or through separate workshops. The advantage of this type 
21

of engagement is that if the Fishery Management Councils 

and stakeholders are involved in the development of the 

models, they may have a greater understanding of the model 

products. 

23

Joint Session of the National Stock and 

Habitat Assessment Workshops

The Joint Session of the National Stock and Habitat Assessment Workshops was held with the intention of improving 

communication and collaboration between the stock assessment and habitat science communities, and represents 

the first time that an interactive meeting of the two groups 

has been held on a national scale. The session began with a 

series of invitational lectures by experts in the fields of stock 

assessment and habitat science to set the stage for the discussions that followed throughout the rest of the meeting. 

Keynote lectures were given by Churchill Grimes and Steven Murawski. Two theme sessions were held, during which 

invited presentations were delivered on the topics “Incorporating habitat information into stock assessments” and 

“Improving calibration and precision of resource surveys 

with habitat information”. Lastly, Joint Session participants 

moved into one of the three breakout sessions to further 

collaborate and discuss topics of mutual interest. Breakout 

Sessions focused on the themes “Using habitat information 

in survey design and analysis,” “Including habitat-specific 

life history rates in population models,” and “Using time series of habitat information in population models.” 

Joint Session Summary: Incorporating Habitat Information in Stock Assessments

Session Organizer: Stephen K. Brown (OST)

Rapporteur: Kristan Blackhart (OST)

Joint Session Top Recommendations

 Habitat data should be integrated into resource survey sampling design where available to improve the precision and efficiency of surveys.

 NMFS should expand its capacity to collect habitat information and develop a comprehensive repository for 

existing and new habitat information. The highest priority to address is expanded habitat mapping and classification.

 Expanded collection of environmental data should occur during existing resource surveys, and development 

and implementation of advanced sampling technologies should continue.

 Cooperation and data sharing should be pursued and existing partnerships strengthened to make the best use 

of available habitat information.

 The accessibility of existing habitat data should be improved to facilitate inclusion in the stock assessment 

and management processes.

Incorporating Habitat Information into Stock 

Assessments

The use of habitat data to inform and improve stock assessments has proceeded slowly, although a number of existing 

examples show promise that the field is moving forward. 

Ample evidence shows that habitat may affect underlying 

stock production and should be considered. Recruitment 

and growth are the most encouraging areas for improvement, although the specified goal of the essential fish habitat mandates is habitat-specific production rates. 

Several examples were given during the theme session of 

theoretical models that relate habitat effects to stock production. In many cases, theoretical models are necessary 

because habitat information is not available at the spatial or 

temporal resolutions necessary for model inclusion. Modeling capability exists at this point to deal with a variety of 

environmental data types and produce highly sophisticated 

models relating a variety of factors to stock production. The 

simulations discussed during the session provide promising 

results and point to the need for additional data collection 

and refined information on the relationships between species and habitat. 
24

Perhaps the next possible step is to begin including a greater 

number of environmental factors that affect the pelagic environment into stock assessments. An increasing number of 

models have begun to incorporate predator/prey effects, but 

continue to ignore environmental effects. A large amount 

of physical oceanographic and environmental data could be 

collected during the course of resource surveys, especially 

acoustic surveys, and some is already being collected. Because of this, increased collection of environmental data 

and integration into stock assessment models would not be 

as difficult as other proposed measures. Such data could be 

used for multispecies assessments as well.

The usefulness of incorporating habitat information into 

stock assessments varies based on a number of factors, especially the species’ life histories. Reducing the uncertainty in 

predictions of stock productivity through the use of habitat 

information is best for stocks with shorter life spans, good 

demographic data, known life stage habitat-specific transitions, and restricted spatial distributions. Another area 

where improved habitat information will be useful to stock 

assessment efforts is the use of habitat-based survey density 

estimates to predict stock abundance; such efforts have been 

successful for species that live in habitats that cannot be surveyed using traditional sampling techniques (e.g. cowcod), 

and also for data-poor stocks where assessment efforts have 

been less successful due to a lack of data or high levels of 

uncertainty in the data (e.g. queen conch).

Improving Calibration and Precision of Resource 

Surveys with Habitat Information

An important area of collaboration between the stock assessment and habitat science communities is the potential 

improvement and refinement of resource surveys using 

habitat information. As the prevalence of spatial management increases, traditional data sources (i.e. fishery dependent) may become less available and there is an increased 

need for fishery-independent data. Integrating habitat data 

into sampling design may improve precision and efficiency 

of surveys. 

One of the simplest ways to integrate habitat data into 

sampling design is to use habitat factors as stratification 

variables. This approach only works in areas that have been 

adequately mapped at a spatial resolution that is sufficient 

for the sampling design. An important consideration is 

sampling allocation—reducing replication where possible 

will increase efficiency and allow for increased areas to be 

sampled. 

A number of advanced sampling techniques, including optical and acoustic technologies, are being developed that 

can be used to advance both habitat and stock abundance 

surveys. Many of these technologies are able to collect environmental and population data concurrently, providing 

data that will be readily available to feed into stock assessments. 

Reports from Breakout Groups

Using Habitat Information in Survey Design and Analysis: Comprehensive mapping and classification, at resolutions that are compatible with stock assessment work, are 

a critical need that must be met before habitat information 

can be incorporated into survey design, analysis, and stock 

assessments. Although substantial habitat information already exists, only a few examples exist of systems (e.g. west 

coast salmonid streams, the Florida Keys reef track) where 

such comprehensive habitat information is available. This 

points to the need both for expanded capacity to collect 

habitat information, and the development of a comprehensive repository for existing information. Such a repository 

would also serve to identify data gaps.

Survey design and analysis can be improved in a number 

of ways by considering habitat information. In the design 

phase, habitat information can be used to facilitate stratification and more efficiently stratify sampling resources. Use 

of habitat data before and during sampling allows for adaptive sampling of patchily distributed species that move in 

response to changing environmental conditions and is required for efficient sampling. Habitat maps can also be used 

to post-stratify survey results or in model-based standardization, although care should be exercised to not de-trend 

true abundance signals due to changing habitat characteristics over time. Habitat information can serve as a proxy or 

index of abundance in assessment models for some stocks. 

Additionally, habitat data may be used to recreate historical 

patterns of abundance, determine initial conditions or carrying capacity, or predict responses to changes in habitat. 

Expanding existing resource surveys to collect increased 

habitat information concurrently with fish data will benefit both habitat and stock assessments. Multibeam habitat 

mapping represents the state of the art for habitat classification, although the optimal technology is likely to be habitat-specific. Continued development of technology that 

will allow efficient sampling of non-trawlable areas, as well 

as methods for blending non-trawl data with trawl data, is 

needed. In areas that are heavily fished, high resolution ves-
25

sel monitoring system (VMS) data can provide important 

information for assessing fishing effects on habitat. Better use of available information, such as ocean circulation 

models, should be pursued to the fullest extent possible for 

applicable resources. Cooperation and data sharing within 

NOAA, with other governmental agencies, and with private industry should be pursued and existing partnerships 

should be strengthened to make the best use of available 

habitat information.

Including Habitat-Specific Life History Rates in Population Models: Different life history rates can be measured 

on a habitat-specific basis, although some rates are better 

suited for use in population models. Growth, recruitment, 

and survival were identified as the life history variables most 

important to modeling population dynamics, although this 

may vary by species. Growth is likely the easiest life history 

rate to measure by habitat type, and can be measured both 

in lab and field studies. Mortality is also likely to be important, although measuring survival is perhaps less feasible 

and species-dependent. Habitat-specific measurements of 

fishing mortality may be attainable if there are differences 

in fishing effort across habitats or in relation to regulatory 

areas.

Determining movement rates of various life history stages 

between habitat types is an essential first step in measuring 

habitat-specific life history rates. This information, in addition to well defined habitats, is necessary for determining 

habitat fidelity. Improved habitat data at the microhabitat 

scale may not be necessary to determine habitat-specific 

vital rates for use in population models; existing factors, 

such as catch, are often aggregated across large areas so vital 

rates could be measured at a similar spatial scale. The scale 

of habitat data does not necessarily need to be finer than the 

scale of the biological data it is used with for the purposes of 

stock assessment. 

Two different general types of models may be used to incorporate spatial variation: single-area models, and spatiallyexplicit models. Spatially-explicit models are more useful 

when habitat-specific life history rates vary substantially or 

when spatial management is used. Spatial models not only 

allow for regional management, but also address the issue 

of local depletion and provide a better fit to spatially-structured data.

Using Time Series of Habitat Information in Population 

Models: Use of environmental time series in population 

modeling has progressed further than other attempts at 

incorporating habitat information into stock assessments. 

A range of examples exist of habitat time series variables 

that have been used in population dynamic models. These 

include temperature-dependent survey catchability (e.g 

Bering Sea flatfish); spatially explicit temperature and chlorophyll (pollock); and eddies and recruitment (sablefish). 

Factors that constrain incorporation of environmental time 

series into assessment models include mismatches between 

the spatial distribution or resolution of habitat data and species ranges and a lack of available information on the linkages between particular species population processes and 

habitat variables. In particular, species-specific conceptual 

models need to be developed to further investigate habitatlinked processes. 

Data availability is another important constraint to the use 

of habitat time series in stock assessments. Although a range 

of habitat data may be available, many stock assessment scientists do not know what is available nor understand how 

to gain access to available data. Improved communication 

between habitat and stock assessment scientists, especially 

at the regional level, will be necessary to improve coordination between the two disciplines: habitat ecologists and 

data managers need to make data more available and easy 

to incorporate into assessments, and stock assessment scientists need to identify the kind of habitat information that 

would be most useful for improving stock assessments, and 

what formats are most appropriate for use in modeling efforts.
26

Joint Session Breakout 1a: Using Habitat Information in Survey Design and Analysis, 

Groundfish/Coastal Pelagic/HMS & Pelagic Groups 

Facilitators: Vincent G. Guida (NEFSC), Paul Spencer (AFSC)

Rapporteur: Mark Sramek (SERO)

Discussions during this breakout session focused on three 

trigger questions: 

 Question 1: What is the current state of the art and future potential for incorporating habitat information into 

survey design and analysis?

 Question 2: How can habitat information improve 

analysis of fishery data?

 Question 3: What new projects are feasible to implement 

in the next five years if funding was available? What are 

longer term research needs?

Groundfish Subgroup (~20 members)

Q1 ~ State of the Art: Most trawl survey designs are based 

on random stratified sampling in which strata are determined by depth, sometimes along with latitude, with no 

consideration for habitat types or boundaries. However, 

in at least one case hydrographic data, including dissolved 

oxygen, are used as covariates during analysis of catch data. 

One exception is the case in the Southern California Bight 

in which rockfish surveys are randomized within habitat 

classes based upon multibeam sonar mapping. 

Q2 ~ Improvement of Analysis: Discussion focused mainly 

on obtaining better estimates of non-trawlable areas with 

video, photo, and acoustic techniques to measure fish abundance on these habitats, as well as long line, pole fishing, 

and pot trapping techniques. Discussion also included how 

habitat knowledge might improve surveys where trawls are 

employed. Of particular importance was the issue of catchability, a parameter that varies with habitat type. Developing catchability values for differing habitats could reduce 

variance of stock estimates, but only if the locations of habitats and their boundaries are known.

Q3 ~ Needs in the Next Five Years:

• Develop improved habitat maps—despite the large areas 

involved and large costs, this would be a huge advantage. 

• Develop technology for the study of non-trawlable areas 

and for blending that data with trawl survey data (“quantitative mixing of apples and oranges”). 

• Add “cheap improvements” where possible. For instance, 

add data collection on to existing surveys, including 

chlorophyll a, zooplankton, and additional physical 

oceanography measurements.

Combined Pelagics Subgroup (Coastal Pelagic and 

HMS/Pelagics; ~15 members)

Since the number of participants for the Coastal Pelagic 

and Highly Migratory Species (HMS)/Pelagic subgroups 

was small, the two were combined into a single Combined 

Pelagics subgroup for breakout discussions. 

Q1 ~ State of the Art: Sardine, anchovy, and mackerel examples include environmental data collection, particularly 

water column data, and these can be used for adaptive sampling (i.e. going where and when the pelagic stocks are). A 

variety of sampling methods, dividing roughly into categories of physical capture (multiple opening and closure nets, 

visual processing systems, conductivity/temperature/depth 

sensors, bottom grabs, etc.), tagging (various kinds), and 

remote sensing (stereo cameras, video plankton recorder, 

various acoustic methods), and combinations of methods 

are in use. As habitat use is patchy and moving in response 

to environmental conditions, efficient survey requires adaptive sampling (i.e. going to where the stocks are rather than 

Top Recommendations

 Technology for the study of non-trawlable areas and for blending non-trawl and trawl survey data should be 

further developed.

 “Cheap improvements” (i.e. adding environmental data collection to existing resource surveys) should be 

added where possible.

 Improved statistical models, simulations, and analytical tools should be developed to gain a better understanding of the temporal dynamics of habitats.
27

to fixed areas or strata). Efficient sampling design therefore 

requires adaptive sampling—the use of habitat data before 

and during surveys to be able to locate and follow areas of 

high probability for target species. 

Q2 ~ Improvement of Analysis: A large amount of data, including circulation models, is available in some regions for 

planning cruise tracks and sampling. Accurate ocean circulation models are important for this purpose, as they can 

provide predictions of habitat conditions months ahead 

of time. These are probably not used to the fullest extent 

possible at this time. In addition to cruise planning, habitat 

information can improve the scaling of larval abundances. 

It can also be used for post-stratification of data after collection to reduce the catch variance. 

Q3 ~ Needs in the Next Five Years: Additional tagging 

studies to track pelagic resources is needed. This is essentially using the animals themselves as sampling platforms. 

Other needs include better statistical models and simulations, better analytical tools, a better understanding of temporal dynamics of habitats. 

Since migrations and spawning events do not always occur 

at prescheduled times (unlike cruise schedules), more “eyes 

at-sea” are needed to catch events as they occur—suggestions are for the use of ships of opportunity, fishing vessels, 

and cooperative programs with other agencies. Also needed 

is a better understanding of causation for movements and 

reproductive events to provide improved predictive power 

to be able to direct surveys more effectively.
28

Joint Session Breakout 1b: Using Habitat Information in Survey Design and Analysis, 

Diadromous/Estuarine Dependent/Reef & Untrawlable Groups 

Facilitators: John F. Walter (SEFSC), Stephen Ralston (SWFSC)

Rapporteur: Terill Hollweg (OHC, Restoration Center)

Overall Summary

The unanimous opinion of the group was that comprehensive mapping and classification are critical for incorporating 

habitat information into survey design, analysis, and improving fisheries assessments. In systems with such mapping, of 

which at least two were identified (i.e. west coast salmonid 

streams and the Florida Keys reef track), a broad suite of 

improvements in sample design, survey analysis, and stock 

assessment can be obtained by considering habitat. Habitat information can improve surveys a priori in the design 

phase through facilitating stratification to more efficiently 

allocate sampling resources. Post-survey improvements can 

be obtained from using habitat maps to either post-stratify 

survey results or in model-based standardization to account 

for factors that the sampling design cannot control. 

The group felt that multibeam habitat mapping represents 

the state of the art for habitat classification, but that the optimal technology (e.g. sidescan sonar, LIDAR [light detection and ranging], aerial photography, and satellite remote 

sensing) will likely be habitat specific. In the short-term, 

substantial habitat information already exists and there is 

a need for a comprehensive repository for existing information, which will serve to identify gaps. Existing fishery 

surveys should be staffed and equipped to obtain habitat 

information to fill in gaps. 

General Recommendations 

1) Expand the capacity of existing fishery survey operations to collect and store habitat data at the same 

time as the collection of fishery data (benthic grabs, 

multibeam, and sidescan mapping capability). 

2) Create a central repository of habitat data, specifically new multibeam data, similar to the Pacific Coast 

Ocean Observing System (PaCOOS; http://oceanwatch.pfeg.noaa.gov/PaCOOS/). The NOAA 

Essential Fish Habitat Mapper (http://sharpfin.nmfs.

noaa) and Multipurpose Marine Cadastre (www.csc.

noaa.gov) may provide useful templates or may be 

potential repositories of information. 

3) Explore the potential to obtain existing data from 

other governmental agencies (e.g. Bureau of Ocean 

Energy Management, Regulation and Enforcement 

[the former Minerals Management Service], U.S. 

Geological Survey) and nongovernmental entities 

(e.g. oil companies). Some partnerships already exist 

(i.e. http://www.gulfofmexicoalliance.org).

4) Create a NOAA-wide statistical support team using 

existing expertise. Sampling design, analysis, and considerations of design changes or modeling in response 

to habitat information may require a high level of 

professional statistical support.

5) Include a ‘habitat’ time series and/or narrative as 

background material in stock assessments (i.e. what 

is known about the habitat, how has it changed, and 

how might the time series of landings and catch per 

unit of effort (CPUE) be interpreted in terms of 

changes in habitat).

6) Caution should be exercised in model-based standardization of survey abundances in light of changing 

habitat characteristics. There is a difference between 

developing habitat models and standardizing survey 

data to account for habitat effects. Model-based 

standardization of survey CPUE for use as indices 

should only account for factors which affect survey 

catchability (i.e. if a trawl fishes differently on mud or 

sand). However, if the proportion of mud is increasTop Recommendations

 The capacity of existing resource surveys should be expanded to collect habitat information concurrently.

 Create a comprehensive central repository for existing and future habitat data, specifically new multibeam 

data, and use to identify current information gaps. The Essential Fish Habitat Mapper or Multipurpose Marine Cadastre may provide useful templates or serve as potential data repositories.

 NMFS should facilitate greater use of vessel monitoring system (VMS) data beyond enforcement. Such data 

provides spatially-explicit information for assessing fishing gear impacts on habitat.
29

ing over time, a standardization model could detrend 

a true abundance signal.

Habitat Subgroup Discussions

The larger breakout group split into smaller subgroups 

based on habitat types for further discussions. The three 

subgroups were: Diadromous, Estuarine Dependent, and 

Reef/Untrawlable.

Diadromous Fishes: Because of the life history bottleneck 

of returning to natal or nursery streams and rivers, the linkage between diadromous fishes and habitat is extremely 

direct. The major issue discussed by the group was NMFS’ 

role in anadromous fish assessment and management, given 

the multiple jurisdictions and entities involved. The group 

felt that the state of the art was a comprehensive mapping 

and classification of all known spawning areas, such as exists for Pacific salmonids. However, while individual states 

have taken various initiatives to map and classify habitats, 

such a comprehensive mapping has not been conducted for 

all east coast diadromous fishes. Nevertheless, substantial 

work has been accomplished by individual states, government agencies (the U.S. Geological Survey, U.S. Fish and 

Wildlife Service), and other entities for which NOAA 

might serve as a strong partner. Further, given the critical 

role that diadromous fishes play in the marine ecosystem, 

explicit consideration of the spawning and nursery habitats 

of diadromous fishes will fall under the NOAA mandate 

for ecosystem considerations. 

Estuarine Dependent: Estuarine dependent species share 

similar logistical difficulties with diadromous fishes, in that 

multiple agencies collect habitat information using different methods. Most estuarine dependent species are managed under state or intrastate management authority. A recommendation from the group is that NOAA may facilitate 

coordination of habitat monitoring, assessment, and classification programs through state-Federal partnerships such 

as the Southeast Area Monitoring and Assessment Program 

(SEAMAP). A particular logistical problem for incorporating habitat information into survey design and analysis is 

the extreme temporal variability of estuaries created by tidal 

and seasonal dynamics. These dynamics complicate presurvey stratification based upon habitat and may elevate the 

importance of post-survey stratification or model-based survey standardization. For example, if a survey cannot sample 

a habitat on all tidal cycles, it may be possible to incorporate 

a tidal cycle model into survey abundance estimates. It was 

the view of the group that comprehensive habitat surveys 

and maps are needed before habitat per se can be used to 

improve resource survey design and analysis.

Reef/Untrawlable: Reef/untrawlable habitats represent 

unique environments for which the state of the art is high 

resolution maps of specific habitats (e.g. Flower Garden 

Banks, Heceta Bank, coral reefs) obtained with multibeam sonar mapping or satellite imagery. The main limitation is that, like estuaries, relatively few habitats have been 

mapped, leaving substantial gaps in the information base. 

Some of these gaps can be filled by collecting data during 

ongoing surveys. Further, much of this high resolution information may have already been collected by the Bureau of 

Ocean Energy Management, Regulation and Enforcement 

(the former Minerals Management Service) and/or oil 

companies and it may be possible to obtain non-proprietary 

versions of the information. As these habitats can be heavily fished, high resolution vessel monitoring system (VMS) 

data also represents state of the art information for assessing 

fishing effects on habitat. Gaps in multibeam habitat mapping represent major impediments to incorporating habitat 

information into surveys and assessments. 

Trigger Questions

Three trigger questions were posed to the group to stimulate and focus discussions. The questions were:

1) What is the state of the art and future potential for 

incorporating habitat information into survey design 

and analysis?

2) How can habitat data improve analysis of fishery 

data?

3) What new projects are feasible to implement in the 

next five years if funding was available? What are 

longer term research needs?

Q1 ~ State of the Art:

 State of the art technology is multibeam habitat mapping, though the best technology (sidescan sonar, aerial 

photography and satellite remote sensing) will likely be 

habitat-specific. 

 Remotely operated vehicle, autonomous underwater 

vehicle, and glider technology can be platforms for 

deployment.

 VMS provides spatially-explicit fishing effort data. 

 Habitat information can be incorporated a priori in 

stratified sampling or a posteriori through post-stratification or modeling.
30

Q2 ~ Improvement of Analysis: 

 Pre-and post-survey gains in sampling efficiency (e.g. 

Bohnsack’s Visual Census of Florida Reefs). Habitat 

mapping can facilitate survey stratification. Survey data 

can also be post-stratified after collection or habitat 

information can be incorporated into model-based abundance estimates.

 Improved standardization of fishery-dependent CPUE 

(coupled with either high spatial resolution catch rate or 

VMS data).

 Improved potential to recreate historical patterns of 

abundance, determine initial conditions or carrying 

capacity and to predict responses to changes in habitat. 

The group identified the following as important research 

questions: 

◉ How has loss of spawning streams reduced carrying 

capacity of diadromous stocks? (Diadromous Fishes)

◉ How has the increase in hard substrate and oil rigs 

affected carrying capacity of red snapper? (Reef/Untrawlable)

◉ How has the loss of oyster reef or seagrass habitat 

affected carrying capacity and function of estuaries? 

(Estuarine Dependent)

• Habitat can serve as a proxy/index for potential abundance in the assessment model.

• Improved understanding of ecosystem changes that have 

occurred during the time series of an assessment model.

Q3 ~ Needs in the Next Five Years: 

• Create/expand central repository of habitat data, 

specifically new multibeam data, similar to PaCOOS in 

the Pacific. 

• Comprehensive mapping of habitat quality of current 

and historic spawning tributaries for the 11 diadromous 

fish species on the east coast of North America.

• Conduct surveys in estuaries to map habitat availability 

and extent.

• Facilitate the greater use of VMS data beyond enforcement. 
31

Joint Session Breakout 2a: Including Habitat-specific Life History Rates in Population 

Models, Groundfish/Reef & Untrawlable/Diadromous Groups 

Facilitators: Richard S. McBride (NEFSC), Eric Bjorkstedt (SWFSC)

Rapporteur: David Dale (SERO)

Three trigger questions were used during this session to engage participants on the subject of including habitat-specific life history rates in population models:

1) What life history rates are useful and feasible to measure on a habitat-specific basis?

2) How can habitat-specific life history rates be incorporated into population models? Does this require 

spatially-explicit models?

3) What new projects are feasible to implement in the 

next five years? What are longer term research needs?

Participants included NMFS scientists and managers identifying themselves as most strongly associated with the 

‘groundfish’ or ‘reef/untrawlable’ categories, with only a few 

associated with diadromous fishes or habitats. The following summary synthesizes the group’s lively and wide-ranging 

discussion in response to the above questions.

The discussion group began by identifying life history variables relevant to population models as well as by defining 

what constitutes ‘habitat’. The following equation captured 

several life history rates of interest:

P = (G + R) - (F + M)

Where P = production, G = growth, R = reproduction (or 

recruitment), F = fishing mortality, and M = natural mortality of a population. Age, size, or ontogenetic stage also 

affect movement between or residency within habitats, 

thereby affecting abundance, distribution, and production 

of fish stocks. 

In terms of the discussion, defining habitat was just as interesting as identifying the life history variables. Characterizing habitat by physical or structural types (e.g. reef, 

mangrove, estuary) was familiar to everyone but further 

discussion revealed the limitations of such static categories. In particular, replicate habitat types are embedded in 

larger-scale environments. Some of these environments may 

be easy to measure, understand, and predict (e.g. latitudinal 

clines in temperature, estuarine salinity gradients, or crossshelf depth zones), whereas others may be less so (e.g. basinscale climate indices such as the Pacific decadal oscillation, 

North Atlantic oscillation, or El Niño-southern oscillation). Time itself is a dimension of habitat, because habitats 

can change over time due to either natural (succession) or 

anthropogenic drivers. Even when systems are stationary 

over long periods, they can exhibit shorter-term dynamics 

of abiotic (seasonal temperatures) or biotic (predator-prey 

fields) components. 

Detailed habitat maps are uncommon, and while this is 

frustrating to habitat ecologists, this is not necessarily an 

obstacle to including habitat-specific vital rates in stock assessments, if the vital rates themselves are not measured at 

a similarly fine spatial or temporal scale. For example, catch 

is often aggregated across large areas or cannot otherwise 

be disaggregated at the microhabitat scale. Thus, improved 

habitat data gained by advances in technology or partnerships may have limited scope to improve opportunities 

for fishery models to use habitat data. On the other hand, 

simple—but well established—data sets of temperature, 

salinity, depth, and ocean-climate indices are particularly 

promising sources of habitat information for incorporating 

into stock assessments in the near term. 

The discussion group tried to generalize some conditions 

Top Recommendations

 Develop reconstructions of historical habitat conditions (analogous to catch reconstructions) to provide 

context for future assessments.

 Hold regional workshops to develop specific, regionally relevant demonstration projects.

 Promote collection of ecosystem data to support comprehensive inclusion of dynamic habitat in future assessments.

 Construct prototype assessment models capable of assimilating data with heterogeneous spatial resolutions.
32

where existing population models could be improved with 

habitat- or spatially-specific data. Most assessment models 

assume a well-mixed stock of individuals that exhibit the 

same average life history. Habitat-specific variability exists, 

but is unspecified, in the data. When habitat can be specified as the source of life history rate variation, then it can 

be used as a basis for converting these overall mean parameters into weighted-means that reflect variability in habitats 

sampled in a manner analogous to stratified abundance estimators. Growth is often the easiest vital rate to determine 

and is therefore the strongest candidate for measuring at 

a habitat-specific scale. Reproduction and movement are 

quantified poorly for most stocks, but examples should be 

developed further where exceptions exist. Estimating natural mortality is likely to remain very difficult to measure. 

However, habitat-specific fishing mortality may be feasible, 

at least if there is strong contrast of fishing effort across spatial gradients or in relation to ‘regulatory’ habitats, such as 

closed or otherwise protected areas. In this regard, the fishing industry’s view of the seascape is another important way 

to characterize habitat.

General concepts from the literature that support the idea 

of subgroups within a population that could be habitatbased are that of fish “platoons” (Phil Goodyear) or “contingents” (Dave Secor). Some more specific examples that 

were discussed during the session included: 

 Sea scallops grow faster in shallower areas of the continental shelf, and slower in deeper waters, so that habitat-specific growth rates are used to predict yields and 

therefore the opening and closing of fishing areas. 

 Bluefin tuna is managed by habitat areas, albeit on a very 

large scale. 

 Fishing mortality rates of hogfish vary along a spatial 

gradient related to fishing effort and this affects demographic patterns of this species in south Florida. 

 New Zealand hoki, a groundfish, was noted as a case 

where spatially structured assessments are being developed, although not based on specific habitat types. 

 A multispecies, end-to-end model in the Bering Sea is 

an active project that will integrate primary production, 

habitat, fishing and markets. 

Ideally, process-oriented studies are used to develop mechanistic models. The findings of such studies are not, however, 

always unequivocal and the data sets relevant for complex 

models may not extend beyond a few years or decades, 

whereas fishing rates may have had significant effects on populations for decades or even centuries. Mechanistic models 

may be the best way to advance confidence in the predictive 

power of NMFS stock and ecosystem assessments, particularly under climate change scenarios that depart from the 

observational record, so continued investment and development are needed. Nonetheless, the mission of NMFS can 

still be met by less sophisticated models, so scientists and 

managers need to fully use what is available today.

Habitat-specific information can be directly injected into 

the stock assessment process through presentations at data 

review meetings or by submitting documents to be included 

in the final assessments. Examples of potential data sources 

or studies include synthesis of ship- or trawl-track data and 

information on habitat recovery rates. It was proposed that 

reconstructions of historical habitat conditions would provide useful context for assessments. When essential habitat 

loss occurs, this will affect rebuilding targets without restoration or mitigation.

Discussion of potential near-term research efforts or demonstration projects yielded the following list of recommendations:

 Examine potential to integrate habitat-weighted average 

vital rates in current assessments. 

 Include presence-absence (or categorical density indices) 

habitat information in assessments.

 Enhance efforts to estimate vital rates with sufficient frequency and spatial coverage to relate these to the habitat 

level within stock boundaries in future assessments. 

 Promote collection of ‘ecosystem’ data, including information on predator-prey interactions to support comprehensive inclusion of dynamic habitat in assessments. 

 Develop habitat reconstructions analogous to catch reconstructions, so that future assessments can move away 

from assumptions that habitat-related quantities (e.g. 

production or capacity) are stationary. 

 Construct prototype assessment models capable of assimilating data with heterogeneous spatial resolutions. 

Such a model can be used to learn how best to ‘scale 

down’ assessment models or ‘scale up’ habitat data by exploring a continuum of model structures (‘global‘ models 

to individual-based models).

 Scale up current, detailed surveys (e.g. remotely operated 

vehicle survey of Heceta Bank) to the stock level to better inform assessments.

 Integrate population models as a tool for understanding 

or predicting the effects of habitat restoration, particularly for diadromous fishes.
33

 Account for insights from the study of marine protected 

areas and associated fisheries. Careful design will be 

required for these studies to account for any trends in 

habitat quality between protected and open areas.

 Integrate outputs from ocean circulation models and remote sensing data, including estimates of production and 

transport, in habitat evaluations and assessments across 

diverse taxa. In doing so, pay close attention to conditions that enable or disable continuity along species’ life 

cycles.

 Where practical, use otolith microchemistry or other 

natural tags as tools for evaluating habitat-specific vital 

rates at scales relevant to assessments.

 Plan future workshops to develop specific, regionally 

relevant demonstration projects.
34

Joint Session Breakout 2b: Including Habitat-specific Life History Rates in Population 

Models, Coastal Pelagic/HMS & Pelagic/Estuarine Dependent Groups 

Facilitators: Jon Brodziak (PIFSC), Lawrence Rozas (SEFSC)

Rapporteur: Joe Nohner (OST)

During this breakout session, participants identified a suite 

of life history rates that were feasible to measure and that 

may be useful for modeling population dynamics. Of these, 

growth, survival, and recruitment rates are thought to be 

both measurable and important for population modeling. 

Although the focus was mainly on single species models 

of population dynamics, the potential importance of multispecies and/or ecosystem models was also recognized. In 

this context, it is thought that measuring life history rates 

of many species by habitat type is a more complex problem, 

but could be approached in a similar manner if habitat type 

was meaningful and clearly defined.

The life history rates that are most useful and feasible to 

measure by habitat type will vary according to the individual species being considered. Nonetheless, growth rate is considered to be the most readily available life history rate to 

measure by habitat type. Growth rates could be measured in 

the laboratory under ideal conditions and compared with 

growth rates measured in the field among various habitat 

types. Mortality rates are also thought to be important, but 

the feasibility of measuring survival is considered to be species-dependent. Possible methods for measuring habitatspecific mortality rates include tethering experiments or 

tagging studies. In addition, the role of habitats in relation 

to natural mortality may be inferred from results of laboratory studies showing effects of habitat characteristics on 

predator-prey relationships.

Other rates include migration rates, predation rates, fishing 

gear capture rates among habitat types, and reproductive 

rates or fecundity. It is noted that population attributes that 

influence life history rates within a habitat type should be 

considered when measuring life history rates. Examples of 

such attributes are the age structure of populations, bioenergetics (assimilation and respiration rates), rates of development at each life history stage, changes in behavior with 

development, presence of disease in populations, gonad 

development, and gender (especially for gender switching 

species).

Understanding movement rates of life history stages among 

habitat types is a crucial first step for determining habitatspecific life history rates. Without an a priori understanding of movement, it is difficult to see how habitat-specific 

rates can be determined with any certainty. For example, if 

habitat is well defined but movement rates among habitat 

types are not known, there would be no clear fidelity of life 

history stage to habitat type. In contrast, if movement rates 

among habitat types are low, as for example, in sessile life 

history stages, then the estimation of habitat-specific life 

history rates would seem to be feasible.

Single species population models are classified into two 

types: 1) models with habitat-specific rates operating on explicitly defined habitat “boxes” representing portions of the 

population using different habitats; and 2) single-area models with weighted averages of life history rates within habitat types in the area. These two model types are thought to 

represent the general approaches being used to incorporate 

spatial variability into population models. Both approaches 

sample specific habitats, with the first utilizing sampling to 

estimate two different rates and the second utilizing stratified sampling to create one overall rate. A specific example 

of a model operating on habitat “boxes” would be an oyster 

population represented by several subareas of reefs, while an 

example of a single-area model would be a rockfish population in a single stock area with life history rate variation 

among habitat types and habitat-averaged life history rates.

Spatially-explicit models are most useful and appropriate 

when habitat-specific life history rates differ substantially. In 

particular, if adult life history stages are sessile, then spatial 

models would be simpler to develop. For species with more 

Top Recommendations

 Population attributes that influence life history rates within a habitat type should be considered when measuring life history rates.

 A crucial first step for determining habitat-specific life history rates is understanding movement rates of life 

history stages among habitat types.
35

mobile life history stages, some information on movement 

rates among habitats would be needed for spatial models to 

be feasible. Another case where spatial models are necessary 

is when population management includes spatial management by subarea. Spatial population models offer advantages and are useful because they allow for regional management, can address the issue of local depletion by region, and 

can provide a better fit to spatially-structured data. 

In terms of the spatial scales that are important for population modeling, rates may vary at different biological 

scales than the scales that are important for fishing fleets 

and/or fishery management. Thus, it is important to consider whether there is a potential mismatch in scale between 

population-scale life history rates and human impacts on 

the population as a whole when formulating population 

dynamics models with spatial heterogeneity in life history 

rates.

While time limited the generation of a complete list, examples of future projects that could be implemented in the 

next five years include: 1) modeling spatial differences in 

life history rates of pink shrimp in South Florida nursery areas and impacts on recruitment dynamics; and 2) modeling 

spatial differences in mortality rates of Chinook salmon between freshwater and tidal rearing habitats by river system 

and the impacts on run size and fish production.
36

Joint Session Breakout 3: Using Time Series of Habitat Information in Population 

Models, All Groups 

Facilitators: Patricia Livingston (AFSC), Kirsten Larsen (OST), Rick A. Hart (SEFSC), Correigh Greene (NWFSC)

Rapporteurs: David Rydene (SERO), Lora Clarke (Office of the Assistant Administrator)

An important first step to take before incorporating habitat time series information into population models is to 

identify population processes most likely to be linked to 

habitat factors. The primary population processes include: 

growth, survival, reproduction, foraging, competition, and 

movement. Observation processes linked to habitat, such as 

survey selectivity, should also be considered. The Fisheries 

and the Environment Program (FATE) has made progress 

in this area, particularly with respect to the incorporation 

of oceanographic indicators into stock assessment, but this 

work should be expanded to include other habitat variables. 

Examples of time series of habitat variables that have been 

incorporated into models include:

 Time series of predator abundance linked to predation 

mortality in multispecies models or single species models 

that include predators. 

 Temperature-dependent growth. 

 Temperature-dependent survey catchability (e.g. Bering 

Sea flatfish). 

 Spatially-explicit temperature, chlorophyll, or eddies and 

recruitment (e.g. pollock, sablefish).

 Oceanographic data and larval dispersal.

Sampling of habitat is also a consideration in development 

of time series. Gear limitations and fixed stations do not always allow for new, expanding, or different aspects of habitat to be sampled. This may vary by ship crew experience, 

availability of funding, and time constraints. It is also important to develop time series data on species ranges. Range 

of available habitat is changing and it will be important to 

link changes in species spatial distributions with changes in 

spatial extent of habitat.

From a management perspective, there is also a need to consider how NMFS can better manage and preserve habitat 

to improve stock status. Managers are interested in understanding what habitats are most important to protect from 

human impacts. Thus, time series of human-induced stressors are also important to develop. Some species have historical time series that could be utilized. One example is time 

series data regarding impediments (e.g. dams, etc.) to diadromous fish movement. Examining the historical forage 

base also has important consequences for rebuilding stocks. 

Another example is data on coastal land use practices (e.g. 

nutrient loading, enhanced turbidity, etc.). Hypoxia is also 

an important consideration. This could directly influence 

mortality, spatial distribution, and growth—lethal and sublethal effects. It is noted that NMFS’ focus on the seafloor 

and benthic effects should be increased. The seafloor is important habitat and certain areas need to be protected for 

shelter.

Question: What are some existing benthic habitat time series data sets that are available?

 Kelp flyover studies on the west coast provide important 

information on changes in the percentage of cover. Such 

data can be used to link availability of refuge to abundance.

 In the Bering Sea there is a survey to monitor the abundance of benthic invertebrates (sponge, coral).

Top Recommendations

 Population processes (e.g. growth, survival, reproduction, etc.) and observation processes (e.g. survey selectivity) that may be linked to habitat factors should be identified.

 Species-specific conceptual models of habitat relationships need to be developed as an initial step towards 

defining habitat-linked population models.

 Data collection should be focused on variables that are likely to be important to population or observation 

processes based on conceptual models or focused experimental studies.

 Habitat scientists should create metadata on habitat time series on a regional basis and make it available to 

the stock assessment community.
37

 There is habitat data (% coral cover, % algal cover) and 

species abundance data for the Florida Keys dating back 

to 1979.

These habitat variables would need to be linked to particular species population processes before they could be used. 

Species-specific conceptual models of habitat relationships 

need to be developed as an initial step towards defining 

habitat-linked population models. 

Difficulties in determining linkages between species responses to habitat changes may occur when there are longterm, weakly quantified changes such as estuarine habitat 

degradation. In some situations, changes may be subtle, 

occur on decadal time scales, and involve multiple habitat 

variables. Thus, relationships may be difficult to understand, particularly if the effects are nonlethal. Identification of sentinel species may be a productive area to focus 

on along with thinking about carrying capacity. With additional steps (lab studies, etc.) these measurements could 

provide the information necessary to understand relationships and to identify critical thresholds. For salmon, there 

are several examples of linking habitat availability (woody 

debris and other factors such as riparian conditions) to 

stock condition. It will be a priority to focus data collections on variables that are likely to be important to population or observation processes based on conceptual models 

or focused experimental studies. Some areas that may prove 

more tractable for study would be those involving relatively 

sessile organisms that have strong habitat associations at a 

particular life history stage.

A major impediment to advancing the incorporation of 

habitat time series into stock assessments is having comprehensive listings and easy access to habitat data. Stock 

assessment scientists generally do not know what habitat 

data is available. Scientists in some regions are developing geographic information system (GIS) layers of habitat 

variables, but there is a need to show that data is useful to 

others before expanding these efforts. One way to advance 

these efforts would be to promote enhanced communication between habitat and stock assessment scientists. Habitat scientists have made considerable progress in the ability 

to predict habitat changes and distributions, but habitat 

scientists are not sure how this will be built into stock assessments. They need to understand what type of habitat 

information is desired and the appropriate form to be useful 

for stock assessments. This would likely need to occur at a 

regional level.

A number of suggestions was made with respect to nearterm areas of research:

 Create metadata on habitat time series on a regional basis 

and make available to stock assessment scientists.

 Create a GIS ocean habitat atlas that would assist stock 

assessment scientists and aid in marine spatial planning 

efforts (note: original data resolution would also need 

to be preserved elsewhere to allow maximum flexibility 

for analytical purposes). In some regions, these atlases 

are available for near shore habitats, but not for offshore 

habitats. Such an atlas would provide useful information 

on spatial distribution and will be important as a transition is made to multispecies and ecosystem management 

plans. 

 On a regional basis, compile a list of existing habitat 

time series and do correlations with residuals from stock 

assessments. 

 Perform studies to predict biogenic habitat type from 

information on geological features. Often broad-scale 

information on geological features is available, but only 

small-scale or patchy information on the biogenic habitat 

associated with geological features. Frequently, it is the 

biogenic habitat that is of the highest interest for linking 

to population processes.

 Conduct studies of local predation and growth rates in 

experimentally-modified habitats. Although laboratory 

studies are useful, it is the in situ, controlled studies of 

fish in various habitat types that may ultimately be more 

informative to help understand the interactions of fish 

relative to these factors in the natural environment and 

help extrapolate findings to population level assessments.

 Develop habitat association models. Demonstrate 

meaningful associations of fish by life history stages with 

habitat and then understand mechanisms of these associations. Certain fish are known to be associated with 

particular habitats (e.g. some rockfish are associated with 

corals and sponges), but additional research is needed 

to understand the purpose or population advantages of 

such associations. Could it be for food, protection, or 

some other benefit? 

 Create spatially-explicit stock assessments for some key 

species.

 Conduct focused habitat studies on species such as grouper or black seabass that are relatively sedentary species 

with habitats that could be quantified.

 Use vessel monitoring system (VMS) data to develop 

time series of spatially-explicit fishing impacts to habitat.
38

 Use a small-scale situation where habitat time series data 

could be collected for stock assessment use as a pilot 

study (e.g. food availability for shrimp, coral availability 

for grouper).

While it is best to have habitat time series data available in 

a format that is usable in a stock assessment model, the conversion of habitat data from unusable to usable forms could 

be a pilot study. 
39

1st National Habitat Assessment Workshop

This session focused on the current state of interactions between the science side (those that produce habitat-related 

information and products) and the management side (those 

that make decisions involving habitat). The goals of this 

session were to share regional experiences and establish a 

framework to improve operational processes, planning, and 

management priorities, in order to provide better quality 

science products for management in an integrated way. The 

session format was comprised of a presentation of the issues, 

a panel discussion, and open plenary commentary.

Assessment of Current Processes

A survey (see Appendix 5) was sent to each of the NMFS 

Regional Offices (RO), Science Centers (SC), and regional 

Restoration Centers (RC). The survey was aimed at understanding how near-term and long-term planning is done to 

determine what science is conducted by NMFS to support 

management decisions. 

Overall, the survey indicated a general lack of organized 

coordination among the SCs, ROs, and RCs. Some of the 

ROs and SCs use informal communications or processes 

for identifying and agreeing upong habitat science priorities. However, in most regions, there is not a clear process 

Session 1 Summary: Current Processes for Providing Habitat Science for Management 

Session Organizer: Peter Colosi (NERO)

Rapporteur: Kristan Blackhart (OST)

Panel Members: Tracy Collier (NOAA Oceans and Human Health Program), Thomas Noji (NEFSC), Jon Kurland 

(AKRO), Bob Hoffman (SWRO), and John Rapp (OHC, Restoration Center)

NHAW Top Recommendations

 Improved communication and coordination is needed between regional Science Centers, Regional Offices, 

and Restoration Centers. These three regional entities should work cooperatively to identify regional information gaps, identify and prioritize research needs, and communicate scientific information.

 Science Centers should continue to be opportunistic with funding sources, but should also promote collaborations and increased efficiency.

 Regional entities should establish defined processes to: 1) jointly identify habitat research priorities on a periodic basis; 2) align habitat research funding decisions with the identified priorities; and 3) maintain open 

lines of communication regarding research planning, research results, and evolving management information 

needs.

 Regional entities should work together to support the implementation of the Habitat Assessment Improvement Plan (HAIP).

for coordinating habitat science between the SCs and ROs 

to meet RO management needs, or between the SCs and 

the RCs to meet RC information needs. A notable exception is the Alaska Regional Office and Alaska Fisheries Science Center, which have developed an essential fish habitat 

(EFH) Research Implementation Plan to capture agreedupon habitat science priorities.

Funding issues play a large role in prioritization discrepancies between the SCs, ROs, and RCs. There is some funding 

support related to EFH to provide habitat science, but this 

is inconsistent across regions and does not cover all areas 

of science or management needs. A large majority of habitat science is opportunistic, often involves competition for 

external funds, and is generally short-term in nature. Management needs for habitat information are commonly reactive and quick response in nature, and may compete with 

ongoing, routine science operations. Many of the ROs and 

RCs feel that they have a limited voice in communicating 

management needs to inform decisions on which habitat 

research projects get funded. However, the general response 

from some SCs was that they receive little direct support to 

conduct habitat-related science, so they pursue the science 

for which they can get funding. In contrast, one SC comment maintained that science priorities should be linked 
40

and applicable to NMFS habitat management. 

The survey did provide a respectable array of examples of 

positive interactions between NMFS habitat science and 

management. Amendments to the Magnuson-Stevens Act 

provide an opportunity to explicitly incorporate fish habitat requirements (and ecosystem processes) into the management process. Other examples include the collaboration 

between west coast scientists and managers to prepare an 

evaluation of EFH for Pacific Coast groundfish, and evaluation of fishery concerns associated with open loop liquid 

natural gas processing facilities in the U.S. Gulf of Mexico. 

The survey asked respondents for suggestions, aside from 

increased funding, to improve current interactions and coordination to provide habitat science support to managers. 

The following improvements were the main conclusions of 

the survey responses:

 ROs, SCs, and RCs should establish processes to identify 

habitat research priorities on a periodic basis (e.g. every 

three years).

 ROs, SCs, and RCs should establish a process to align 

habitat research funding decisions with the identified 

priorities.

 ROs, SCs, and RCs should establish processes to maintain open lines of communication regarding habitat 

research planning, research results, and evolving management information needs.

Panel Discussion: Proposing Alternatives to the 

Current Processes

Funding: The availability of funds (or lack thereof ) to conduct habitat science is an ongoing issue across all regions. 

It is clear that substantial levels of additional funding are 

needed, but unlikely to be available at the desired level in 

the near-term. Until then, is it possible to reprogram existing funds to better align with habitat-related priorities? 

One possibility is to use stock assessment base funding to 

address issues related to answering species productivity 

related to habitat, the products of which would seem to 

benefit assessment and habitat science programs as well as 

habitat management. SCs should continue to be opportunistic with funding sources, but should also promote collaborations and increased efficiency. To make the best use 

of available funding, better prioritization of research needs 

is essential. A disconnect between priorities and funding 

makes NMFS less influential in habitat/ecosystem assessment than it could be, and more vulnerable to legal action. 

It is important to move the emphasis and funding back to 

prevention rather than the current situation which necessarily focuses more on “putting out fires.” The agency as a 

whole can help by better coordination of funding opportunities between programs. For the long-term, a core capacity 

needs to be developed to provide funding to address habitat 

science issues.

Communication: It is obvious that increased and improved 

communication between the science and management sides 

is needed. The respective roles in this process would be that 

managers would not tell scientists how to do habitat research, but do need to be more integrated and articulate to 

identify information gaps and research priorities, and make 

the best use of available funding. Scientists, then, would be 

in a position to address and translate needs into a research 

product or service context. Communication about funding 

and research plans needs to be improved between the ROs, 

SCs, and RCs. RO and RC staff needs to better communicate their research needs to the SCs. SC staff need to better 

communicate scientific information and research results to 

RO and RC staff in ways that are useful to the management 

process. 

Disconnect between Regional Offices and Science Centers:

Scientists working in the SCs are obligated to publish the 

results of their research in peer-reviewed scientific journals. 

Evaluations and promotions are often based on one’s publication record. Publications are also influential in acquiring 

funding from external sources, which is often necessary to 

conduct habitat-related research. Additionally, standing in 

the scientific community, achieved in part through publication, is crucial for wider acceptance of agency-generated 

science and defending against lawsuits. While the ROs and 

RC acknowledge the need to publish, the consensus is that 

this obligation should not be an obstacle to priority setting 

for making information available to management. Greater 

efforts need to be made on the part of the SC staff to disseminate results and provide tools to RO and RC staff in 

ways that will better meet their needs. This can be facilitated, if the need for science support is clearly articulated by 

managers and a dialog with habitat scientists takes place to 

confirm mutual understanding of that need.

Another area of disconnect between the ROs and SCs is 

a mismatch in the time line between science and management. The RO often has immediate needs and short turnaround times on their information requirements, whereas 

responding to the need is often beyond the capability of 

the SC which works on a longer-term perspective. Focus-
41

ing exclusively on short-term research needs is in conflict 

with providing the research and products that are needed 

for overall management needs. A solid science foundation 

with core habitat expertise is needed in order to rapidly respond to management needs and provide the information 

that is often urgently needed by the RO. Staff in the ROs 

and RCs need to level their expectations about how fast the 

SCs can and should provide quality science information. At 

the same time, it was noted that there are probably some science services that can be provided in the near term to bring 

these gaps together to provide management needs. 

Implementation of the Habitat Assessment Improvement 

Plan: The ROs, SCs, and RCs should work together to 

support the implementation of the Habitat Assessment Improvement Plan (HAIP). The NMFS Headquarters Offices 

(OST, OHC) should provide leadership in this arena, and 

ensure that the HAIP and associated initiatives remain on 

the agenda of the NMFS Science Board and other agency 

leadership. Staff in the ROs and SCs can also help advance 

the HAIP by investing the time needed to show agency 

leaders that staff are serious about making the best use of 

existing habitat research funds—demonstrate that the RO 

and SC are in sync regarding habitat science, they have a 

plan that includes priorities, and the priorities directly support the agency’s mission.
42

Participants in this breakout session were asked to focus 

on two key questions. The first question, “How do Regions 

and Centers work together to provide and improve science 

for the foundation pieces of our work?” was discussed thoroughly during the panel discussion so a majority of time was 

spent focusing on Question 2. Overall, the consensus regarding current Region-Center interactions is that they are 

variable and inconsistent between regions, and only Alaska 

has a semiformal process.

Question 2 was rewritten slightly to state: “How can WE

better respond to emerging on demand and foundational 

science to support more effective habitat management 

(through stock assessment, integrated ecosystem assessment, essential fish habitat, coastal marine spatial planning, 

etc)?” Overall, the main topics that need to be addressed 

the improvement of: 1) communication; and 2) the identification and prioritization of needs. In general, Restoration 

Center (RC) interests were included together with the Regional Office (RO). 

Communication needs to be improved across the RC, ROs, 

Science Centers (SCs), individual Capabilities, and Line 

Offices. Ideas for methods of improvement included:

 Create an inventory of personnel and expertise, which 

could possibly augment the NOAA directory with a 

search function for expertise. This would allow staff and 

managers to easily find the experts on particular topic 

nationwide. Each individual’s link could include a brief 

explanation of research interests, projects, and possibly 

a list of recent publications. Keeping the site passwordprotected would reduce concerns about potential public 

NHAW Session 1 Breakout Group A: Evaluating Current Science Center, Regional 

Office, and Restoration Center Interactions 

Facilitator: Karen Abrams (OHC)

Rapporteur: Allison Candelmo (NEFSC)

harassment of individuals working on controversial topics. A recent enhancement to the internal NOAA Staff 

Directory (https://nsd.rdc.noaa.gov/nsd/intsearch), the 

NOAA Personal Professional Profile System, will be useful along these lines by allowing researchers and resource 

managers to search out staff with needed expertise or 

working on relevant research projects.

 Establish communication guidelines with a set of operational rules and processes for RO-SC communication.

 Establish a liaison at each RO and SC.

 Distribute existing newsletter/staff notes through previously mentioned liaisons.

 Implement routine meetings with RO and SC staff and 

leadership at least every 1–2 years. 

ROs and SCs need to speak with one voice about habitat 

science priorities. To improve the identification and prioritization of habitat science needs, ROs and SCs need 

to: 1) schedule routine meetings of staff and managers; 2) 

articulate management priorities; and 3) identify prioritization criteria. This approach is used in Alaska to develop 

an annual research implementation plan for essential fish 

habitat that provides a guideline for prioritizing needs and 

allocating funding. This product is reviewed annually and 

is used to establish science priorities based on management 

priorities. Such an approach can be used to help get the “hot 

topics” funded and research underway promptly and to respond opportunistically to external funding. Additionally, 

it is important that priorities identified by the Regional Offices and Science Centers are aligned with Fishery Management Council needs.

Top Recommendations

 Communication among regional entities needs to be improved. This could be accomplished by: 1) establishing regional communication guidelines; 2) identifying a habitat liaison at each Regional Office/Science 

Center/Restoration Center; and 3) implementing routine regional habitat coordination meetings.

 Regional entities should improve identification and prioritization of habitat science needs by: 1) holding 

routine coordination meetings; 2) identifying prioritization criteria; and 3) articulating management priorities.
43

NHAW Session 1 Breakout Group B: Evaluating Current Science Center, Regional 

Office, and Restoration Center Interactions 

Facilitator: Michael Parke (PIFSC)

Rapporteur: Ronald L. Hill (SEFSC)

Key Question: How Should (Do) Regional Offices 

and Science Centers Work Together to Provide and 

Improve Science For the Foundation Pieces of Our 

Work?

Discussions during this breakout session focused largely 

on improving communications and the flow of funding 

between Regional Offices (ROs), Science Centers (SCs), 

regional Restoration Centers (RCs), and Fishery Management Councils (FMCs). Communications and working 

relationships run the gamut from casual phone calls or 

“water cooler consultations”, to e-mail requests—generally 

through established chains of command—for document 

review or needed scientific input, and on to requests for 

long-term data accumulation and analysis. Time frames for 

these interactions range from minutes or days to multiple 

months or years. At times there may be some urgency to 

a formal request for science information; these often arise 

from some urgent need originating from outside the agency. 

Many of the breakout session participants felt that shortterm communications occurred with ease, although these 

types of interactions are generally facilitated by collocation, 

proximity, or familiarity with the scientist involved. There 

was some concern among participants that even informal 

requests could become overwhelming as information needs 

become more intense. The longer-term, more formal processes are often cumbersome, or correct protocols may not 

be well defined, and there is less willingness to pursue scientific support through these means. Some communications are hampered by staff in the ROs, RCs, and FMCs not 

knowing who in the SCs have the necessary expertise. 

There was also considerable discussion over defining mechanisms, accepted and approved by RO and SC management, 

to efficiently obtain needed scientific support.

Some of the group members pointed out that these same 

discussions have been going on for a long time (~30 years) 

and might very well recur in the future unless something 

significant happens. Suggestions included agency reorganization at various levels, such as placing the SCs under the 

control of the RO (again) to ensure they are responsive to 

regional needs. This would provide greater control of the 

“purse strings” to ensure priority needs get adequate attention. One strength of this approach would be that funding 

requests/budgets being pushed up to Congress would be 

aligned and more offices would support linked requests; 

currently too many little pieces (i.e. programs) ask for money in an unorganized way. Various discussions were spawned 

from these suggestions but ultimately there did not seem to 

be a lot of support for this reorganization idea. There was 

strong support for guidelines to be well defined (more or 

less codified), so that knowledge of the process will not be 

lost when senior staff leave the agency or retire. As an alternative to reorganization, it was suggested that some of this 

can be accomplished through integrated ecosystem assessments (IEAs). The compromise positions included:

 Develop a structure to address short-term and long-term 

habitat needs, with input from SCs; 

 Use the recent liquid natural gas analysis as a model for 

the process needed for gathering and transmitting habitat science; and 

 There should at least be parallel structure within the 

SCs and ROs—habitat contact staff in each to facilitate 

better communication. The point was made that there 

are habitat coordinators in the various centers, but their 

roles obviously need to be further defined and/or highlighted.

Top Recommendations

 Regional entities should meet on a regular basis to facilitate planning and information sharing, improve 

communication, and coordinate habitat science priorities.

 Providing scientific support to meet management needs should be part of habitat scientists’ performance 

plans.

 The Habitat Assessment Improvement Plan (HAIP) should be used as the organizing structure for obtaining 

support and coordinating regional needs.
44

The group expressed concern that scientists within the SCs 

can tend to become focused on managers needs for stock assessment data and analysis. Supervisors within the SCs need 

to acknowledge that ROs have multiple information needs 

(e.g. Sustainable Fisheries, Habitat Conservation, Restoration Center, Protected Resources) with several parallel missions. They also need to include the FMCs and headquarters offices and their related scientific needs. Mandates from 

different directions and different needs are often expressed; 

each one carries different weights and can shift a scientist’s 

priorities. Some priorities may come with funding while 

others often do not, and funding is not always aligned with 

priorities. ROs need to seek accountability for funding invested. They may need to rework outcomes and deliverables 

associated with ongoing funding. Habitat science research 

programs per se often do not exist, and are not funded at 

the SCs.

Further discussion centered on the need for meetings between scientists, between scientists and managers, and between scientists and RO habitat staff. The National Habitat 

Assessment Workshop was the first national level meeting of 

habitat scientists and managers; similar workshops should 

be supported by the habitat program in the future. 

The final issue of the discussion focused on the data needs 

of habitat managers. Some participants questioned the 

availability and accessibility of SC data, and there was some 

feeling that the ROs do not know what data SCs have or 

how to gain access. The question was posed whether data 

were really needed or whether analysis relative to a particular question was needed. SC data are generally available 

from SC scientists and analysis and interpretation is usually 

published through the peer-reviewed literature. Although 

the publication of findings was generally appreciated and 

supported, since peer-review processes tend to lend greater 

credence to research findings, ROs often need science information in a more accessible format—simple access, data 

tables, and interpretations of data that relate to their current 

project. 

Key Question: If There Were One Thing to Change 

What Would It Be?

Members of the group were asked to identify one thing 

they would like to change in the way habitat science is supported by the SCs/agency. Once the elements were listed 

participants were asked to vote on their preferred change 

and identify whether it could be accomplished with current 

funding or whether it would require additional funding. 

Each group member voted and the ranked items are listed 

in order below:

1) Identify and develop a standing capacity at the SC 

to respond to RO/RC/FMC requests for work and 

support (may require additional funding).

2) Develop the data management structure/architecture 

to provide access to SC data and decision support 

tools to ROs/RCs/FMCs (requires additional funding).

3) Need regular (regional) meetings between the 

SC/RO/RC/FMC to share information on work, 

expertise, future/current needs and strategic planning 

(with IEA/HAIP as organizing vehicles, especially 

for medium- and long-term needs) (requires additional funding).

4) Develop points of contact for habitat science for RO 

and FMC inquiries with control of dollars and supervision (may not require additional funding).

5) Need short and intermediate response personnel in 

the SC so they can support needs and apply the science to specific needs. These tasks need to be added 

into performance plans.

Recommendations

 There should be meetings between the RO and SC once 

or twice a year to facilitate planning and information 

sharing, preceded by internal discussions within the RO 

to prioritize habitat science and information needs.

 There should be a means for the RO to track information expertise within the SC. Some sort of directory or 

a web page might work (for example, see the GulfBase 

Directory at http://gulfbase.org/person/). The NOAA 

Personal Professional Profile System, a recently developed augmentation in the internal NOAA Staff Directory (https://nsd.rdc.noaa.gov/nsd/intsearch), allows 

NOAA users to search out staff with needed expertise or 

working on relevant research projects and may become 

useful for improving communication as it becomes 

populated with information on staff expertise, research 

interests, and current projects.

 Managers in both the RO and SC should be aware of 

all the work SC scientists do in support of habitat, and 

recognize that more work could be done with adequate 

fiscal support.

 Providing scientific support for RO/RC/FMC, particularly in the area of habitat science, should be part of 

habitat scientists’ performance plans on par with peer-
45

reviewed publications.

 There should be defined mechanisms or protocols outlining how to obtain scientific support when it is needed. 

There should be simple ways to approach SC scientists 

for simple questions and more formal ways to address 

more complex or time consuming needs. For example, 

a phone call may suffice for quick answers, an e-mail 

request copied to both lab and office directors may be 

used for a task requiring a few days, and a formal memo 

from the Regional Administrator to the SC Director 

requesting work that requires more than that. This sort 

of exchange does currently occur for many tasks (e.g. in 

the SEFSC/SERO, generally for SF needs).

 Work requests should be explicit about degree of needs 

and deadlines.

 There should be better defined official Points of Contact 

in the SCs and ROs/ RCs/FMCs.

 The communication process has to be a dynamic conversation that is formalized but can be modified when new 

situations arise.

 Potentially meet at the level of large marine ecosystem. 

 Priorities crossover, so IEAs could give a cross-boundary 

base of knowledge. 

 Shift gears to regular meetings between the SCs, ROs, 

RCs, and FMCs, with the focus of the meeting to get 

science more in line with management needs. 

 Do a better job planning; for example, schedule tasks 

and priority activities with upcoming FMC needs or 

habitat needs. This can be done for nonfishing needs as 

well as fishing needs. Better planning can give greater 

lead time for SCs to address habitat needs.

 ROs need “tool kits” to apply to their management 

issues. Many SC’s are working towards decision frameworks. The Northwest and Alaska regions are leading the 

way on that approach. 

 Geospatial tools are required for habitat science. Some 

are available but hard to find. Most SCs have that expertise on hand and are working to make that available 

in some areas. There has not been a lot of support for 

the development of regional (RO and SC) geographic 

information systems (GIS) capabilities and many ROs 

have gone to the National Ocean Service (NOS) for that 

support, which has drawn funding away from SCs that 

could have helped to develop additional tools for habitat 

science. Most SCs and some ROs have been moving in 

that direction, but priorities are not always aligned with 

habitat needs, although they could be with a shift in 

funding. One way to generate habitat support is with 

repeat business.

 Use the Habitat Assessment Improvement Plan (HAIP) 

as the organizing structure for this relationship. It gives 

the structure of coordinating goals, meeting both SC and 

RO habitat goals. The HAIP thus should be used as a 

rallying issue to garner more support and funding.
46

NHAW Session 1 Breakout Group C: Evaluating Current Science Center, Regional 

Office, and Restoration Center Interactions 

Facilitator: Mike Sigler (AFSC)

Rapporteur: Ben Laws (OPR)

What is the Objective? 

The objective is to fulfill the mandates provided in the Magnuson-Stevens Act, Endangered Species Act, and Marine 

Mammal Protection Act; to provide the basic information 

necessary for managed species; and to implement the Habitat Assessment Improvement Plan (HAIP).

How Can NMFS Improve the Way That Centers and 

Habitat Managers Work Together to Improve the 

Scientific Foundations of Habitat Work?

The group agreed upon a regional approach to improved 

collaboration and coordination between the science enterprise and habitat managers (Regional Offices, Restoration 

Center; Figure 1). Regular, institutionalized coordination 

of effort would involve appropriate personnel meeting, with 

managers contributing a prioritized understanding of management science ‘wants’, and research managers contributing an understanding of Science Center (SC) capabilities 

and a current inventory of research projects referenced to 

the principal investigators. 

Attempting this style of coordination can create a more proactive, forward thinking approach for managers. Over time 

this will result in closer alignment of management needs 

with SC projects and research time lines. This collaboration 

would carry significant benefit, as discussed below.

References may be made to management ‘needs’ for scientific support, but in reality managers may understand the 

types of activities for which they need scientific support 

without understanding what products might provide that 

support or what research is necessary to provide those products. Interaction with SCs can help gain clarity with regard 

to what management ‘wants’ support for and what is needed 

to provide that support.

A comparison of prioritized management needs with current SC activities would have at least two benefits: 1) Regional collaborators would identify ongoing or projected 

SC activities that may not be targeted towards provision 

of management support, but that could either directly, or 

through some reasonable application of flexibility, be able 

to satisfy an identified science need; and 2) the comparison 

would help to highlight gaps in support. Needs should be 

evaluated on a 3–5 year moving time frame. Managers will 

not always know all needs on that time frame, but many 

core needs can be identified. Management understanding 

of research directions can produce efficiencies of effort by 

adding value to existing survey efforts, for example.

Once gaps are identified, the next step would involve an 

evaluation of SC capacity. If capacity exists to fill a previously unexamined gap in provision of needed support, it 

should be a relatively easy fix. If capacity is lacking, the SC 

can determine the desirability of building the needed capacity, and build it into future funding strategies. If the same 

gaps are present on an annual basis, it could clarify whether 

the SC should seek to develop that capacity. If the capacity 

to undertake research in certain arenas or provide certain 

products lies outside a SC’s purview, then the group can begin to evaluate options for obtaining support from external 

sources (e.g. the U.S. Geological Survey, NOAA’s National 

Centers for Coastal Ocean Science, academia, consulting 

companies).

Top Recommendations

 Comparisons of prioritized management needs with current Science Center activities should be made at the 

regional level to improve coordination and identify gaps. An evaluation of Science Center capacity should 

also be included in this analysis.

 Further coordination amongst Science Centers should be performed at the NMFS Science Board level to 

provide the basis for national collaboration.

 A simple information clearinghouse (i.e. a list of current research and expertise available) should be created 

to help identify opportunities for improved efficiency.
47

GIS-based Information

EFH

RO, FMC

Consultations

RO

Monitoring

RC, RO

Long-term Capacity

SC Research Teams

Research Plan

Research Priorities

Research Funds

RO, RC, FMC

Communication

Communication

Figure 1. Regional approach to improved collaboration and coordination between Science Centers (SCs), Regional Offices (ROs), regional Restoration Centers (RCs), and Fishery Management Councils (FMCs).

This collaboration would provide an improved understanding of SC capabilities, but would also enable more clarity 

with regard to where specific expertise lies. Knowing who 

investigators are for specific research types will enable more 

staff level communication, which can often solve some simple requests for information. An institutionalized mechanism for interpersonal interaction between managers and 

scientists will bring to light general expertise that might not 

be revealed in a list of investigators.

The timing and form of these collaborations will need to 

be determined on a regional basis. The science and management groups will additionally have to determine regional 

criteria for joint priorities.

Further coordination amongst SCs should be performed 

at the NMFS Science Board level. It is not reasonable to 

expect any given SC to have sufficient expertise in all areas 

that regional managers operate. This national collaboration 

can provide managers with knowledge of where expertise in 

certain areas resides and how to tap into it.

How Can NMFS Work Together to Better Provide 

the On-demand Support Managers Often Require, 

and How Can NMFS Better Provide Support For 

Emerging Issues?

The group determined that, as above, much improvement 

can be gained through increased communication and coordination. Staff level interaction can be useful, but requires 

some formalization to be an accepted tool for on-demand 

support. Ad hoc staff level requests can cause problems 

when supervisors are unaware of requests, and agreements 

to provide support. Up to date, operational lists of expert 

points of contact for specific issues that may require on-demand support can help to solve this problem.

SCs and managers should agree upon data products that are 

of interest to SCs and of use to managers; these can help 

provide on-demand support. Periodic meetings would enhance the staff level communication discussed above, and 

ensure that data products provide significant value. Examples include Alaska’s ShoreZone fish atlas and the west 

coast’s Pacific Coast Ocean Observing System (PaCOOS) 

effort.
48

Supporting emerging needs will involve joint strategic planning, budget initiatives, and the collaboration and coordination discussed above. One avenue to address these issues 

might be through a regular National Stock and Habitat Assessment Workshop.

Notes

 One of the main points identified is better communication. Most of the people here got into this field to make 

a difference and many managers have a scientific background, while some scientists are managers of research. 

These dual roles can help bridge the communication gap.

 The SWRO recently provided the SWFSC with a science 

priorities list, while the SWFSC has its own priorities 

based largely on long-term needs and needs from the Pacific Fishery Management Council (FMC). One way to 

approach regional coordination would be to get together 

with the entities’ respective priorities and attempt to 

prioritize needs as a group. Where there are mismatches, 

the group can examine justifications for those priorities 

and consider how to improve coordination.

 To put the idea of ‘science needs’ in context, habitat 

managers must consider that Sustainable Fisheries and 

Protected Resources also have management needs for 

science. Not all of these needs will be satisfied due to 

current capacity, and the SC has to decide what can get 

accomplished. There may be some needs across the management spectrum that will have commonalities; the SC 

could capitalize on that to create efficiencies in science 

provision.

 Attempting this style of coordination can create a more 

proactive, forward thinking approach for managers. 

Over time this will result in closer alignment of management needs with SC projects and research time lines. 

The mismatch of time scales often results in significant 

disconnect and a situation where managers ignore the 

need to understand their own priorities and scientists ignore the need to provide scientific support to managers.

 One simple benefit of better coordination will be the 

discovery of certain synchronicities, where the SC may 

be conducting research that already addresses, or could 

be modified to address, management needs.

 Separate from a formalized coordination process, a 

simple information clearinghouse could help identify 

opportunities for efficiency. SCs could make a list of 

current research available such that, even without new 

long-term funding, a current awareness of research projects and knowledge of who is conducting that research 

can help.

 SCs must agree about the ability and willingness to be 

flexible with habitat projects. When opportunities to address priority management needs through minor changes 

to research plans, NMFS should take advantage of these 

opportunities. Even with external funding there can be 

lot of flexibility as long as agency goals are addressed.

 A first step towards an institutionalized plan for research 

in the region will be to compare management priorities 

with SC capabilities. To keep this to a manageable effort, 

it will be necessary to limit scope to habitat management 

needs.

 The essential fish habitat steering committee that previously existed in the Northeast was an effective way to 

bring these needs and capabilities to the table in a way 

that draws FMCs into the process. FMCs can potentially 

bring funding as well.

 A priorities list on the scale of 3–5 years is good for SC 

time lines, but it will also be useful to have a short-term 

‘go to’ list in cases where there may be ship time available 

for surveys and need something quick to plug into it.

 What should be time of response? It depends. Studies need planning and sufficient time to gather data. 

However, staff to staff communication can be helpful for 

quicker questions and is mostly not employed as much as 

it should be. It would be very helpful to have established 

point of contact experts in certain subject areas. 

 The HAIP exists as a broad national framework for providing habitat science, but was never meant to provide 

regional level specifics. The type of communication that 

is proposed at the regional level can show what the most 

urgent needs of managers are, enabling a discussion of 

whether the SC can address that need or, if not, how that 

need can be satisfied. 

 Any given SC cannot expect to be an expert in every 

single field. It would be helpful to identify nationally 

where certain expertise lies, where it is best housed, and 

how to gain access to that expertise. 

 The goal of HAIP is to address needs identified by mandates. What should the criteria be for setting up priorities, given this reliance on mandates? Overall agency 

criteria should always be met first.

 The sources of funding is one easy criterion to narrow 

focus; otherwise multiple priorities may split SC time 

and energy (including in-house priorities, FMC needs, 

states needs, etc.).

 The Restoration Center (RC) has gotten good use of 

collaboration in project monitoring, e.g. Maine project 
49

with 11 species, but only two managed species—the SC 

brings Atlantic salmon expertise, the Regional OfficeProtected Resources Division has expertise with alewives, and the RC has expertise in geomorphology.

 It is critical to have specific priority list of needs. There 

are a variety of ways SCs can help provide that information; when sampling scientists get all kinds of information and could add value to ongoing projects, but this 

cannot be accomplished without knowledge of priority 

needs. 

 A lack of legitimate prioritization efforts forces operations to be based on the ‘emergency list’ because the 

appropriate context is lacking to guide efforts. 

 To aid in short-term support, collaboration with regular 

contacts could be institutionalized along with a list of 

points of contact for certain subject areas. Interpersonal 

contact can help expose different areas of expertise that 

is not currently known; people often have expertise that 

they are not currently using in practice.

 There must be some control on staff level interactions, 

though, or supervisors lose understanding of what staff 

have committed to, and are unable to effectively manage 

expectations for products as well as workload.

 Development of data products can help with data 

management as well as helping to solve some short-term 

requests. Applications that meet certain management 

needs and can speed up response times could be built.

 Fact sheets on research, web pages, white papers, and web 

accessible products can help meet some short-term information requests, but this requires resources to create and 

maintain material.
50

NHAW Session 1 Breakout Group D: Evaluating Current Science Center, Regional 

Office, and Restoration Center Interactions 

Facilitator: Susan-Marie Stedman (OHC)

Rapporteur: Terill Hollweg (OHC, Restoration Center)

The plenary and panel speakers preceding the breakout 

group discussions all made the point that currently, the limited communication that does occur between the Science 

Centers (SCs), Regional Offices (ROs) and regional Restoration Centers (RCs) is very ad hoc. Participants pointed 

out that ad hoc communication is not necessarily bad, and 

in many cases this kind of communication can work well. 

Collocation of RO/RC staff with SC staff is important to 

establish personal relationships and open lines of communication. However, these relationships and open lines of 

communication do not exist in all SCs, so it was agreed that 

more formally established communication processes and 

opportunities are needed.

The current lack of a mandate from NOAA that the SC and 

RO/RC should be working closely together was mentioned 

as a major reason it is not currently occurring. Sustainable 

fisheries are perceived as the top priority for the agency, and 

the SCs see supporting stock assessments as their first priority. A complicating factor is the lack of dedicated funding 

to support habitat research. A small amount of funding is 

available through essential fish habitat (EFH) funds, but it 

is not enough to support a robust and responsive habitat 

research program in the SCs. When small amounts of funds 

do become available for discreet projects, the RO/RC often finds that local universities or contractors are better 

equipped than the SC to provide results on a short time 

line. The SCs are frustrated when they see NOAA funding 

going to outside institutions.

There also seem to be differences in focus and philosophy 

when it comes to science in the SCs and ROs/RCs. Some 

staff believes all science done by the SC should be applied 

science that relates to the NOAA mandates to protect, restore, and manage living marine resources. Others disagree, 

believing that the role of the SC is to provide unbiased data. 

A compromise suggestion was that the SC should be collecting information that can be used to build models of fisheries and their response to all influences, including changes 

in habitat.

The group agreed that a plan for moving forward has to 

include processes for improving communication through 

regular meetings of the SC, RO, RC, and Fishery Management Councils (FMCs), joint priority setting, exchanges of 

publications and lists of expertise/interest, and collocation 

or rotational assignments of staff wherever possible. Hiring or assigning a staff person whose responsibility it is to 

coordinate SC/RO/RC activities was also suggested as an 

effective way to ensure follow through on promises to communicate more often. It was agreed that SCs should have 

the right of first refusal for any funding that becomes available for habitat science.

It was agreed that the SC/RO/RC should develop a common goal for habitat science and management, perhaps 

with a common currency like ecosystem services, valuation, 

or production. There needs to be recognition of the mutual 

benefits of improved coordination. The SC should build 

a framework to help address habitat questions and stock 

questions together. Another avenue for cooperation (and 

perhaps funding) would be pre-spill and response planning—many habitat maps are about ten years out of date. 

Once that information has been generated, it needs to be 

housed somewhere and searchable in a context that makes 

it useful for answering management questions. Rather than 

trying to build that system all at once, it may be best to start 

with a pilot project and build from there.

Top Recommendations

 Science Centers should have the right of first refusal for any funding that becomes available for habitat science.

 Science Centers should build a framework to help address habitat and stock status questions concurrently.

 Regional entities should create working lists of available habitat expertise, recent habitat-related publications, 

current research, data sources and access points, and sources of funding.
51

Summary

 Recognize that the RO/RC needs to change as much as 

the SC.

 Improved communication is important to establish common goals and frameworks.

 Clearly establish mutual benefits.

 Establish a habitat science culture with mutual understanding of roles.

 Annual meeting of RO, RC, SC and FMCs.

 Undertake a set of pilot projects to build relationships 

and establish processes.

 Establish a data framework (for example, pre-spill planning).

 Create a working list of expertise/interests and funding 

sources.
52

This session focused on strategies to develop long-term capacity to improve the ability of habitat science to support 

management needs. The panelists were asked to consider 

the importance of maintaining a core of habitat expertise 

at the Science Centers (SCs) and what the funding implications were. Further, the panelists discussed what mechanisms, partnerships and capacities should be available to 

develop better and more responsive habitat science. How 

does habitat science feed into essential fish habitat (EFH) 

designation, protection of habitat from fishing and nonfishing activities, restoration of degraded or stressed habitats, Fishery Management Councils (FMCs), etc.? How can 

habitat science address performance outcomes, verification, 

and prioritization of management activities? 

Interactions between Science Centers and Habitat 

Managers 

The session discussion on the survey responses (see Appendix 5) indicated that there is not a defined or formal longterm priority setting process between the SCs and habitat 

management with the aim of building capacity for habitat 

science in support of management, although some regional 

practices do notably exist. The panel suggested processes, 

observations and insights to spark discussion and promote 

progress in this respect, as noted below. This session also 

provided context for regionally focused breakout groups 

during the workshop.

In the arena of regional fishery management, there is some 

organized science-management coordination in place. It is 

not surprising that fairly well defined processes are in place 

for interacting with the FMCs—implementation of the 

NHAW Session 2 Summary: Proposing Strategies for the Development of Habitat 

Science Capacity and the Incorporation of Habitat Science into Management

Session Organizer: Thomas Noji (NEFSC)

Rapporteur: Kirsten Larsen (OST)

Panel Members: Peter Colosi (NERO), Miles Croom (SERO), Perry Gayaldo (OHC), Stephen K. Brown (OST), and 

Pace Wilber (CSC)

NHAW Top Recommendations

 Low cost steps should be taken in the near-term to promote development of long-term habitat science capacity.

 Formal processes should be established for improved communication, coordination, and planning and priority setting at the regional level and applied in an ecosystem context to all areas of habitat programs.

 NMFS’ Restoration Program should have an increased role in the regional habitat dialog.

EFH management mandate in the Magnuson-Stevens Act 

depends on fruitful partnership. These regional sciencemanagement fora serve to inform fishery management planning for EFH designations as well as assessments of fishing 

and non-fishing impacts. For example, the Alaska region 

has a forum in which the managers meet periodically with 

the SC to address science needs and prioritize how EFH 

funds will be spent, and what products and services will be 

provided to meet operational priorities. In the Southeast, 

Northeast, and Southwest, regional needs are more likely 

addressed and partnerships established in venues that are 

focused and driven by Fishery Management Plan (FMP) 

amendments and National Environmental Policy Act 

(NEPA) needs, not specifically by habitat issues. However, 

the important dialog between SC habitat scientists and 

managers is less formal in some regions, for instance, in the 

Southeast and Northwest, and it is not undertaken in the 

Pacific Islands. Further, the scope of action is often limited 

to specific issues and sectors and lacks a holistic ecosystembased approach. 

The panel recommended that a process for fruitful dialog between habitat scientists and managers should be established 

in all regions and applied in an ecosystem context to all areas of a habitat program. It was agreed that habitat management should be an integrated continuum and practiced in 

an ecosystem approach. More specifically, it was also agreed 

that EFH designations developed in a consultative format 

with the FMCs are required: 1) to manage fishing gear impacts within Council FMPs; 2) to prioritize threats to living 

marine resources’ habitat; and 3) to promote stewardship 

engagement in many venues across the nation. It was noted 

that the agency’s restoration program should be part of the 
53

regional dialog. 

Management Needs and the Operational Dichotomy 

of Habitat Science vs. Management

There are important needs from which the sound habitat 

management intended by the Magnuson-Stevens Act and 

envisioned by the Habitat Assessment Improvement Plan

(HAIP) is shaped. Some long-term needs requiring science products, services, and partnering are: a) the capacity 

to handle routine, short turnaround requests; b) planned 

special investigations; c) emerging issues; d) agency drivers 

(e.g. ecosystem-based management, marine spatial habitat 

management); e) knowledge gaps (e.g. habitat services, productive capacity of habitats); and f ) strategic partnering in 

stewardship (e.g. hydro power expertise, guidance for impact analysis). 

Importantly, it was acknowledged by the panel that it is 

sometimes difficult for habitat scientists to meet the often 

urgent requests by habitat managers. Partially, this is due to 

the scientist’s training and ethic to perform rigorous, comprehensive and ‘bullet proof ’ investigations before coming 

to a conclusion. This all too often requires more time than 

the habitat manager can afford, if regulatory deadlines are 

to be met. 

It was recommended that, to the extent possible, habitat 

scientists should be cognizant of the meaning of “best available science” in the sense that sometimes advice must be 

provided based on (a limited) availability of data, even if it 

is provided with that caveat. Further, it was agreed that, to 

the extent possible, habitat managers should be cognizant 

of the constraints on the capabilities of habitat scientists, 

when designing management strategies and management 

plans. It was also noted that FMC science support may 

need to be expanded to include non-SC experts, particularly when the capacity to respond in a timely manner does 

not exist at an SC. 

Funding Implications

It was acknowledged that funding is a factor in determining 

capacity of habitat science, but that there are low-cost steps 

that can be taken in the near term to promote development 

of long-term capacity. Improving dialog and coordination 

between habitat science and management should lead to 

more effective planning, reduction in redundant efforts and 

more efficient implementation of management actions. 

It was recommended that a concerted discussion among the 

NMFS partners, initially at the regional level (and later at 

a national level), take place to identify fruitful partnerships 

and interactions to improve the overall effectiveness and 

economy of operations of the ‘habitat enterprise’. In each region this should include the SC, Regional Office and Restoration Center. 
54

NHAW Session 2 Breakout Group A: Evaluating Strategies for the Development of 

Habitat Science Capacity and the Incorporation of Habitat Science into Management 

Facilitator: Karen Abrams (OHC)

Rapporteur: Allison Candelmo (NEFSC)

This breakout session discussed two questions focusing on 

building habitat science capacity, both using current resources, and with potential new funds. The first question 

was “How do we build capacity to meet our habitat science 

needs with our current resources?” Basic information dissemination and an increase in the accessibility of data and 

communication is an important step towards building capacity with current resources. To this end, creation of a national database of ongoing projects and research (for examples, see databases maintained by the Northwest Fisheries 

Science Center and National Coastal Data Development 

Center) would be vitally useful. The NOAA Personal Professional Profile System, a recently added enhancement to 

the internal NOAA Staff Directory (https://nsd.rdc.noaa.

gov/nsd/intsearch), will be useful by allowing researchers 

and resource managers to search out staff with needed expertise or working on relevant research projects. Additional 

implementation of technology transfers and the synthesis 

of existing information are also important. The data translation of the Estuarine Living Marine Resources (ELMR) 

report is a good example of the transfer of what was a very 

large report into an Excel spreadsheet to establish a source 

of data that is able to be readily incorporated into research 

and management. This was implemented with support from 

the staff from the Biogeography Branch of the Center for 

Coastal Monitoring and Assessment. 

Another important step is redirecting current resources to 

align with agreed upon habitat science priorities and needs. 

Improvement of the administration and processing of funding to streamline and expedite the efficient use of year-end 

NOAA funds is also necessary. Without efficient internal 

procedures, staff may be forced to use outside sources such 

as universities to process and store funds, which can be difficult in some regions. Money management issues are a real 

problem in some regions, particularly those that do not 

have a well established joint program with a university. It 

can severely hamper field work and forces use of contractors 

and other outside sources.

A third step to building current capacity is to tap into existing NOAA staff at other Science Centers (SCs) with particular expertise to meet the jointly developed habitat science 

needs and priorities. Implementing staff transfers between 

the Regional Offices (ROs) and SCs would give people the 

opportunity to work in different units and gain insight on 

both the science and management sides, while also improving communication and need prioritization. Employees 

from the RO that are collocated within the SC are often 

more productive and happier with their work.

The second question asks “How do we build capacity to 

meet our habitat science needs in the context of potential 

new resources?” The first step focuses on implementing the 

Habitat Assessment Improvement Plan (HAIP) to add the 

staff resources necessary to do the research required to meet 

NMFS’ habitat science needs. Implementation of the HAIP 

requires: 1) refining and prioritizing the objectives outlined 

in the document, to make them more tangible and establish 

a realistic first step; 2) creating regionally-specific habitat 

research plans; and 3) linking habitat research to topical 

priorities such as coastal and marine spatial planning. It will 

be necessary to increase staffing depth in the SCs by creating additional entry level positions. A large amount of habitat information and projects could be generated by lower 

level positions, with senior scientists stepping in to refine 

projects and analysis as necessary. Improved partnerships 

(with other SCs/academic institutions/states) are needed, 

as well as some sort of a marketing strategy to use these partnerships to build support, collect the data, and create the 

products. Such improved partnerships could and should be 

used to help lobby for support and funding.

Top Recommendations

 NMFS should create a national database of ongoing habitat projects and research.

 Staff transfers and other interactions should be considered to improve communication and build current 

capacity.
55

Conclusions

There are capacity improvements that can be made with 

current resources and should be pursued. Improvements 

should not depend exclusively on uncertain new resources. 
56

NHAW Session 2 Breakout Group B: Evaluating Strategies for the Development of 

Habitat Science Capacity and the Incorporation of Habitat Science into Management 

Facilitator: John P. Manderson (NEFSC)

Rapporteur: Terra Lederhouse (OHC)

Summary

The discussion focused on what is needed to develop longterm capacity for habitat assessment, using the context of 

the Deepwater Horizon oil spill. The most important questions were: 

1) What habitat science information would have been 

the best to have on hand before the spill (i.e. what 

would have been most useful for determining baseline conditions); and

2) What might the rapid response for assessing damage 

be? 

Three key points emerged from the discussions: time scales, 

valuation of ecosystem services, and habitat simulation 

models.

Time Scales: The time scales of habitat science and management are not always in agreement—managers often need 

information with quick turnaround times, while scientists 

need sufficient time to develop quality science products. 

Habitat managers need to collaboratively develop a coherent set of long-term goals and recognize that scientists need 

time to achieve those goals. At the same time, scientists may 

be able to shorten their time scales to build the science using the principal of parsimony and the understanding that 

managers cannot wait for the most sophisticated “model”. 

Valuation of Ecosystem Services: The response variate for 

habitat science should be the valuation of ecosystem services or how specific habitats enhance the survivorship (S

= 1 - μ) of key species in the ecosystem. To be more realistic, economists and managers need to convert this equation 

into more practical terms ($ = 1 - μ). In the context of the 

oil spill, much more information is needed about the relative ecological value of different habitats, including pelagic 

habitats, to understand how to minimize the impacts of different mitigation strategies (e.g. are the ecological costs of 

reduced survivorship in deep and offshore habitats due to 

dispersants actually smaller than the ecological costs of tar 

balls on the beach). 

Habitat Simulation Models: Habitat scientists need to 

move beyond small-scale empirical studies towards building broad-scale general habitat simulation models with estimates of uncertainty, analogous to stock assessment models. 

The response may be a habitat-specific index of ecosystem 

services. These models may operate as habitat-specific ecosystem models.

Notes

 A key question is how to develop more long-term capacity in the Science Centers to meet NMFS’ management 

needs?

 NMFS needs to improve its ability to predict impacts 

when catastrophic events occur. For instance, after the 

Gulf of Mexico oil spill, capacity was lacking to answer 

questions on the effects of oil and dispersants on marine 

resources, despite the fact that oil development has been 

occurring in the area for years. 

 One possible solution is an emergency response program 

with funding that carries over from year to year. Such a 

program needs to have both a long-term planning aspect 

and an immediate response aspect. The long-term aspect 

could prepare maps and other products that aid in preparations and long-term planning. Some of this may already exist (e.g. Environmental Sensitivity Index maps), 

but may be limited in availability or completeness.

 To make the best management decisions, managers need 

to know the science and be able to weigh trade offs between alternatives. Ecosystem service valuation is essential to feed into this. Providing this kind of new informaTop Recommendations

 Habitat managers need to collaboratively develop a set of long-term goals.

 Habitat scientists should move towards building broad-scale general habitat simulation models with estimates of uncertainty.
57

tion would require new staff, and could be appropriate 

for the proposed emergency response program. Information on ecosystem real dollar values often resonates with 

politicians and the public, which can then translate into 

increased funding opportunities.

 Habitat is defined in many levels and scales, and appropriate frameworks should be developed for habitat 

assessments. When the Regional Offices (ROs) ask the 

Science Centers (SCs) what their ability is to predict 

something, the SCs do not have the tools necessary with 

respect to habitat.

 A number of ways to build capacity were discussed. These 

include:

◉ Five years ago the west coast essential fish habitat 

(EFH) requirement forced the SCs to build capacity 

immediately. Could the oil spill be used as an opportunity to increase habitat science capacity in a similar 

way?

◉ Can action agencies fund the data collection systems 

needed—possibly through a “tax”?

◉ A better term than habitat is needed—possibly “seascape”.

 EFH Tier 3 identifications are needed. That will provide 

the reference information that managers often need 

immediately. SCs have performed a lot of useful empirical studies, but they have not expanded the studies into 

regional models. Once Tier 3 information is available, 

habitat biologists in the ROs can do most of the analyses 

required in response to regulatory actions. However, 

managers in the ROs will also need help with impact 

evaluations.

 Managers will always need to make decisions without 

knowing all that they would like to know. The SCs have 

limited capacity to provide information. Collaboration is 

needed to set priorities for what habitat questions should 

be answered in both the short-term and long-term. The 

following is a potential list of prioritized habitat science 

needs:

◉ Data to inform coastal and marine spatial planning.

◉ Habitat assessments.

◉ Upcoming impacts: renewable ocean energy; aquaculture.

◉ Synthesis of existing information into useful forms.

◉ Habitat maps, refined EFH maps, vulnerable habitats 

in relation to fishing gear impacts and other potential 

impacts.
58

NHAW Session 2 Breakout Group C: Evaluating Strategies for the Development of 

Habitat Science Capacity and the Incorporation of Habitat Science into Management 

Facilitator: Mike Sigler (AFSC)

Rapporteur: Ben Laws (OPR)

How Does NMFS Develop More Long-term Capacity 

in the Science Centers to Meet Management Needs?

Define: What is long-term capacity? Long-term capacity is 

the capability to conduct monitoring, forecasts, and mapping. Where does NMFS need to build capacity? Science 

Centers (SCs) may want to grow capacity in areas where 

they did not operate previously (e.g. restoration science). 

Long-term capabilities to build within NMFS must be 

identified. 

Communication: SCs and restoration managers should 

work to develop closer relationships. Much of the needed 

restoration science work is closely aligned with SC time 

lines, including long-term monitoring. Scientists and managers need better communication about priorities and about 

funding opportunities and streams.

Priorities: The group had some discussion about prioritizing offshore versus nearshore activities, but realized that 

this would be variable from region to region. Emerging 

issues, such as those related to alternative energy, will be 

priorities. One primary recommendation was to utilize the 

priorities identified in the Habitat Assessment Improvement 

Plan (HAIP), and reference these going forward.

What products or states are desirable? Managers need comprehensive, accessible databases that can reduce response 

time and alleviate the need for some staff level communication. The goal is to achieve information at levels identified 

as essential fish habitat (EFH) Level 4, or HAIP Tier 3.

Other consensus needs identified were evaluation of the effectiveness of restoration as well as of the implementation 

of other habitat activities.

Most habitat science funding now is minor relative to the 

scope of the need; the only foreseeable answer may be the 

implementation of HAIP with full funding. This will not 

happen immediately, but if it is pursued efficiently and with 

determination it may provide a phased, realistic answer to 

funding issues.

Notes

 The only SC with known, regular EFH research funding 

is Alaska—where does this money in other regions go? A 

clearer understanding of allocation of EFH funds would 

be helpful.

 Certain types of research or work that the Restoration 

Center (RC) is interested in are more amenable to the 

longer time scale of research than the quick turnarounds 

required by consultations. Long-term monitoring (5–10 

years), baseline assessments, and 5–10 year monitoring 

might be areas where the RC could work with SCs. The 

SCs should be asked whether they want to build this 

type of capacity.

 There is room for more interaction between SCs and 

the RC; few regions currently do this. It is important to 

begin building these relationships, rather than assuming 

they exist, as the RC has a great need for fisheries studies. The time frame is often not an issue, RC issues are 

usually not especially political, and funding streams are 

often sufficient for these needs.

 Much SC work is often focused on forecasts, trends, 

scenarios, and policy options, or integrated ecosystem 

assessments and helping councils with ecosystem-based 

fisheries management. The SC work also includes monitoring.

 Part of capacity development must be comprehensive, accessible geospatial databases and ways of getting products 

out. However, staff time can be an issue in development, 

and inappropriate use is a big concern.

Top Recommendations

 Science Centers and regional Restoration Centers should work to develop closer relationships and improved 

communication.

 Priorities identified in the Habitat Assessment Improvement Plan (HAIP) should be utilized and referenced 

moving forward.
59

 Long-term capacity also applies to communications, specifically with regard to institutional memory. With staff 

turnover, people come in unaware of issues on a technical 

level. To this end, succession planning, legacy data sets 

and personal knowledge, and lost professional experience 

must be considered.

 In cases where restoration is possible, key long-term 

questions revolve around the effectiveness of various 

restoration actions. Some kind of science-based review 

process is needed for evaluating the effectiveness of various actions. This may not be necessary on a project by 

project basis, but in general it is necessary to know the 

most effective way to allocate resources to restoration.

 The HAIP recommendations should be considered and 

referenced when prioritizing stocks and locations for 

research. These can help to analyze data inadequacies in 

their respective habitats, and to develop a plan for better 

using new technologies to address these inadequacies.

 There is a need to address where funding is coming from, 

and how to restructure work when there is no money 

coming for it, other than for habitat-related stock assessment.

 Managers often have no say over where habitat money 

goes or what deliverables it creates.

 What are the next steps following monitoring? Who 

evaluates data and to what use will it be turned? The RC 

integrates monitoring into a feedback loop that helps 

determine how projects are done and what type of projects are done; it is important that scientists analyze and 

disseminate, but also feed back mechanistically into this 

program-building aspect of the work.
60

NHAW Session 2 Breakout Group D: Evaluating Strategies for the Development of 

Habitat Science Capacity and the Incorporation of Habitat Science into Management 

Facilitator: Susan-Marie Stedman (OHC)

Rapporteur: Terill Hollweg (OHC, Restoration Center)

The group began by discussing current impediments to 

building long-term capacity for habitat science, with the 

intention of developing solutions to overcome the impediments once they are identified. Many of the themes discussed in the short-term capacity session were repeated, 

particularly the lack of dedicated funding and high-level 

NOAA support for habitat science. Many expressed the 

opinion that, even if new funding were made available for 

habitat science, without oversight and involvement from 

high levels in NOAA, the money would end up going to 

stock assessment. 

The lack of an outside constituency also hampers NMFS’ 

attempts to raise awareness about the need for more habitat science. The Restoration Center (RC) is an exception—

they have built a good constituency that helped them to get 

a large amount of funding under the American Recovery 

and Reinvestment Act of 2009. Working with the RC to 

adopt or adapt their techniques for building outside support would be a good idea.

Partnering with stock assessment scientists was discussed 

as one way to get ship time, but there are some difficulties 

because habitat sampling often requires stopping whereas 

stock sampling usually requires constant motion, and seasonal sampling may not occur at optimal times for both interests. There are also new restrictions on using volunteers 

that has made it harder to use them for collecting data. In 

some cases, Science Center (SC) staff are discouraged from 

working outside their geographic regions.

The overall solution proposed was for the SC and Regional 

Office (RO)/RC to work together to build a plan/framework for long-term habitat science capability. This framework would be designed to answer the priority questions 

about ecosystem interactions and productive capacity. Habitat characterization and assessment need to be recognized 

as essential components of this framework. Not all regions 

should have the same capabilities—sharing expertise across 

regions would be explicitly encouraged. The framework 

would encourage a shared vision and purpose for habitat 

science within the agency that would maintain the link to 

fisheries management.

It was agreed that long-term science capacity consists of 

four things—people, expertise, infrastructure, and funding. All of these things are needed for an effective habitat 

science program. Flexibility and adaptability are also key 

because it is impossible to know what tomorrow’s habitat 

challenges will be. 

Partnering with NOAA’s National Ocean Service (NOS) 

has been used by some staff as a way of getting habitat science done, but most felt that being beholden to NOS for 

help was not a good way to build NMFS science capacity. 

Using stock assessment funds, such as those that will be 

available to enhance habitat information to Tier 3, should 

be pursued through implementing the Habitat Assessment 

Improvement Plan. SCs should consider hiring new staff to 

act as data interpreters and synthesizers for RO/RC staff, so 

researchers do not have to take time away from research to 

do this. ROs should revisit getting funding from applicants 

for applied science questions, the way that the U.S. Fish and 

Wildlife Service does and NMFS used to.

Top Recommendations

 The habitat science community should work with partners in the NOAA Restoration Center to adopt or 

adapt their techniques for building outside support.

 Science Centers should consider adding staff specifically to interpret and communicate information to habitat managers and Restoration Center staff.

 Sharing expertise across regions should be explicitly encouraged.
61

Session 3 consisted of breakout groups, separated by region, 

focusing on ways to implement the proposed short- and 

long-term solutions in each region. After each breakout 

group concluded their discussions, the larger group reconvened for presentations from each group and an overall discussion of the regional implementation ideas. 

Although each region approaches management issues from 

a different perspective and faces its own set of unique challenges, a set of recurring themes emerged from the regional 

discussions. Across all regions, improved communications 

and coordination between the science side (i.e. the Science 

Centers) and the management side (i.e. the Regional Offices and regional Restoration Centers, and also the Fishery 

Management Councils) was the top priority. Some regions 

even suggested a formalized process such as a science-management coordination team be established for communication and coordination between the Science Centers (SCs) 

and Regional Offices (ROs). Many regions felt that regular, formal meetings between habitat staff would be an important step towards improving communications, and two 

regions (Alaska and the Northeast) tentatively proposed 

holding the first habitat coordination meetings for their 

regions in October 2010. In addition to providing habitat staff a chance to better establish relationships and learn 

more about each other’s roles, such meetings would provide 

a venue for improved planning between the SCs and ROs. 

Another important step for all regions to take is to better 

define and communicate needs and priorities. ROs need to 

better define the scope of their science needs, prioritize these 

needs, and clearly communicate these priorities to the SCs. 

NHAW Session 3 Summary: Implementing Proposed Solutions Regionally

Rapporteur: Kristan Blackhart (OST)

NHAW Top Recommendations

 Regional entities should make efforts to improve communication and coordination between science and 

management on habitat science issues. An important step would be implementing regular, formal meetings 

between regional habitat staff.

 Habitat science needs and priorities should be defined by the regional entities in a cooperative manner.

 At the regional level, science and management staff should work together to identify current funding streams 

and look for opportunities to align identified priorities with existing funding or redirect funding to better 

meet needs.

 Regions should support implementation of the Habitat Assessment Improvement Plan (HAIP) by supporting development of national HAIP budget initiatives and by incorporating the HAIP into regional habitat 

research plans and developing regional HAIP implementation plans.

Likewise, the SCs should better define their capabilities, including existing tools, data, products, and publications, and 

make this information readily available to RO staff in usable 

formats so the RO can take full advantage of existing SC 

capabilities. SCs should also identify their habitat science 

priorities, and SCs and ROs should work together to collectively develop a combined list of regional priorities. Such 

a process could evolve into a formal work planning process 

between the SCs and ROs, a suggestion echoed by several of 

the regional breakout groups.

Funding issues were widely discussed across the regional 

breakout groups, and the consensus was that for habitat 

science and management needs to be met, a significant increase in funding is necessary. Since the prospects for large 

increases in funding in the immediate future are limited, 

prioritization of needs is critical. At the regional level, SC 

and RO staff should work together to identify current 

funding streams and look for opportunities to align priorities with existing funding or redirect funding to better meet 

needs. Improved coordination of habitat science priorities 

between the SCs and ROs will also allow staff to be better prepared for opportunistic funding opportunities when 

they arise.

Several of the regional groups discussed the recently published Habitat Assessment Improvement Plan (HAIP) and 

agreed that regional support will be important to the overall implementation and success of the plan. Suggestions for 

support at the regional level included: incorporating the 

HAIP into regional habitat research plans; supporting the 

development of nationwide HAIP budget initiatives (by 
62

providing regional information, etc.); developing regional 

implementation plans for the HAIP; and considering habitat research in support of stock assessment improvement.
63

NHAW Session 3 Breakout: How To Implement the Proposed Solutions in the 

Northeast Region 

Facilitators: Thomas Noji (NEFSC), Peter Colosi (NERO)

Rapporteur: Ben Laws (OPR)

Summary

A very conscious decision was made to focus the Habitat 

Assessment Improvement Plan (HAIP) on stocks listed in 

the Fish Stock Sustainability Index (FSSI), not because the 

HAIP is irrelevant outside that scope, but for purely tactical 

reasons. It is necessary to focus efforts to get off the ground. 

Similarly, any regional plan needs to begin by focusing on 

three things: 1) core duties and routine responsibilities; 

2) an understanding of how resources are allocated to ‘fire 

drills’; and 3) a process for strategic or long-term planning. 

There are certain things that can be foreseen, although the 

specifics may change.

The HAIP is an operational national framework, but will 

be implemented regionally. To develop the granularity necessary for definition of regional coordination, an iterative 

process must be developed, in which regional participants 

interact to anticipate emerging needs and identify future 

science needs.

This points to the need for a formalized process for communication and coordination. Managers in the Regional 

Office (RO) must internally determine what their priorities 

are, before consulting with the Science Center (SC). Managers and SCs must consult to evaluate the type of services 

or information that are needed and to look at what type of 

product is necessary to provide that, before devising a plan 

to develop that product. It is important to speak with one 

voice in terms of the message to the Fishery Management 

Councils (FMCs). Operationally, the most must be made 

out of the resources that are available, in addition to plans 

to strategically to develop capacity.

The three regional entities (SC, RO-Habitat Conservation 

Division, and regional Restoration Center) agree to have a 

meeting in the fall (tentatively October). Each entity will 

begin preparations soon to bring their piece to the table. 

The goal is to develop and institutionalize a repeatable process. Toward this end, the SC should inform the RO and 

regional Restoration Center (RC) about scientific capabilities, current research foci and emerging science needs, and 

the RO and RC managers should inform the SC what the 

most pressing management needs are and are expected to 

be. Notably, past calls for a plan have resulted in lists but 

little lasting action. Each of the three groups will give short 

presentations on their core responsibilities to facilitate understanding on capabilities and expertise.

Notes

Process: A lot of discussion has centered on ways to interact, 

but what is really needed?

Mapping assistance is needed to help with emerging issues 

such as siting of offshore renewable energy, as well as help 

setting up monitoring plans to understand impacts from 

noise, community structure changes, benthic impacts, etc.

If specific projects are able to be funded through the SC it 

would be great, but real-time advice on these issues is very 

helpful.

A consistent need exists for more life history work, especially for very young stages and for trophically important 

species.

How should questions and requests for assistance be expressed? Are there extant data that might serve management 

needs if it were appropriately packaged and interpreted? 

The SC feels that they need specific examples of what is 

needed rather than general requests for more life history 

work. Essentially, managers must internally determine what 

Top Recommendations

 NERO managers should give habitat scientists at the NEFSC specific examples of their habitat science 

needs, rather than general requests.

 The regional entities should meet in the fall of 2010 to develop and institutionalize a repeatable process for 

planning and coordination.
64

their priorities are before comparing with SC capabilities. 

With specific requests, SC can evaluate a question, reference the query to what information may be available, and 

then determine whether the need for new study is practical. 

Managers and SCs must consult to evaluate the type of services or information that are needed, and then look at what 

type of product is necessary to provide that, finally devising 

a plan to develop that product. A small team could develop 

such a science plan as a compendium of sorts; it is undesirable to reinvent this on a project by project basis.

Increased face to face interaction, on at least an annual basis, 

would help to facilitate more collaborative work, beginning 

with a more macro-scale of overlap between needs, expertise and capacity. Each group would need to bring certain 

things to the table, e.g. managers bring a prioritized list of 

needs and SC brings a list of current activities, projects, and 

capabilities. With this foundation regions can identify efficiencies and areas where cooperative work is already occurring, as well as evaluate areas where improvements could be 

made or outside solutions may be necessary.

Several SC staff suggested a need for increased focus on 

modeling. A realistic look at the ocean and the footprint 

of all that NMFS needs to understand underscores that 

all objectives cannot be achieved through empirical study. 

Targeted empirical studies can be conducted to test model 

outputs, but it is hugely expensive to do assessments everywhere. A workable modeling framework is needed; this may 

initially require building ‘bad’ models with a high degree of 

uncertainty as a starting point.

All of this points to the need for formalized process for 

communication and coordination. Interactions are happening, but have not been made formal or put into an agreedupon plan. Once this happens, priorities can be advanced 

and a way forward can be figured out. Another aspect of 

closer coordination must be a mechanism to bring in the 

FMCs. What do FMCs expect from the RO?

To clarify, managers may often be able to prioritize what 

they want, whereas consultation with SCs may be necessary 

to understand what is actually needed in order to satisfy 

those wants. 

Perhaps this process can help regions develop a framework 

to quantify allocation of resources. Using tools in engaging 

stakeholders can help NMFS to communicate its positions 

when dealing with recreational and commercial sectors, 

which often put it in the position of fighting about pieces, 

while the pie shrinks.

Meetings can help by encouraging managers to do more 

forward thinking about what needs are in terms of products 

and services; regular interactions will cause managers to 

look further out and should become a longer-term planning 

tool where needs will consistently be on the list discussed 

with SCs. Needs are often expressed on a shorter term, reactionary scale; with a more proactive approach long-term 

needs will be identified over time and regions can work towards developing capacity to deal with them.

Managers cannot know everything that will be needed two 

years from now, due to emerging issues, but a hard look at 

longer-term priorities will identify known or existing issues 

(e.g. renewable energy, EFH updates, and information necessary to minimize fishing impacts).

Scientists often do not feel like habitat managers are their 

clients, while managers often feel there is no customer/client relationship between them and the SC. Clearly, perceptions need to change to implement this working model of 

coordination. A more formal relationship, similar to the 

one that exists between the SC’s stock assessment biologists 

and RO fishery management staff, needs to be developed. 

In that case, there are clear responsibilities that are understood between the SC and the RO and each party understands what the other party needs and works together to 

accomplish the needed tasks. A three-way client/customer 

relationship, between habitat managers, the SC, and the 

FMCs, should be established. 

The HAIP can be a means to produce better consultations, 

and should be considered in the process. In this regard, 

habitat scientists and managers need to look at provisions 

of the HAIP strategically. There is an inherent argument to 

be made for using HAIP-based science capacity advances 

to serve NMFS programs (e.g. by better supporting consultations). Effective programmatic approaches and funding 

support for the science/management partnership can be 

realized. 

How can the habitat community do a better job of being 

opportunistic? One fundamental way may be to develop 

better structure to hold, access, and use information that 

already exists. NMFS must be strategic, and get out of the 

mode of worrying about individual projects. A much bigger 

vision is needed in order to operationally make the most of 

what is available, and to institutionalize the process so it is 

repeatable.
65

One opinion expressed was that scientists and managers often feel a certain disconnect because their stated missions 

are very different. It may be necessary to go back and restructure mission statements to reflect the mandates that 

link the regional entities together. 
66

NHAW Session 3 Breakout: How To Implement the Proposed Solutions in the 

Southeast Region 

Facilitators: Tom Minello (SEFSC), Pace Wilber (SERO)

Rapporteur: Kirsten Larsen (OST)

The discussions in this breakout group were wide-ranging 

but mainly directed towards increasing interaction and 

communication between the SEFSC, the SERO, and the 

Restoration Center (RC). With the recognition that increased research funding is not imminent, most of the solutions discussed are achievable with little or no funding support. However, a list of high priority SERO science needs 

and the development of a more formal list proposed to help 

guide scientific research if new funds become available were 

discussed. The role of the SEFSC Habitat Coordinator 

(Tom Minello) was also discussed. This position was established by the SEFSC Science Director as a clearinghouse 

for SERO and RC contacts with the SEFSC, and most of 

the SERO and RC participants are aware of the position. 

However, relatively few of the scientists working on habitat 

research in the SEFSC are aware of the position. Perhaps 

this is not unusual, since most communications have been 

between the Habitat Coordinator and Directors of the various Laboratories and Divisions in the Center. A point of 

contact has been established in most SEFSC Divisions for 

habitat-related issues to help improve this aspect of communication within the SEFSC. These points of contact are: 

Doug DeVries (Panama City Lab), Todd Kellison (Beaufort 

Lab), Mike Schirripa (Sustainable Fisheries Division), and 

Jim Bohnsack (Protected Resources and Biodiversity Division). It was apparent, however, that improved communication regarding habitat issues is needed within the SEFSC as 

well as between the SEFSC and SERO. Because the need 

for improved communication was acknowledged by all participants, various approaches were discussed to meet this 

need, including: 1) the development of written summary 

documentation of SEFSC research products; 2) a prioritized list of SERO information needs; 3) a strategy to improve communication through meetings; and 4) new ways 

to use the internet and e-mail. A summary of discussions for 

each of these issues follows.

Documentation of SEFSC Research Products

The staff of the SERO and the RC needs improved access 

to the research products being developed by the SEFSC 

and by the larger scientific community (including NOAA’s 

National Centers for Coastal Ocean Science, or NCCOS). 

While the staff of the SERO and RC are trained scientists, 

they have little time to spend reviewing scientific literature. 

In addition to the obvious (but funding constrained) solution of providing more time for such reviews, the SEFSC 

has initiated efforts to summarize recently developed research products pertinent to SERO and RC needs. A document has already been developed providing summaries or 

abstracts of habitat science publications from the Fishery Ecology Branch of the Galveston SEFSC Laboratory 

(2005–present), and an effort is underway to provide this 

information from all SEFSC laboratories. In addition, the 

Habitat Coordinator agreed to pursue the inclusion of publications from Beaufort’s NCCOS research group, and that 

contact has been initiated. Some discussion also centered 

around using key words in a searchable database and posting 

this product on the SEFSC web page. In addition to providing information to the SERO and the RC on what research 

is being conducted, this effort will help SEFSC staff know 

what research their scientific peers are conducting.

Identifying and Prioritizing SERO Information 

Needs

Problem: The SEFSC is not fully aware of the science needs 

of the SERO and RC staff or their priorities. 

There are opportunities during the course of SEFSC research projects to modify procedures or methods without 

negatively affecting project objectives or costs. In some instances, such modifications might be useful in providing 

Top Recommendations

 A formal list of high priority SERO science needs should be developed to help guide scientific research if 

new funds become available. 

 SEFSC scientists should improve access and availability of the habitat science products they develop.

 Annual habitat science coordination meetings should be held, perhaps in conjunction with the regular 

SERO manager meetings to reduce meeting costs. Staff from the SEFSC, SERO, and RC should participate.
67

information to the SERO or RC staff without additional 

cost. The ability of SEFSC scientists to provide such information, however, requires better communication regarding priority needs of the SERO and RC. In this regard, the 

SERO agreed to draft a document summarizing these priority needs. Some of these long-term needs are identified 

in the Fishery Management Plans and in a diadromous fish 

report coming out soon. Other scientific needs discussed 

in the meeting include: 1) effects of mining sand from ebb 

tidal shoals; 2) the fishery value of tidal freshwater habitats 

for species such as white shrimp; 3) seagrass restoration; 4) 

how to protect shallow coral reefs; 5) freshwater inflow and 

effects of major river diversions; 6) impacts of alternative 

energy projects; 7) maps of essential fish habitat; and 8) impacts of open and closed loop liquid natural gas facilities.

Increased Communication through Meetings

There was much discussion about the benefits of meetings 

between the SEFSC and the SERO (and RC) to discuss science projects and science needs. The last meeting specifically held to address this question was in Beaufort more than 

ten years ago. The general consensus was that such meetings 

would be beneficial, allowing valuable interactions between 

scientists and managers. Because the cost of holding meetings on a regular basis is an issue, the suggestion was made 

to coordinate them with regular SERO manager meetings 

that have been held over the past three years. Assuming that 

these annual meetings within the SERO habitat office will 

continue, recommendations were made to hold the meetings at different SEFSC laboratories each year and expand 

the agenda to include presentations from the host laboratory and other SEFSC scientists available to attend. Over 

several years following this approach, the regional habitat 

managers could be exposed to most habitat research being 

conducted in the SEFSC with a relatively small increase in 

meeting costs.

There was also some discussion about coordinating meetings 

between the SERO, SEFSC, and RC in association with the 

National Habitat Assessment Workshop (NHAW). An extra day following the NHAW could be devoted to regional 

issues. This approach has the advantage of more readily including staff from the RC. If the NHAW continues to be 

held in association with the NSAW, such a meeting also 

could potentially include stock assessment scientists, and 

this was considered highly desirable by some in the meeting. The downside of such an approach could be the lack 

of funds to support broad participation in future NHAW 

meetings.

Increased Communication through Web Sites and 

E-mail

Many of the SEFSC labs have web sites with summaries of 

research projects and links to publications. Some labs are in 

the process of developing web sites and these efforts should 

be encouraged. These web sites can be accessed through the 

main SEFSC web site (http://www.sefsc.noaa.gov), and 

the use of this resource should be advertised and encouraged. The development of a new habitat science web page 

(as discussed above) on the SEFSC web site will also help 

to consolidate and make recent information more readily 

available. It is anticipated that the regional science needs 

document will be posted on this page as well.

One suggestion for improving communication among everyone in the Southeast region and in NOAA in general 

would be to make some simple changes to the NOAA Locator. This suggestion had strong support within the group 

and would involve adding basic information on research interests and perhaps current research projects to the Staff Directory. Because the NOAA Locator is password protected, 

this information would be for internal NOAA use and not 

be available to the public. The group suggests including recent photographs of personnel as well. This simple effort 

would be very beneficial in allowing NOAA staff to connect 

with each other. The NOAA Personal Professional Profile 

System, a recently developed augmentation in the internal 

NOAA Staff Directory (https://nsd.rdc.noaa.gov/nsd/intsearch), has already implemented some of these suggested 

enhancements. The system allows NOAA users to enter information about their expertise, research interests, and current projects, and to search out staff with needed expertise 

or working on relevant research projects.

An additional suggestion for improving communication 

within the Southeast would be to develop a ListServ for 

habitat science. We will investigate the development of such 

a ListServ either through the SERO or the SEFSC to allow 

broadcasting of habitat news of interest among scientists 

and managers.

Additional Funding for Habitat Research

The issue of inadequate funding for habitat science was discussed. Most of the habitat science in the SEFSC is conducted through reimbursable funding from a variety of 

funding sources, and while the objectives are aligned with 

NOAA research goals, they often are not aligned with immediate SERO or RC needs. SERO managers can often 
68

identify research funding sources for particular projects of 

interest, and communicating this information to the appropriate scientists can help bridge this gap between scientists 

and managers.

Efficient Use of Funds

From a programmatic perspective, a major obstacle to using funds efficiently is not having an effective administrative 

vehicle for using end of year funds (arrival of funds late in 

the fiscal year also is a problem, but outside NOAA’s control). Partner agencies often can “bank” or carry over funds 

to subsequent years, but this has been difficult for SEFSC 

scientists. As a result, end of year funds within the SERO 

and RC often go to other agencies. While initially the funds 

on a per project basis may be small, after this occurs for a 

few years, a substantial expertise base and professional relationship is developed, which is becomes difficult to ignore 

when more stable funding appears. The use of Cooperative 

Research Units and Cooperative Ecosystem Studies Units 

(http://www.cesu.psu.edu/) was discussed as one solution 

to this problem. An initial step may be to examine this cooperative unit with respect to SERO and RC needs and 

advise SERO and RC administrative and technical staff on 

the requirements for moving funds to the cooperative unit. 

The review also would identify expertise gaps in the cooperative unit that might be addressable via revisions to the 

cooperative agreement or be included in future cooperative 

agreements. 
69

NHAW Session 3 Breakout: How To Implement the Proposed Solutions in the Alaska 

Region 

Facilitators: Mike Sigler (AFSC), Jon Kurland (AKRO)

Rapporteur: Terra Lederhouse (OHC)

Habitat Assessment Improvement Plan

As implementation of the Habitat Assessment Improvement 

Plan (HAIP) progresses, Alaska staff should provide regional information in support of budget initiatives and other 

information requests. An Alaska plan should be developed 

to implement the HAIP when funding becomes available 

(i.e. identifying first steps, etc.). HAIP needs should also be 

incorporated into an updated Alaska habitat research plan, 

and considerations should be made for habitat research that 

supports improvement of stock assessments.

Essential Fish Habitat Research Plan

The Essential Fish Habitat (EFH) Research Plan should be 

updated, incorporating HAIP material, the recent revision 

of North Pacific Fishery Management Council research 

priorities, and the recent 5-year review of Alaska EFH. The 

plan should recognize the habitat science needs of both 

nearshore and offshore research topics, taking into account 

nearshore EFH consultation requirements. 

Habitat Coordination Meetings

Alaska staff working on habitat-related issues should hold 

annual or biennial meetings to: 1) increase awareness in the 

Regional Office of recent Science Center habitat research 

activities, connections to management priorities, and plans 

for future research; 2) increase awareness for Science Center staff of Regional Office habitat information needs; and 

3) identify habitat science priorities. The first meeting will 

possibly be held in October 2010 and should be attended 

by all Alaska Regional Office (AKRO) Habitat Conservation Division staff, Restoration Center staff (Ammann, 

Koski), and Alaska Fisheries Science Center (AFSC) staff 

(Newport: Hurst, Ryer; Seattle: Gaichas, Hoff, Lowe, McConnaughey, McDermott, Ormseth, Rooper, Yeung, Zimmerman; Juneau: Farley [salmon EFH], Harris, Heifetz, 

Johnson, Lindeberg, Lorenz, Rice, Shotwell, Sigler, Stone, 

Thedinga; Kodiak: Conrath, Foy, Knoth). Mike Sigler and 

Jon Kurland will develop further plans for the first meeting. 

At the habitat coordination meeting, Regional Office and 

Science Center staff should each identify and present their 

habitat science priorities, and then collectively develop 

a combined regional list of priorities. Current funding 

sources should also be identified, and participants should 

discuss potential venues for new funding and ways for both 

the Regional Office and Science Center to tap into new resources. Additionally, Regional Office staff should describe 

mandates and activities so Science Center staff has a better 

understanding of the kind of information needs of management.

Funding

NMFS staff in Alaska should develop a mechanism for Regional Office and Science Center staff to discuss and coordinate proposals to non-EFH funding sources before they 

are submitted. Doing so would create proposals that are 

stronger and more focused towards management needs. Beyond EFH resources, funding sources for habitat science in 

Alaska include: the Restoration Center; hydropower; and 

the North Pacific Research Board. An additional source of 

potential funding for habitat science lies with the Bureau of 

Ocean Energy Management, Regulation and Enforcement 

(BOEMRE; the former Minerals Management Service). 

Top Recommendations

 Alaska regional staff should provide support for implementation of the Habitat Assessment Improvement 

Plan (HAIP), including development of an Alaska implementation plan and incorporating HAIP-defined 

needs into an updated Alaska habitat research plan. 

 Alaska habitat staff should hold annual or biennial coordination meetings to increase communication and 

jointly identify habitat science priorities. The first such meeting will be held in the fall of 2010.

 Alaska habitat staff should develop a mechanism to coordinate on funding proposals for non-essential fish 

habitat funding sources before proposals are submitted.
70

BOEMRE annually requests that the AKRO comment on 

the types of studies that are needed in Alaska to contribute 

to its annual studies plan. An AKRO–AFSC coordinated 

response is completed each year. The AKRO and AFSC 

should also consider a mid-level managers meeting with 

BOEMRE to discuss opportunities for NMFS to conduct 

BOEMRE-funded fish habitat research related to BOEMRE environmental impact assessments. Such research 

efforts would be useful for the AKRO Habitat Conservation Division in evaluating the effects of BOEMRE development activities. 
71

NHAW Session 3 Breakout: How To Implement the Proposed Solutions in the 

Northwest Region 

Facilitators: Michael Tehan (NWRO), W. Waldo Wakefield (NWFSC)

Rapporteur: Kristan Blackhart (OST)

Summary

The Northwest regional leadership will be briefed on the 

outcomes of the workshop, and concurrence sought with 

the development of an action plan to improve regional 

management and Science Center coordination in support 

of habitat science in the region. 

Among the short-term steps discussed in the breakout session are:

• Develop mechanisms (meeting, video calls, org charts, 

etc.) to better inform both the Regional Office (RO) and 

the Science Center (SC) on the organizational structure 

of each entity to better familiarize each side regarding the division structure, staff, areas of responsibility, 

etc. Similarly, interregional coordination needs to be 

improved to address coast-wide management issues that 

are of interest to both the Northwest and Southwest 

ROs/SCs.

• The RO needs to better define the overall scope of science needs associated with each management Division, 

to better inform the SC of the breadth of the collective 

needs. This would include the short-term requests for 

project reviews to emerging needs that will require longterm research or tool development to support habitat 

protection and recovery actions. 

• The SC similarly should define its capabilities, by Division and Program, including existing tools, products and 

publications (including interactive web resources) so 

that the RO staff can take full advantage (which should 

reduce the immediate need for short-term assistance in 

many circumstances (self-service).

• The RO and SC should collectively review the current 

patterns and avenues by which the RO seeks habitat 

science support, including the types of products and 

assistance, and evaluate whether a more formal coordination process should be developed and implemented. In 

doing so, the RO and SC should clearly define the roles 

of each entity (i.e. where is the line between scientists 

doing habitat project reviews and habitat biologists doing research). 

• The RO should develop a comprehensive list of habitat 

science needs, arrayed from brief telephone assistance 

for specific projects on one end of the continuum, to 

multiyear research investigations on the other, to form 

the basis of a formal work planning discussions between 

the RO and SC. 

• The RO and SC should identify existing funding streams 

for the center, including funds currently targeted at 

essential fish habitat, habitat, and stock assessment, and 

identify opportunities to both align regional habitat 

science needs with the existing science budget lines and 

consider opportunities to redirect other funding streams 

to better meet the RO’s habitat science needs. 

Armed with the results of the actions above, the RO and SC 

should develop a formal planning process to provide forums 

and points of contact where these coordination activities 

can take place. The RO already participates in the development of the SC’s five year strategic research plan; however, 

more frequent planning coordination should be pursued. 

Top Recommendations

 Northwest Regional Office staff should develop an action plan to improve regional management and Science 

Center coordination in support of habitat science in the region. 

 Northwest regional staff should develop a formal planning process to provide forums and points of contact 

where coordination activities can take place.
72

NHAW Session 3 Breakout: How To Implement the Proposed Solutions in the 

Southwest and Pacific Island Regions 

Facilitators: Mary M. Yoklavich (SWFSC), Michael Parke (PIFSC)

Rapporteur: Joe Nohner (OST)

Discussions during this breakout session focused on implementing the ideas generated throughout the workshop in 

the Southwest (SW) and Pacific Islands (PI) Regions. The 

goal of the discussion was to achieve better awareness, communication, understanding, coordination, and collaboration amongst the Science Centers (SCs), Regional Offices 

(ROs), regional Restoration Centers (RCs), and Fishery 

Management Councils (FMCs). In particular, each of these 

groups needs to identify their research and management 

priorities and communicate how these priorities are established and achieved.

In the near term, several opportunities for improved communication between the SCs, ROs, RCs, and FMCs were 

identified. Suggestions included exchanging a list of recent 

publications through librarians, increased data sharing, and 

updated web pages to reflect the science and management 

activities being carried out by staff. A distribution list for 

newsworthy items already exists at the Southwest Fisheries Science Center, so it may be possible to simply expand 

the distribution list. A need for points of contact to serve 

as subject area experts was identified by managers, who 

suggested a contact list managed by a gatekeeper. An interoffice habitat team composed of SC, RO, RC, and FMC 

personnel could serve to facilitate communication amongst 

offices and identify opportunities for collaboration. Similar species-specific science teams exist in the Pacific Islands 

Region, so the creation of an interoffice regional habitat 

team is feasible. This team would be able to identify points 

of contact and habitat liaisons within the SC, RO, RC, and 

FMC. Collocation of staff from these offices would greatly 

increase understanding of science products, management 

needs, and the opportunities for improved collaboration 

amongst offices. Such collocation of staff could occur on a 

short-term, informal basis, as well as through longer-term, 

more formal arrangements such as rotational and permanent assignments.

Examples of potential areas for collaboration would be 

aquaculture (PI and SW) and restoration (SW), where 

significant habitat science and monitoring needs currently 

exist. In the past, some of these operations have been conducted through joint institutes and contractors. SCs were 

overlooked due to assumed lack of capacity, but SCs potentially had the resources to do this type of research and 

monitoring. There is a need to be prepared for opportunistic funding sources such as refining essential fish habitat 

(EFH) and hydrologic study. A joint budgeting process, or 

at least planning sessions, to address budget reconciliation 

would address the constraints faced in the provision and 

prioritization of habitat science.

With regard to the provision of science, managers indicated 

that decision support tools are useful, but not necessary. 

A more cost effective approach in many cases may be the 

simple transfer of data or scientific conclusions, which can 

be interpreted by the managers. A starting point for this 

would be to adopt protocols that provide access to peer-reviewed and grey literature habitat science and to publicize 

this amongst other offices.

There are disconnects between the SCs and the ROs/RCs/

FMCs involving time scales, geographic areas (inshore versus offshore), and focal species, but these differences can be 

addressed through improved planning. For instance, emerging areas of concern, such as EFH and hydrology, are likely 

to require significant scientific input on short time scales. 

To meet that demand, managers must anticipate the types 

of information that they will need and communicate it to 

the habitat scientists as soon as possible. Without this lead 

time, habitat scientists cannot plan, fund, and execute the 

research to adequately accommodate science requests from 

managers. In addition, there is a need to address the fundamental incentive structures. 

Top Recommendations

 Regional entities should identify their research/management priorities and communicate to each other how 

these priorities are established and achieved. 

 A joint budgeting process, or at least planning sessions, are needed to address budget reconciliation and the 

constraints faced in the provision and prioritization of habitat science.
73

Long-term means to achieve effective habitat-related science 

and management will hinge on the successful implementation of the Habitat Assessment Improvement Plan (HAIP) 

and concomitant funding. As indicated by the HAIP, a major limiting factor in the amount of habitat science being 

conducted is available funding. The breakout group supported full implementation of the budget initiatives presented in the HAIP as a necessary step to fully accomplish 

NMFS’ habitat science and management goals. 

75

ABC acceptable biological catch

ACL annual catch limit

AFSC Alaska Fisheries Science Center

AKRO Alaska Regional Office

ASTWG Advanced Sampling Technology 

Working Group

AUV autonomous underwater vehicle

B biomass

BOEMRE Bureau of Ocean Energy Management, 

Regulation and Enforcement (former 

Minerals Management Service)

BSAI Bering Sea and Aleutian Islands

CPUE catch per unit of effort

EFH essential fish habitat

ELMR Estuarine Living Marine Resources

F fishing mortality

FATE Fisheries and the Environment program

FMC Fishery Management Council

FMP Fishery Management Plan

FSSI Fish Stock Sustainability Index

GIS geographic information system

HAIP Habitat Assessment Improvement Plan

HAPC habitat area of particular concern

HMS highly migratory species

IEA integrated ecosystem assessment

M natural mortality

MPA marine protected area

MSY maximum sustainable yield

NEFSC Northeast Fisheries Science Center

NEPA National Environmental Policy Act

Common Acronyms

NERO Northeast Regional Office

NHAW National Habitat Assessment Workshop

NMFS National Marine Fisheries Service

NOAA National Oceanic and Atmospheric 

Administration

NSAW National Stock Assessment Workshop

NWFSC Northwest Fisheries Science Center

NWRO Northwest Regional Office

OFL overfishing limit

OHC Office of Habitat Conservation 

OPR Office of Protected Resources

OSF Office of Sustainable Fisheries 

OST Office of Science and Technology

PaCOOS Pacific Coast Ocean Observing System

PIFSC Pacific Islands Fisheries Science Center

PIRO Pacific Islands Regional Office

RC NMFS regional Restoration Center

RO NMFS Regional Office

SC NMFS Science Center

SEAMAP Southeast Area Monitoring and 

Assessment Program

SEFSC Southeast Fisheries Science Center

SERO Southeast Regional Office

SS Stock Synthesis

SSC Scientific and Statistical Committee

SWFSC Southwest Fisheries Science Center

SWRO Southwest Regional Office

VMS vessel monitoring system

Z total mortality

77

National Stock Assessment Workshop Steering Committee

William Michaels OST, Chair

Ray Conser SWFSC Gerard DiNardo PIFSC

Sandra Lowe AFSC Richard Methot OST, NWFSC

Mike Prager SEFSC Fred Serchuk NEFSC

Ian Stewart NWFSC Douglas Vaughan SEFSC 

National Habitat Assessment Workshop Steering Committee

Stephen Brown OST, Chair

Kristan Blackhart OST Peter Colosi NERO 

Miles Croom SERO Gerry Davis PIRO

Correigh Greene NWFSC Bob Hoffman SWRO

Jon Kurland AKRO Kirsten Larsen OST

Ben Laws OPR (formerly OHC) Tom Minello SEFSC

Joe Nohner OST Thomas Noji NEFSC

Michael Parke PIFSC Bob Stone AFSC

Michael Tehan NWRO Waldo Wakefield NWFSC

Mary Yoklavich SWFSC

Appendix 1: Steering Committees

79

Appendix 2: Meeting Agendas

National Stock Assessment Workshop

Monday, May 17 

8:30 Welcome

8:40 Perspectives on current issues in fish stock assessments Methot

Theme Session A: Understanding the Trade Off Between Simple and Complex Models

9:00 Simple spreadsheet: Population models and policy simulations Lombardi, Walters, Allen, Pine

9:20 Determining yields for data-poor stocks using a DCAC-based stock reduction analysis of catch history Dick, 

MacCall

9:40 Concluding discussions for Session A

10:00 Break

Theme Session B: Quantification of Uncertainty From Model Structure and Retrospective 

Patterns

10:30 Addressing cohort strength related ageing error in fisheries stock assessment Hamel, Stewart

10:50 Modeling recruitment along the continuum from data-poor to data-rich Taylor, Methot

11:10 Management strategy evaluation of a retrospective fix Legault

11:30 Reconciling uncertain and conflicting trends in petrale sole abundance Haltuch, Hastie, Hicks, Whitmire

11:50 Concluding discussions for Session B

12:00 Lunch

Theme Session C: Addressing Uncertainty Due to Key Parameters, Especially Natural 

Mortality

13:00 Estimating stock-recruitment steepness from life history information: A case study of North Pacific bluefin tuna, 

Thunnus orientalis Brodziak, Mangel, DiNardo

13:20 Incorporating egg predation by haddock into a population model for Atlantic herring Richardson, Hare, Walsh

13:40 An independent estimate of natural mortality for Atka mackerel using tagging data McDermott, Ianelli, Lowe

14:00 Do marine protected areas improve the ability to estimate biological parameters using an integrated stock 

assessment model? Garrison, Punt

14:20 Concluding discussions for Session C

14:40 Review objectives for breakout sessions

15:00 Break

15:30 Breakout Sessions

Session 1: Protocols for ABC recommendations in data-poor situations

Session 2: Methods for quantifying uncertainty in assessments, including proxies for unmeasured variance 

components

Session 3: Evaluation of performance for ABC control rules; risk analysis; management strategy evaluation

Session 4: Addressing long-term climate/ecosystem factors affecting stock assessment and habitat

17:00 Reports from breakout sessions and concluding discussions

17:30 Adjourn
80

Wednesday, May 19

Theme Session D: Incorporating Statistical Uncertainty From Sampling Error

13:00 Specification of observation error variances G. Thompson

13:20 A hierarchical model to estimate relative catchability at size Miller

13:40 Mixture distribution models of Pacific rockfish schooling behavior Thorson, Stewart

14:00 Acoustical-optical surveys of coastal pelagic species, with emphasis on Pacific sardine, using improved allocation 

of effort, multifrequency acoustic methods, and a towed stereo camera system Zwolinski, Cutter, Demer

14:20 Trawl survey designs for reducing uncertainty in biomass estimates for patchily-distributed species Spencer, 

Hanselman, McKelvey

14:40 Concluding discussions for Session D

15:00 Break

Theme Session E: Developing a Comprehensive Approach For Characterizing Uncertainty

15:30 Calculating the uncertainty in fishery assessment forecasts Methot

15:50 Some aspects of scientific uncertainty in west coast stock assessments Ralston, Punt

16:10 Dominant sources of scientific uncertainty in recent Gulf of Mexico stock assessments—implications for ACLs 

Cass-Calay, Powers

16:30 Estimating scientific uncertainty in ABC control rules for Bering Sea Aleutian Islands (BSAI) crab stocks Turnock, 

Foy, Hollowed, Punt, Rugolo, Stram

16:50 Incorporating uncertainty into ABC control rules for Bering Sea Aleutian Islands (BSAI) crab stocks Stram, Punt, 

Turnock, Rugolo, Foy, Hollowed

17:10 Utilizing environmental information to reduce recruitment uncertainty in the Alaska sablefish stock assessment 

Shotwell, Hanselman, Foley

17:30 Adjourn

18:30 Poster Session

Thursday, May 20

Theme Session E: Developing a Comprehensive Approach For Characterizing Uncertainty, 

Continued

8:20 The relationship between MSY fishing rates (FMSY) and productivity indices Cope, Patrick, Methot

8:40 Quantifying the trade off between precaution and yield in fishery reference points Hart

9:00 A review of harvest policies: Understanding the relative performance of control rules Deroba, Bence

9:20 Setting allowable biological catch for stocks with reliable catch data only Berkson, Barbieri, Cadrin, Cass-Calay, 

Cooper, Crone, Dorn, Friess, Kobayashi, Miller, Patrick, Pautzke, Ralston, Trianni

9:40 Management uncertainty in the context of annual catch limits Millikin, Tromble

10:00 Concluding discussions for Theme Session E

10:15 Break

10:45 Breakout Sessions

Session 1: Protocols for ABC recommendations in data-poor situations

Session 2: Methods for quantifying uncertainty in assessments, including proxies for unmeasured variance 

components

Session 3: Evaluation of performance for ABC control rules; risk analysis; management strategy evaluation

Session 4: Addressing long-term climate/ecosystem factors affecting stock assessment and habitat
81

12:00 Lunch

13:00 Breakout Sessions, Continued

15:00 Break

15:30 Reports from breakout sessions and concluding discussions

16:30 Adjourn

Joint Session of the National Stock and Habitat Assessment 

Workshops

Tuesday, May 18

Invitational and Keynote Lectures

8:30 Welcome Sutter

8:40 Identifying the role of habitat science in NMFS Cyr

9:00 Developing and implementing the Habitat Assessment Improvement Plan Yoklavich

9:20 Building and funding a national Habitat Science Program in NMFS S. Brown

9:40 Stock assessment 101: Getting to ABC Methot

10:10 Break

10:30 Keynote Lecture: Informing and improving stock assessments with marine habitat information Grimes

Theme Session G: Incorporating Habitat Information into Stock Assessments

11:15 A framework for incorporating climate impacts on pelagic ocean habitats into stock assessments Hollowed, Greig, 

Logerwell, Wilson

11:30 Incorporating the effects of an environmental regime shift in an assessment of Atlantic menhaden population 

dynamics Quinlan, Schueller, Vaughan

11:45 Insights for stock assessment and empirical prerecruit indices from an environmentally forced individual-based 

model of early life history stages for west coast rockfishes Bjorkstedt, Ralston

12:00 Lunch

13:00 A habitat-specific approach for incorporating environmental variation into stock forecasting models C. Greene, 

Hall, Beamer, Pess

13:15 Integrating habitat change and population dynamics: Using the Shiraz framework to evaluate salmon recovery 

efforts Jorgensen

13:30 Can habitat-based densities predict stock status in a heavily fished Caribbean gastropod? Hill, McCarthy, 

Appeldoorn

13:45 Can we use habitat information to derive prior distributions for virgin biomass of deepwater groupers and 

tilefish? Walter, Cook, Lombardi, Quinlan

14:00 Using statistical modeling and Ocean Observing Systems to identify fish habitat at broad scales: Potential 

applications for spatial planning, estimation of natural mortality, and reducing fisheries bycatch Manderson, 

Kohut, Palamara, Grey, Oliver

14:15 Break

Theme Session H: Improving Calibration and Precision of Resource Surveys with Habitat 

Information

14:45 Incorporating satellite derived environmental data with Gulf of Mexico pelagic longline observer data for the 

evaluation of bluefin tuna relative abundance and distribution patterns C. Brown, Ramírez López, Quinlan
82

15:00 Expansion of Atlantic croaker (Micropogonias undulatus) larval habitat on the northeast U.S. continental shelf 

Walsh, Richardson, Hare, Marancik

15:15 Habitat-specific survey methods to improve assessments of rockfishes off California and Alaska Yoklavich, 

O’Connell

15:30 Integrating benthic community structure data into a stratified random sampling design to improve reef fish 

abundance estimates in the Northwestern Hawaiian Islands Helyer, Williams

15:45 Collaborative Optically-assisted Acoustical Survey Technique (COAST) for surveying the distributions, 

abundances, and lengths of demersal fishes, by species Demer, Butler, Cutter, Stierhoff, Byers, Murfin, Renfree, Mau, 

Sessions

16:00 Using mesohabitat information to improve abundance estimates for west coast groundfish: A test case at Heceta 

Bank, OR Wakefield, Clemons, Stewart, Whitmire

16:15 Modeling habitat relationships for rockfish to improve fishery-independent survey biomass estimates Rooper, 

Martin, Spencer

16:30 Advances in conducting spatially-explicit, fishery-independent, ecosystem-based reef fish and habitat assessments 

Bohnsack, Ruttenberg

16:45 Concluding discussions

17:00 Adjourn

18:30 Poster Session

Wednesday, May 19

8:15 Keynote Lecture: Are we running out of fish? And where will they live? Murawski

9:00 Charge to breakout groups, move to breakout rooms

9:15 Breakout Sessions

Session 1: Using habitat information in survey design and analysis

Session 2: Including habitat-specific life history rates in population models

Session 3: Using time series of habitat information in population models

9:45 Breakout groups subdivide by habitat/species

10:40 Break

11:00 Report from breakout groups

12:00 Lunch

National Habitat Assessment Workshop

Wednesday, May 19

13:00 Welcome Montanio

13:15 Keynote Lecture: Confronting the ghosts of Christmases past: A new context for habitat assessments Boreman

13:45 Outline session goals and objectives

Habitat Science in Support of Management, Session 1

14:00 Presentation: An assessment of current processes for providing habitat science for management

14:45 Panel Discussion: Proposing alternatives to the current processes

15:30 Break

15:50 Charge to breakout groups 
83

16:00 Breakout Sessions: Evaluating current Science Center, Regional Office, and Restoration Center interactions

17:00 Report from breakout groups

17:30 Adjourn

18:30 Poster Session

Thursday, May 20

8:15 Welcome 

Habitat Science in Support of Management, Session 2

8:30 Presentation: How do we develop long-term capacity in the Science Centers to meet management needs?

9:15 Panel Discussion: Proposing strategies for the development of habitat science capacity and the incorporation of 

habitat science into management

10:00 Break

10:15 Breakout Sessions: Evaluating strategies for the development of habitat science capacity and the incorporation of 

habitat science into management

11:15 Report from breakout groups

12:00 Lunch

Habitat Science in Support of Management, Session 3

13:00 Breakout Sessions, organized by region: How do we implement the proposed solutions in our region?

15:00 Report from breakout groups

15:45 Break

16:00 Summary presentation: Highlighting meeting accomplishments and identifying the next steps for habitat science 

and management

16:30 Concluding remarks

17:00 Adjourn

85

Appendix 3: NSAW & NHAW Participants

Karen Abrams OHC, Habitat Protection Division Karen.Abrams@noaa.gov

Michelle Bachman New England Fishery Management Council mbachman@nefmc.org

Gretchen Bath Martin SEFSC, Beaufort Laboratory Gretchen.Bath.Martin@noaa.gov

Jim Berkson SEFSC, RTR Unit at Virginia Tech Jim.Berkson@noaa.gov

Thomas Bigford OHC, Habitat Protection Division Thomas.Bigford@noaa.gov

Eric Bjorkstedt SWFSC, Fisheries Ecology Division Eric.Bjorkstedt@noaa.gov

Kristan Blackhart OST, Assessment and Monitoring Division Kristan.Blackhart@noaa.gov

James A. Bohnsack SEFSC, Miami Center Jim.Bohnsack@noaa.gov

John Boreman North Carolina State University John.Boreman@ncsu.edu

Eric Breuer OST, Marine Ecosystems Division Eric.Breuer@noaa.gov

Jon Brodziak PIFSC, Fishery Biology and Stock Assessment Division Jon.Brodziak@noaa.gov

Elizabeth Brooks NEFSC, Resource Evaluation and Assessment Division Liz.Brooks@noaa.gov

Joan Browder SEFSC, Miami Center Joan.Browder@noaa.gov

Craig Brown SEFSC, Miami Center Craig.Brown@noaa.gov

Stephen K. Brown OST, Assessment and Monitoring Division Stephen.K.Brown@noaa.gov

David Bruce OHC, Chesapeake Bay Office David.Bruce@noaa.gov

Michael Burton SEFSC, Beaufort Laboratory Michael.Burton@noaa.gov

Allison Candelmo NEFSC, Ecosystems Processes Division Allison.Candelmo@noaa.gov

Shannon L. Cass-Calay SEFSC, Miami Center Shannon.Calay@noaa.gov

John Catena OHC, Restoration Center John.Catena@noaa.gov

R. Christopher NEFSC, Ecosystems Processes Division Chris.Chambers@noaa.gov

Chambers

Louis A. Chiarella NERO, Habitat Conservation Division Lou.Chiarella@noaa.gov

Dezhang Chu NWFSC, Fisheries Resource Analysis and Monitoring Dezhang.Chu@noaa.gov

 Division

Antonie Chute NEFSC, Resource Evaluation and Analysis Division Toni.Chute@noaa.gov

M. Elizabeth Clarke NWFSC, Fisheries Resource Analysis and Monitoring Elizabeth.Clarke@noaa.gov

 Division 

Lora Clarke Office of the Assistant Administrator Lora.Clarke@noaa.gov

Julia E.R. Clemons NWFSC, Fisheries Resource Analysis and Monitoring Julia.Clemons@noaa.gov

 Division

Tracy Collier NOAA Oceans and Human Health Program Tracy.K.Collier@noaa.gov

Angela B. Collins Florida Fish and Wildlife Conservation Commission Angela.Collins@myfwc.com

Mathias J. Collins OHC, Restoration Center Mathias.Collins@noaa.gov

Peter Colosi NERO, Habitat Conservation Division Pete.Colosi@noaa.gov

Ray Conser SWFSC, Fisheries Resources Division Ray.Conser@noaa.gov

Thomas D. Cooney NWFSC, Conservation Biology Division Tom.Cooney@noaa.gov

Name Affiliation E-mail 
86

Name Affiliation E-mail 

Jason M. Cope NWFSC, Fisheries Resource Analysis and Monitoring Jason.Cope@noaa.gov

 Division

Sean Corson OHC, Chesapeake Bay Office Sean.Corson@noaa.gov

Miles Croom SERO, Habitat Conservation Division Miles.Croom@noaa.gov

Ned Cyr OST, Director Ned.Cyr@noaa.gov

David Dale SERO, Habitat Conservation Division David.Dale@noaa.gov

Gerry Davis PIRO, Habitat Conservation Division Gerry.Davis@noaa.gov

Bryan DeAngelis OHC, Restoration Center Bryan.DeAngelis@noaa.gov

David A. Demer SWFSC, Fisheries Resources Division David.Demer@noaa.gov

Jonathan J. Deroba NEFSC, Resource Evaluation and Assessment Division Jonathan.Deroba@noaa.gov

Doug DeVries SEFSC, Panama City Laboratory Doug.DeVries@noaa.gov

E.J. Dick SWFSC, Fisheries Ecology Division Edward.Dick@noaa.gov 

Gerard DiNardo PIFSC, Fishery Biology and Stock Assessment Division Gerard.DiNardo@noaa.gov

Chris Doley OHC, Restoration Center Chris.Doley@noaa.gov

Matt Eagleton AKRO, Habitat Conservation Division Matthew.Eagleton@noaa.gov

Alan Everson PIRO, Habitat Conservation Division Alan.Everson@noaa.gov

Kari Fenske SEFSC, Southeast Data, Assessment, and Review Kari.Fenske@safmc.net

Scott Ferguson PIFSC, Protected Species Division Scott.Ferguson@noaa.gov

Gary Fitzhugh SEFSC, Panama City Laboratory Gary.Fitzhugh@noaa.gov

David G. Foley SWFSC, Environmental Research Division Dave.Foley@noaa.gov

Claudia Friess Ocean Conservancy cfriess@oceanconservancy.org

John Froeschke Gulf of Mexico Fishery Management Council john.froeschke@gulfcouncil.org

Graciela Garcia-Moliner Caribbean Fishery Management Council graciela_cfmc@yahoo.com

Thomas M. Garrison University of Washington gtommy@u.washington.edu

Perry Gayaldo OHC, Restoration Center Perry.Gayaldo@noaa.gov

Todd Gedamke SEFSC, Sustainable Fisheries Division Todd.Gedamke@noaa.gov

Vladlena V. Gertseva NWFSC, Fishery Resource Analysis and Monitoring Vladlena.Gertseva@noaa.gov

 Division

Steve Giordano OHC, Chesapeake Bay Office Steve.Giordano@noaa.gov

Joseph Godlewski NEFSC, Fisheries and Ecosystems Monitoring and Analysis Joseph.Godlewski@noaa.gov

 Division

Stanley Gorski NERO, Habitat Conservation Division Stanley.W.Gorski@noaa.gov

Correigh Greene NWFSC, Environmental Conservation Division Correigh.Greene@noaa.gov

Karen Greene NERO, Habitat Conservation Division Karen.Greene@noaa.gov

Churchill B. Grimes SWFSC, Fisheries Ecology Division Churchill.Grimes@noaa.gov

Vincent G. Guida NEFSC, Ecosystems Processes Division Vincent.Guida@noaa.gov

Melissa A. Haltuch NWFSC, Fisheries Resource Analysis and Monitoring Melissa.Haltuch@noaa.gov

 Division

Owen Hamel NWFSC, Fisheries Resource Analysis and Monitoring Owen.Hamel@noaa.gov

 Division

Alonzo Hamilton SEFSC, Mississippi Laboratory Alonzo.N.Hamilton@noaa.gov
87

Name Affiliation E-mail 

David S. Hanisko SEFSC, Mississippi Laboratory David.S.Hanisko@noaa.gov

Dana H. Hanselman AFSC, Auke Bay Laboratories Dana.Hanselman@noaa.gov

Jeanne Hanson AKRO, Habitat Conservation Division Jeanne.Hanson@noaa.gov

Rick A. Hart SEFSC, Galveston Laboratory Rick.Hart@noaa.gov

James D. Hastie NWFSC, Fisheries Resource Analysis and Monitoring Jim.Hastie@noaa.gov

 Division

Dennis Heinemann Ocean Conservancy DHeinemann

 @oceanconservancy.org

Jason Helyer PIFSC, Coral Reef Ecosystem Division Jason.Helyer@noaa.gov

Daniel Hennen NEFSC, Resource Evaluation and Assessment Division Daniel.Hennen@noaa.gov

Allan Hicks NWFSC, Fisheries Resource Analysis and Monitoring Allan.Hicks@noaa.gov

 Division

Ronald L. Hill SEFSC, Galveston Laboratory Ron.Hill@noaa.gov

Tom Hoff Mid-Atlantic Fishery Management Council thoff@mafmc.org

Bob Hoffman SWRO, Habitat Conservation Division Bob.Hoffman@noaa.gov

Anne B. Hollowed AFSC, Resource Ecology and Fisheries Management Anne.Hollowed@noaa.gov

 Division

Terill Hollweg OHC, Restoration Center Terill.Hollweg@noaa.gov

Brian Hostetter OHC, Restoration Center Brian.Hostetter@noaa.gov

Thomas F. Hourigan OHC, Habitat Protection Division Tom.Hourigan@noaa.gov

Staci Hudy Virginia Tech sfhudy@vt.edu

John Iliff OHC, Restoration Center John.Iliff@noaa.gov

Larry Jacobson NEFSC, Resource Evaluation and Assessment Division Larry.Jacobson@noaa.gov

Michael Jech NEFSC, Fisheries and Ecosystems Monitoring and Analysis Michael.Jech@noaa.gov

 Division

Jeff Jorgensen NWFSC, Conservation Biology Division Jeff.Jorgensen@noaa.gov

Isaac Kaplan NWFSC, Conservation Biology Division Isaac.Kaplan@noaa.gov

Stephen Kasperski AFSC, Resource Ecology and Fisheries Management Stephen.Kasperski@noaa.gov

 Division

Charles Keith NEFSC, Resource Evaluation and Assessment Division ckeith@mercury.wh.whoi.edu

Todd Kellison SEFSC, Beaufort Laboratory Todd.Kellison@noaa.gov

Jon Kurland AKRO, Habitat Conservation Division Jon.Kurland@noaa.gov

Debra Lambert OSF, Domestic Fisheries Division Deb.Lambert@noaa.gov

Richard Langton NEFSC, Ecosystems Processes Division Rich.Langton@noaa.gov

Kirsten Larsen OST, Assessment and Monitoring Division Kirsten.Larsen@noaa.gov

Ben Laws OHC, Habitat Protection Division Benjamin.Laws@noaa.gov

Terra Lederhouse OHC, Habitat Protection Division Terra.Lederhouse@noaa.gov

Hui-Hua Lee PIFSC, Fishery Biology and Stock Assessment Division Huihua.Lee@noaa.gov

Chris Legault NEFSC, Resource Evaluation and Assessment Division Chris.Legault@noaa.gov

Steve Lindley SWFSC, Fisheries Ecology Division Steve.Lindley@noaa.gov

Brian Linton SEFSC, Sustainable Fisheries Division Brian.Linton@noaa.gov
88

Name Affiliation E-mail 

Patricia Livingston AFSC, Resource Ecology and Fisheries Management Pat.Livingston@noaa.gov

 Division

Linda Lombardi SEFSC, Panama City Laboratory Linda.Lombardi@noaa.gov

Sandra A. Lowe AFSC, Resource Ecology and Fisheries Management Sandra.Lowe@noaa.gov

 Division

Clyde L. MacKenzie, Jr. NEFSC, Ecosystems Processes Division Clyde.MacKenzie@noaa.gov

John P. Manderson NEFSC, Ecosystems Processes Division John.Manderson@noaa.gov

Garry Mayer OHC, Senior Scientist Garry.Mayer@noaa.gov

Richard S. McBride NEFSC, Fisheries and Ecosystems Monitoring and Analysis Richard.McBride@noaa.gov

 Division

Kevin McCarthy SEFSC, Sustainable Fisheries Division Kevin.J.McCarthy@noaa.gov

Bob McConnaughey AFSC, Resource Assessment and Conservation Engineering Bob.McConnaughey@noaa.gov

 Division

Sean McDermott NERO, Habitat Conservation Division Sean.McDermott@noaa.gov

Susanne McDermott AFSC, Resource Ecology and Fisheries Management Susanne.McDermott@noaa.gov

 Division

Carey McGilliard University of Washington careymcg@u.washington.edu

Kara Meckley OHC, Habitat Protection Division Kara.Meckley@noaa.gov

Richard D. Methot, Jr. OST, Assessment and Monitoring Division Richard.Methot@noaa.gov

Dave Meyer SEFSC, Beaufort Laboratory Dave.Meyer@noaa.gov

William L. Michaels OST, Assessment and Monitoring Division William.Michaels@noaa.gov

Tim Miller NEFSC, Resource Evaluation and Assessment Division Timothy.J.Miller@noaa.gov

Mark Millikin OSF, Domestic Fisheries Division Mark.Millikin@noaa.gov

Tom Minello SEFSC, Galveston Laboratory Tom.Minello@noaa.gov

Melissa Monk Louisiana State University mhedge1@tigers.lsu.edu

Pat Montanio OHC, Director Pat.Montanio@noaa.gov

Paula Moreno SEFSC, Mississippi Laboratory Paula.Moreno@noaa.gov

Roldan Munoz SEFSC, Beaufort Laboratory Roldan.Munoz@noaa.gov

Steven A. Murawski Director of Scientific Programs & Chief Scientific Advisor Steve.Murawski@noaa.gov

James M. Nance SEFSC, Galveston Laboratory James.M.Nance@noaa.gov

Julie Neer SEFSC, Southeast Data, Assessment, and Review Julie.Neer@safmc.net

Redwood W. Nero SEFSC, Mississippi Laboratory Woody.Nero@noaa.gov

Joe Nohner OST, Assessment and Monitoring Division Joe.Nohner@noaa.gov

Thomas Noji NEFSC, Ecosystems Processes Division Thomas.Noji@noaa.gov

Michael Parke PIFSC, Operations, Management and Information Division Michael.Parke@noaa.gov

Frank Parrish PIFSC, Protected Species Division Frank.Parrish@noaa.gov

Wesley S. Patrick OSF, Domestic Fisheries Division Wesley.Patrick@noaa.gov

Beth Phelan NEFSC, Ecosystems Processes Division Beth.Phelan@noaa.gov

Kevin Piner PIFSC, Fishery Biology and Stock Assessment Division Kevin.Piner@noaa.gov

Adam Pollack SEFSC, Mississippi Laboratory Adam.Pollack@noaa.gov

Clay Porch SEFSC, Sustainable Fisheries Division Clay.Porch@noaa.gov
89

Name Affiliation E-mail 

John A. Quinlan SEFSC, Miami Center John.A.Quinlan@noaa.gov

Stephen Ralston SWFSC, Fisheries Ecology Division Steve.Ralston@noaa.gov

John Rapp OHC, Restoration Center John.Rapp@noaa.gov

Jeff Rester Gulf States Marine Fisheries Commission jrester@gsmfc.org

Jeep Rice AFSC, Auke Bay Laboratories Jeep.Rice@noaa.gov

David E. Richardson NEFSC, Ecosystems Processes Division David.Richardson@noaa.gov

John Rooney PIFSC, Coral Reef Ecosystem Division John.Rooney@noaa.gov

Chris Rooper AFSC, Resource Assessment and Conservation Engineering Chris.Rooper@noaa.gov

 Division

Lawrence Rozas SEFSC, Galveston Laboratory Lawrence.Rozas@noaa.gov

Lou Rugolo AFSC, Resource Assessment and Conservation Engineering Lou.Rugolo@noaa.gov

 Division

Patrick Rutten OHC, Restoration Center Patrick.Rutten@noaa.gov

David Rydene SERO, Habitat Conservation Division David.Rydene@noaa.gov

Courtney Saari Louisiana State Univerisity cnosac1@tigers.lsu.edu

Marlowe Sabater Western Pacific Fishery Management Council mgsabater@yahoo.com

Steven Saul University of Miami ssaul@rsmas.miami.edu

Korie Schaeffer SWRO, Habitat Conservation Division Korie.Schaeffer@noaa.gov

Christina Schobernd SEFSC, Mississippi Laboratory Christina.Schobernd@noaa.gov

Amy M. Schueller SEFSC, Beaufort Laboratory Amy.Schueller@noaa.gov

Joseph E. Serafy SEFSC, Miami Center Joe.Serafy@noaa.gov

Manoj Shivlani Center for Independent Experts shivlanim@bellsouth.net

S. Kalei Shotwell AFSC, Auke Bay Laboratories Kalei.Shotwell@noaa.gov

Christina Show SWFSC, Fisheries Resources Division Christina.Show@noaa.gov

Mike Sigler AFSC, Habitat and Ecological Processes Program Mike.Sigler@noaa.gov

David Somerton AFSC, Resource Assessment and ConservationEngineering David.Somerton@noaa.gov

 Division

Paul Spencer AFSC, Resource Ecology and Fisheries Management Paul.Spencer@noaa.gov

 Division

Mark Sramek SERO, Habitat Conservation Division Mark.Sramek@noaa.gov

John Stadler NWRO, Habitat Conservation Division John.Stadler@noaa.gov

Susan-Marie Stedman OHC, Habitat Protection Division Susan.Stedman@noaa.gov

Jennifer Steger OHC, Restoration Center Jennifer.Steger@noaa.gov

Andi Stephens NWFSC, Fisheries Resource Analysis and Monitoring Andi.Stephens@noaa.gov

 Division

David K. Stevenson NERO, Habitat Conservation Division David.Stevenson@noaa.gov

Ian J. Stewart NWFSC, Fisheries Resource Analysis and Monitoring Ian.Stewart@noaa.gov

 Division

Kevin Stierhoff SWFSC, Fisheries Resources Division Kevin.Stierhoff@noaa.gov

Diana L. Stram North Pacific Fishery Management Council Diana.Stram@noaa.gov

Emily Susko Virginia Tech esusko@vt.edu
90

Rusty Swafford SERO, Habitat Conservation Division Rusty.Swafford@noaa.gov

Brendan Sylvander NWFSC, Operations, Management, and Information Brendan.Sylvander@noaa.gov

 Division

Kathleen Szleper OST, Ecosystem Assessment Program Kathleen.Szleper@noaa.gov

Cody Szuwalski University of Washington c.s.szuwalski@gmail.com

Ian G. Taylor OST, Assessment and Monitoring Division Ian.Taylor@noaa.gov

Michael Tehan NWRO, Habitat Conservation Division Mike.Tehan@noaa.gov

Charles H. Thompson SEFSC, Mississippi Laboratory Charles.H.Thompson@noaa.gov

Grant G. Thompson AFSC, Resource Ecology and Fisheries Management Grant.Thompson@noaa.gov

 Division

James T. Thorson University of Washington jimthor@uw.edu

Howard Townsend OHC, Chesapeake Bay Office Howard.Townsend@noaa.gov

Jack Turnock AFSC, Resource Ecology and Fisheries Management Jack.Turnock@noaa.gov

 Division

Sue Tuxbury NERO, Habitat Conservation Division Susan.Tuxbury@noaa.gov

Douglas S. Vaughan SEFSC, Beaufort Laboratory Doug.Vaughan@noaa.gov

W. Waldo Wakefield NWFSC, Fisheries Resource Analysis and Monitoring Waldo.Wakefield@noaa.gov

 Division

Harvey J. Walsh NEFSC, Ecosystems Processes Division Harvey.Walsh@noaa.gov

John F. Walter SEFSC, Miami Center John.F.Walter@noaa.gov

Curt E. Whitmire NWFSC, Fisheries Resource Analysis and Monitoring Curt.Whitmire@noaa.gov

 Division

Pace Wilber SERO, Habitat Conservation Division Pace.Wilber@noaa.gov

Chris Wilson AFSC, Resource Assessment and Conservation Engineering Chris.Wilson@noaa.gov

 Division

Mary M. Yoklavich SWFSC, Fisheries Ecology Division Mary.Yoklavich@noaa.gov

Name Affiliation E-mail 
91

Appendix 4: Abstracts

*denotes presenting author

Keynote and Invited Speakers

Perspectives on current issues in fish stock assessments

Richard D. Methot, Jr.

Office of Science and Technology, Seattle, WA

It has been ten years since development of the Marine Fisheries Stock Assessment Improvement Plan. In that time, the Expand 

Annual Stock Assessment (EASA) budget line has grown from $1.7M in 2001 to $50.9M in 2010 and is now nearly 25% 

of NMFS total expenditures for fish catch and stock monitoring and assessment. This budget line supports recreational and 

commercial catch monitoring programs, fishery-independent surveys, stock assessment staff and programs, and several national endeavors: Advanced Sampling Technology, Assessment Toolbox (recently expanded to Assessment Methods and to 

include competitive projects and AD Model Builder support), Center for Independent Experts, Species Information System 

(which contains summary information on all stock assessments and status determinations), Fisheries Scientific Computing 

System (which collects and manages survey data at-sea), Sea Grant fellowships in population dynamics (recently expanded 

to support 6 new students per year), and Fisheries and the Environment. In 2005, the Fish Stock Sustainability Index (FSSI) 

was created as a performance measure to track the assessment and management of 230 selected stocks. The growing EASA 

budget has enabled us to increase the number of FSSI stocks with adequate assessments from 100 in 2001 to 139 in 2010. 

Another major boost to our capability has been the recapitalization of the NOAA fleet of fishery survey vessels, with the 

fourth new vessel, the Bell M. Shimada, becoming operational this year and a fifth vessel is due in 2013. The demand for 

more frequent and better assessments of more stocks continues to increase. A major current challenge for our stock assessment enterprise is to meet the expectations of the National Standard 1 Guidelines. This basically means that assessment 

outputs need to more comprehensively calculate uncertainty in model outputs to support risk analysis with respect the 

probability that a proposed catch limit will prevent overfishing. In parallel, the Fishery Management Council’s Scientific 

and Statistical Committees (SSCs) are developing protocols for using these assessment results as they specify the level of acceptable biological catch that will prevent overfishing. National SSC workshops in 2008 and 2009 provided an opportunity 

for representatives from the SSCs and from NMFS assessment programs to work together on these issues. Some additional 

challenges facing the assessment community include: providing assessments for data-weak stocks; continuing to develop 

data methods to link assessments to ecosystem/habitat/environment processes; building more spatial structure into the assessments to better engage with marine spatial planning, including marine protected areas; and improving fishery-independent survey information through increased use of advanced technology and cooperative surveys.

Identifying the role of habitat science in NMFS

Ned Cyr

Office of Science and Technology, Silver Spring, MD

The continuing loss of marine and coastal habitats has been identified in the Magnuson-Stevens Act (MSA) as one of the 

“greatest long-term threats to the viability of commercial and recreational fisheries”. The National Marine Fisheries Service 

(NMFS) has a mandated responsibility, via the MSA and other habitat-related legislation, to sustain marine fisheries and 

associated habitats. This requirement defines a unique role for NMFS in addressing the marine fisheries aspects of habitat 

science and providing the habitat information necessary to support informed management decisions. NMFS is working to 

develop a coordinated habitat science program that will deliver sound habitat science and make habitat information read-
92

ily available for use by fishery managers. Improved habitat science information will find a wide number of uses throughout 

NMFS, including managing essential fish habitat, habitat restoration, stock assessment, integrated ecosystem assessment, 

coastal and marine spatial planning, understanding climate change, and ecosystem-based fishery management.

Developing and implementing the Habitat Assessment Improvement Plan

Mary M. Yoklavich

SWFSC, Santa Cruz, CA

The Habitat Assessment Improvement Plan (HAIP) is the first nationally coordinated plan to focus on the marine fisheries 

aspects of habitat science. It addresses the lack of knowledge regarding the association of marine species and their habitats, 

which impedes effective fisheries and habitat management, protection, restoration, and stock assessment. Questionnaire 

responses from NMFS managers and scientists indicated a lack of habitat-specific data, staff to collect such data, and knowledge of interactions within the ecosystem. The HAIP establishes the framework for NMFS to coordinate habitat research, 

monitoring, and assessments and to increase support for habitat science. The goals of the HAIP are to: 1) assist NMFS in 

developing a habitat science program; 2) improve our ability to identify essential fish habitat (EFH) and habitat areas of 

particular concern; 3) provide information needed to assess impacts to EFH; 4) reduce habitat-related uncertainty in stock 

assessments; 5) facilitate a greater number of stock assessments that explicitly incorporate ecosystem considerations and spatial analyses; 6) contribute to assessments of ecosystem services (i.e. the things people need and care about that are provided 

by ecosystems); and 7) contribute to ecosystem-based fishery management, integrated ecosystem assessments, and coastal 

and marine spatial planning.

Building and funding a National Habitat Science Program in NMFS

Stephen K. Brown

Assessment and Monitoring Division, Office of Science and Technology, Silver Spring, MD

The team charged with developing the Habitat Assessment Improvement Plan (HAIP) has completed this task, which required about two years from start to finish. The NMFS Science Board has asked that this excellent team continue to work 

on implementing the HAIP. This will be a more complex task in which the HAIP team, and NMFS as a whole, will have less 

control over events and outcomes. Success will depend on persistence, creativity and flexibility, and the merit of the ideas we 

generate and the initiatives we pursue. 

The HAIP provides recommendations that should be addressed. We will need to develop new budget and staffing initiatives, 

because it is obvious that additional funding is needed. It is also apparent that existing partnerships will have to be strengthened, and new partnerships developed. On one hand, it’s no secret that the Federal budget is under considerable strain, so 

funding for new programs, no matter how important they may seem, is likely to be quite limited in the foreseeable future. 

On the other hand, many entities within NMFS, within other NOAA line offices, and in other federal and state agencies, 

as well as in academia and the private sector, have needs for better habitat science. They also have resources, expertise, and 

potential sources of funding to bring to the table. 

The HAIP contains other recommendations that can be implemented with little or no new funding. Many of these require 

changes in how we do business and how we relate with one another. Holding the 1st National Habitat Assessment Workshop (NHAW), bringing together habitat scientists, stock assessment scientists, and habitat managers involved with habitat 

protection and habitat restoration is an important first step in bringing about these changes. This should be followed by 

concerted efforts to carry out ideas generated at the NHAW, as well as efforts to follow up on other recommendations of 

the HAIP. These include developing criteria to prioritize stocks and geographic areas that would benefit from habitat assessments, identifying and prioritizing data inadequacies for stocks and their habitats, implementing demonstration projects 
93

(we are already doing this), convening additional regional and national workshops focused on habitat science and management issues, etc.

In the Forward to the HAIP, John Boreman, the recently retired Director of the NMFS Office of Science and Technology 

and prime instigator of the HAIP, closes by saying, “Now that we finally have the ball in play, let’s not drop it.” I’m looking 

forward to the group in this room, and to our colleagues around the agency and around the nation, to taking up this challenge. It will be hard work, but it will be worth it.

Stock assessment 101: Getting to ABC

Richard D. Methot, Jr.

Office of Science and Technology, Seattle, WA

Fish stock assessments provide the quantitative basis for implementing the National Standard 1 Guidelines of the Magnuson-Stevens Reauthorization Act of 2006. Assessments determine the abundance of a fish stock and the level of fishing 

mortality it is experiencing relative to sustainable levels. Thus, assessment results are key to determining whether or not a fish 

stock is overfished and for forecasting a level of catch that would obtain optimum yield from the fishery while preventing 

overfishing, or, in the case of a previously overfished stock, would rebuild the stock to a level capable of producing maximum 

yield. Assessments analyze three fundamental types of information. First is catch, which is the amount of fish being removed 

from the stock by commercial and recreational fisheries, including discarded bycatch. Second is a measure of stock abundance or a time series trend of relative stock abundance. These data are best obtained from fishery-independent surveys with 

high degree of standardization and statistically designed coverage of the range of the stock, but in many cases the catch rate 

(catch per unit of effort) of the fishery is processed to serve as a proxy for a fishery-independent survey trend. Third is life 

history information (natural mortality, growth and reproduction). Stock assessment models combine these data to estimate 

how large the stock must have been in order to have displayed the observed abundance information while experiencing the 

observed level of fishery removals and conditioned on the biological characteristics of the stock. Assessments typically deal 

with the fish stock as a uniform, essentially well-mixed entity. One important role of fish-habitat studies is to determine the 

degree to which this unit stock, well-mixed assumption is too simple to provide useful management advice over the broad 

spatial scale of the assessment. Questions regarding marine spatial planning, including marine protected areas, need more 

spatially-explicit fish stock assessment models.

Where there is a time series of young fish surveys or a time series of age and size composition data, assessment models are 

also able to estimate annual levels of fish recruitment. Recruitment fluctuates naturally from year to year due to a variety of 

climate, habitat and environmental factors, the details of which are rarely known. Where there is a sufficiently long time series of these recruitment estimates, it is sometimes possible to estimate the relationship between spawner abundance and the 

expected (mean) level of recruitment produced by these spawners. Typically, average recruitment does not decline until the 

spawning stock is much depleted and this compensatory resilience (aka steepness) is the productivity that sustains fisheries. 

Fish habitat studies have a key role in determining the life stage(s) at which this compensation principally occurs, but absent 

this detailed information the spawner-recruitment model treats the transition from spawner abundance to recruitment (at 

age 1 or so) as a one-step, black-box process. The ability to estimate this steepness parameter strongly depends on being able 

to observe recruitment over a wide range of spawner abundance levels, on observing enough years so that the mean recruitment signal can be detected from annual fluctuations, and on there not being long-term climate/ecosystem/habitat changes 

that may also affect mean recruitment levels thus are confounded with the spawner-recruitment relationship. Given these 

challenges, most assessments are not able to estimate steepness so provide fishery management advice in terms of maintaining a spawner abundance level that is in the range of 30–50% of unfished levels. Investigation of the suite of habitat and 

ecosystem factors that create a recruitment event from the fecundity of the spawning stock remains an important ecological 

challenge.
94

Informing and improving stock assessments with marine habitat information

Churchill B. Grimes*, Stephen Ralston, John C. Field, Brian Wells, and Mary M. Yoklavich 

SWFSC, Santa Cruz, CA

Habitat degradation and destruction have long been recognized as among the principal causes of declining marine fish 

stocks. However, it was not until the 1996 reauthorization of the Magnuson-Stevens Fishery Conservation and Management Act that NMFS was given statutory responsibility to incorporate habitat considerations into Fishery Management 

Plans. Since that time the use of habitat information by scientists to inform and improve stock assessments has proceeded 

at a slow pace. For this presentation we define habitat as the space in which any life stage of fish species live as defined by 

any relevant physical and biological variables. For example, pelagic habitat might be described by such variables as upwelling, Ekman transport, sea surface temperature, chlorophyll concentration, and ocean environmental indices (e.g. the Pacific 

Decadal Oscillation or El Niño-Southern Oscillation), and benthic habitat by substratum type (e.g. rock, clay, or reef ), bottom temperature, depth, and vegetative cover (e.g. kelp or seagrass). Several species and habitat types will be used as examples 

of how habitat variables affect distribution, growth, recruitment, and natural and fishing mortality and potentially could be 

used to improve stock assessments.

Are we running out of fish? And where will they live?

Steven A. Murawski

Director, Scientific Programs and Chief Science Advisor, Silver Spring, MD

NOAA Fisheries Service is responsible for managing the nation’s marine fisheries, and for providing the best available science upon which management decisions must be based. Recovery of depleted fishery populations has become a consistent 

and increasingly important theme in national and international environmental negotiations and commitments regarding 

sustainability. We are not running out of fish, but we recognize that there are real concerns to be addressed for sustaining 

our fisheries in the future, and for increasing the economic and social benefits we obtain from them. We know that many of 

stocks are being sustainably fished, but that quite a few are not. We also know what we do not know. The U.S. Ocean Policy 

Task Force specifically has called for the “protection, maintenance, and restoration of populations and essential habitats supporting fisheries, protected species, ecosystems, and biological diversity” to support ecosystems as one of its priority objectives. More and better data, and more broadly based management approaches for managing our nation’s marine ecosystems, 

are needed. It is clear that if we are to recover the majority of stocks classified world-wide as “overfished”, it will take a more 

holistic, adaptive and ecosystem-based approach to fishery recovery that incorporates trophic dynamics, habitat protection 

and restoration, and climate effects, and is sensitive to life history and previous impacts of fisheries on stock resilience. Science supporting the implementation of ecosystem-based principles chiefly requires information on species interactions, climate-species relationships, and habitat-species dependencies. Basic habitat information including where important habitat 

is located and its condition are lacking for many species, and traditional assessment methods can not be used for many stocks 

due to habitat challenges. In addition, these basic categories of habitat science are needed to conduct integrated ecosystem 

assessments, which are poised to boost the successful application of ecosystem-based management (EBM). Without such 

information, environmentalists urge precautionary management, while existing use sectors demand more specificity in the 

issues to be considered under the EBM rubric, as well as an accounting of how current management fails to address important issues. A new, more effective, consistent, and politically supported stock recovery paradigm is necessary if society is to 

eventually meet its articulated sustainability goals for global fisheries. 
95

Confronting the ghosts of Christmases past: A new context for habitat assessments

John Boreman

North Carolina State University, Department of Biology; formerly Director, Office of Science and Technology

The concept of a habitat assessment workshop is not new. Several similar attempts have been made by NMFS over the past 

25 years—all have failed. Reasons for the failures include lack of standardized methods for habitat assessments, an essentially 

undefined role for habitat assessment in NMFS, and, most importantly, lack of buy-in from NMFS leadership. What is different this time, and how can the problems that plagued past attempts be avoided? 

National Stock Assessment Workshop

Theme A: Understanding the Trade Off Between Simple and Complex Models

Simple spreadsheet: Population models and policy simulations

Linda Lombardi1,3*, C. Walters2,3, M. Allen3, and W.E. Pine3

1

SEFSC, Panama City, FL; 2University of British Columbia, Fisheries Centre, Vancouver, BC; 3University of Florida, 

School of Forest Resources and Conservation, Fisheries and Aquatic Sciences Program, Gainesville, FL

The simplest way to learn population dynamics is to use spreadsheet models. Spreadsheets allow the user to explicitly control 

the number and type of input parameters. Model complexity can range from surplus production and delay difference models 

incorporating recruitment anomalies, to Stock Synthesis and virtual population analysis involving age-specific growth, mortality, fecundity, selectivity and vulnerability vectors. Visually, basic graphics display how manual manipulations of parameters (e.g. exploitation, catchability, stock-recruitment relationship) affect the overall population levels. Alternative policy 

scenarios involving increased exploitation, closed areas, or changes in minimum size limits can also be simulated. Maximum 

likelihood parameter estimation and policy optimization can be done simply using the efficient Solver GRG algorithm. 

These methods are not only a useful tool for beginner assessment scientists but can be implemented by advanced modelers 

to test the results of more complicated assessment models. Simple spreadsheet stock assessment models can also provide a 

common platform for fisheries analysts and stakeholders to examine assessment model design, assumptions, uncertainties 

and outputs, given that spreadsheets are commonly used by citizen stakeholders in their daily lives.

Determining yields for data-poor stocks using a DCAC-based stock reduction analysis of catch history

E.J. Dick* and Alec MacCall 

SWFSC, Fisheries Ecology Division, Santa Cruz, CA

We describe a method for determining reasonable yield for data-poor species. Data requirements include estimates of annual 

catch, approximate natural mortality rate and age at maturity. The method produces management reference points concerning yield (overfishing limit [OFL] and maximum sustainable yield [MSY]) and biomass (Bunfished, BMSY, and Bcurrent). The 

approach merges stochastic stock-reduction analysis (Walters et al., 2009) and depletion-corrected average catch (DCAC; 

MacCall, 2009), and is useful when only catch and basic life history data are available. Uncertainties in natural mortality, 

stock dynamics, optimal harvest rates, and stock status are incorporated using Monte Carlo simulation. Comparison of 

model outputs to data-rich stock assessments suggest that our method is effective, along with DCAC, for estimating sustainable yields for data-poor stocks with variable, but not highly episodic, recruitment.
96

Theme B: Quantification of Uncertainty from Model Structure and Retrospective 

Patterns

Addressing cohort strength related ageing error in fisheries stock assessment 

Owen Hamel* and Ian J. Stewart

NWFSC, Seattle, WA

Age data are important in stock assessment for estimation of parameters such as growth rate, age of maturity, fecundity at 

age, natural mortality rate and recruitment. Unfortunately, age estimates are often subject to considerable error. Even given 

modern otolith annulus counting techniques, there continues to be substantial uncertainty in ages as shown by double read 

analysis as well as various validation methods. Ageing uncertainty is typically included in stock assessments via lab- or eraspecific ageing-error matrices, which generally result in improvements in both parameter estimation and fits to age data. In 

the course of the 2009 Pacific hake (Merluccius productus) stock assessment, however, poor fits to strong year classes were 

consistently seen, despite the use of ageing error matrices. We concluded that the most likely mechanism underlying these 

poor fits was the heretofore suspected tendency for structures with uncertain age determinations to be assigned to predominant year classes. The Pacific hake stock is characterized by infrequent strong year classes, typically surrounded by average 

and below average cohorts. This results in reduced misageing of strong year classes, and perhaps increased misageing of adjacent year classes. Results from the most recent Pacific hake stock assessment demonstrate the advantages of this technique 

through improved fitting of age data, and therefore improved estimation of year class strength. The ‘strong cohort effect’ is a 

potential problem for any species with appreciable ageing imprecision and a high degree of recruitment variability.

Modeling recruitment along the continuum from data-poor to data-rich

Ian G. Taylor1,2* and Richard D. Methot, Jr.3

1

NWFSC, Seattle, WA; 2University of Washington, Seattle, WA; 3Office of Science and Technology, Seattle, WA

Many stocks have adequate data, at least for recent years, to indicate that annual variability in recruitment plays a role in 

population dynamics, but insufficient data to precisely estimate recruitment values for all years with known removals. In 

these cases, the use of a spawner-recruit relationship with a penalty on deviations in recruitment provides a middle ground 

between biomass dynamics models and models with freely estimated recruitment in all years. The variability in the recruitment estimates around the spawner-recruit curve is shown to be a function of both the underlying population process and 

the amount of information in the data about this process. Therefore the data-richness needs to be accounted for in making 

a bias adjustment to the lognormal distribution typically used to model recruitment variability because the mean of the 

lognormal distribution is a function of the variance. A method of using the standard error of the estimated recruitment 

deviation parameters to refine this bias adjustment is presented.

Management strategy evaluation of a retrospective fix

Chris Legault

NEFSC, Woods Hole, MA

Retrospective patterns in a stock assessment are an indication of model mis-specification, where a parameter or a process has 

a temporal component that is not included in the model dynamics. Three commonly investigated sources of retrospective 

patterns are: 1) misreporting of catch; 2) a change in the natural mortality rate; and 3) a change in the survey catchability. 

Each of these sources can be used in a population simulator to create data sets for stock assessment models that will exhibit 

retrospective patterns similar to those observed in actual assessments. The timing of the change can be identified using a 
97

moving window analysis. However, the true source of the retrospective pattern cannot be identified. One approach to reduce the retrospective pattern is to split the survey time series at the time identified through the moving window analysis. A 

management strategy evaluation (MSE) is used to evaluate the consequence of applying this retrospective fix when the true 

source of the retrospective pattern is one of the three described above. The MSE uses the population simulator, virtual population analysis, and age-based projection programs from the NOAA Fisheries Toolbox along with a simple management 

rule to compare the ability to achieve the desired management objective with and without the retrospective fix. Preliminary 

results indicate that splitting the survey time series works as a retrospective fix no matter which of the three sources is the 

cause of the retrospective pattern.

Reconciling uncertain and conflicting trends in petrale sole abundance

Melissa A. Haltuch*, James D. Hastie, Allan Hicks, and Curt E. Whitmire

NWFSC, Seattle, WA

Petrale sole are a commercially important flatfish that migrate seasonally between feeding and spawning grounds, and have 

recently been declared overfished. The summer trawl survey shows a decline in petrale sole abundance since 2005 similar to 

the unstandardized summer catch per unit of effort (CPUE) from the fishery. However, many stakeholders disagree that 

petrale sole abundance has been declining, instead choosing to focus on the unstandardized winter CPUE that shows a 

strong increase beginning in 2000. The assessment attributes the increasing trend in winter CPUE to management actions 

that forced the fleet to: 1) increase fishing effort during the winter; and 2) conduct winter fishing in locations with high 

historical catch rates. Standardized fishery CPUE was not used in the assessment due to changing management regulations 

beginning in the late 1990s and the high likelihood of a winter CPUE index showing hyper-stability due to the fishery focusing on the aggregated spawning stock. Given the potential discrepancy between the assessment results and the experience 

of the groundfish fleet, particularly during the winter fishing season, and the limited conclusions that can be drawn from 

unstandardized CPUE, this work explores the utility of the summer and winter fishery CPUE series as indices of abundance 

for the petrale sole stock assessment. The ultimate goals are to determine if an adequate index of abundance can be created 

using fishery CPUE, and to address the uncertainty due to the discrepancy between the fishery-independent and fisherydependent data sources and therefore the perceived stock assessment uncertainty.

Theme C: Addressing Uncertainty Due to Key Parameters, Especially Natural Mortality

Estimating stock-recruitment steepness from life history information: A case study of North Pacific bluefin 

tuna, Thunnus orientalis

Jon Brodziak1*, Marc Mangel2, and Gerard DiNardo1

1

PIFSC, Honolulu, HI; 2University of California, Santa Cruz, Center for Stock Assessment Research, Santa Cruz, CA

The relationship between spawning stock and the resulting offspring added to the population (recruitment) is a fundamental research problem in fisheries science. The steepness of the stock-recruitment relationship is commonly defined as the 

fraction of unfished recruitment obtained when spawning biomass is 20% of its unfished level. Steepness has become widely 

used in fishery management, where it is usually treated as a statistical quantity. Here, we investigate the reproductive ecology 

of steepness, using biomass dynamics and age-structured models with compensatory recruitment dynamics. We show that 

if one has sufficient life history information to construct a density-independent population model then one can derive an 

associated estimate of steepness. Thus, steepness cannot be chosen arbitrarily. Given that survival of recruited individuals 

fluctuates randomly within a stock, a prior distribution for steepness can be estimated using Monte Carlo simulation and 

information about early life history survival and demographic parameters. We apply our approach to estimate a Bayesian 

prior distribution for steepness of North Pacific bluefin tuna (Thunnus orientalis) and discuss an extension for depensatory 

recruitment dynamics. We show that assuming that steepness is unity when recruitment is considered to be environmentally 
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driven is not biologically consistent and leads to the wrong scientific inference.

Incorporating egg predation by haddock into a population model for Atlantic herring

David E. Richardson*, Jonathan A. Hare, Harvey J. Walsh

NEFSC, Narragansett, RI

Predation on the early life stages of marine fishes may be a source of interannual and multidecadal variability in recruitment. 

However, quantifying predation-related mortality of eggs and larvae has proven difficult, hampering attempts to incorporate 

predation into population models. We developed an egg predation model to estimate the survival rate of Atlantic herring 

eggs on Georges Bank from haddock predation. The model assumed that larval herring abundance was a function of herring 

spawning stock biomass and egg survival from haddock predation, and that haddock exhibit a type III functional feeding response. Model parameters were estimated with time series of larval herring abundance, haddock predation intensity and herring spawning stock biomass from 1971–2005. The egg predation model was then incorporated into a herring population 

model that included a Beverton-Holt model describing the relationship between larval abundance and recruitment at age 2 

years, and parameters accounting for growth, maturity, natural mortality and fishing mortality (F). The population model 

indicates that Georges Bank Atlantic herring have alternate stable equilibrium population levels and that fishing mortality 

or changes in haddock predation intensity can drive the population between high and low states. The model also indicates 

that a population collapse can occur even if fishing is maintained well below FMSY. More specifically, the model predicts that 

the Georges Bank herring population will collapse with the recent recovery of the Georges Bank haddock population, a 

prediction that is supported by the declining abundance of herring since 2006 in a compilation of 14 fisheries-independent 

time series. These findings highlight the importance of integrating species interactions into population models.

An independent estimate of natural mortality for Atka mackerel using tagging data

Susanne McDermott*, James N. Ianelli, Sandra A. Lowe

AFSC, Seattle, WA

The importance of reliable natural mortality (M) estimates has long been recognized for stock assessments as applied for 

fisheries advice. M is often confounded with other parameters (e.g., selectivity and catchability) and tagging studies hold 

promise to avoid these problems. For Atka mackerel (Pleurogrammus monopterygius) assessments in Alaska, M estimates 

have been derived from life history parameter correlates. Information outside the assessment is needed to configure appropriate prior distributions of M. Tagging data provide a means to estimate natural mortality independent of fishery or life 

history data. In this study a model of three years of tagging data from two distinct aggregations in the Aleutian Islands is 

proposed to estimate natural mortality. Preliminary results indicate that tagging data can provide supplemental information 

to stock assessments. However, more data are needed to validate assumptions from the tagging model (e.g. that the estimates 

reflect a long term average for the population or apply only for the period areas considered in the study).
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Do marine protected areas improve the ability to estimate biological parameters using an integrated stock 

assessment model?

Thomas M. Garrison1* and André E. Punt2

1

University of Washington, Quantitative Ecology and Resource Management, Seattle, WA; 2University of Washington, 

School of Aquatic and Fishery Sciences, Seattle, WA

Marine protected areas (MPAs) have gained popularity recently as an effective tool for the conservation and long-term 

protection of marine resources. However, their effectiveness from a traditional fisheries management perspective remains 

equivocal. One of the argued fisheries management benefits of an MPA is that because there is no fishing inside of the protected area, it may be possible to precisely estimate the rate of natural mortality and better determine growth and maturity 

rates, parameters that are often assumed prespecified in a stock assessment. This study aims to assess the degree to which 

having an MPA increases the ability to directly estimate these parameters in a integrated stock assessment model (Stock 

Synthesis), how long it would take for these benefits to be reflected in improved estimates of management quantities (e.g. 

BMSY), and the extent to which these improvements will be reduced or lost if there is spillover of adults from the MPA. An 

age- and length-structured two-area simulation model has been parameterized for two generic fish with contrasting life 

histories, a short-lived high-productive and long-lived low-productive species. This model forms the basis for a Monte Carlo 

simulation which examines the benefits of data from an MPA on estimation performance for Stock Synthesis. Preliminary 

results indicate that the extent of improvement in estimation of growth and maturity parameters from an MPA are slight 

compared to directly estimating these quantities using fishery data. Estimation of natural mortality from an MPA, however, 

does substantially improve estimation. 

Theme D: Incorporating Statistical Uncertainty from Sampling Error

Specification of observation error variances

Grant G. Thompson

AFSC, Resource Ecology and Fisheries Management Division, Seattle, WA

Except for pure process error models, all stock assessment models require specification of observation error variances. However, there appears to be no consensus among practitioners as to how this should be done. One school of thought holds 

that the specified variances should be equal to the values implied by the respective sampling designs. A problem with this 

approach is that the distributional assumptions included in ‘off the shelf ’ stock assessment packages may not correspond to 

the actual sampling designs. For example, most stock assessment packages assume that age/size composition data are drawn 

from a multinomial distribution, but actual sampling may violate the multinomial assumption. In such cases, it is necessary 

to compute a multinomial sample size that produces a variance equal to that from the actual sampling distribution. An 

example will be given in this talk. A second school of thought holds that the specified variances should be larger than those 

implied by the respective sampling designs, so as to compensate for any process error not included explicitly in the model. 

These larger values are typically determined within the stock assessment model itself by iterative reweighting. However, this 

practice is at best an approximation, as it can be shown that adjusting observation error variances cannot compensate completely for unmodeled process error. Moreover, this practice has the effect of adding parameters to the model, thus tending 

to increase the variances of estimates in general. As an alternative, this talk will demonstrate that it is better to model the 

process error explicitly.
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A hierarchical model to estimate relative catchability at size

Tim Miller

NEFSC, Woods Hole, MA

Annual trawl surveys supply important information on relative abundance to stock assessment models. Sometimes the vessel 

or gear changes due to new technology or aging equipment and the new vessel/gear configuration will sample populations 

differently from the old one. To use both sources of information, we must measure the differences in catchability of the old 

and new survey gear/vessel configurations. The catchability of a survey is often thought of as a constant value across all tows 

made with a particular gear/vessel configuration, but it can vary from tow to tow due to random variation in the environment and towing procedures. In most cases, the problem will be further complicated by differences in catchability across 

sizes of individuals. At the Northeast Fisheries Science Center, the Henry B. Bigelow replaced the Albatross IV in 2009 as the 

bottom trawl survey vessel and new gear and fishing protocols were also implemented. Over the course of 2008, a paired-tow 

study was conducted to provide conversion factor estimates for catches made by the two vessels. We present a beta-binomial 

model that allows estimation of size-specific conversion factors and illustrate the method with an example.

Mixture distribution models of Pacific rockfish schooling behavior

James T. Thorson1* and Ian J. Stewart2

1

University of Washington, School of Aquatic and Fisheries Sciences, Seattle, WA; 2NWFSC, Seattle, WA

Seven Pacific rockfish (Sebastes spp.) are currently listed as overfished. These and other rockfish species are constraining to 

fisheries management owing to target and nontarget catch limits. Indices of abundance for rockfish are frequently derived 

from a bottom trawl survey that occasionally yields extraordinary catch events (ECEs), in which catch per unit area is much 

greater than usual. ECEs strongly violate index standardization model assumptions, and removing or including them can 

cause considerable changes in the indices of abundance used in stock assessments and potentially affect stock assessment 

results. We hypothesize that ECEs result from trawl catches of fish schools. In this study, we develop models for positive 

catch rates of rockfish from the bottom trawl survey using a mixture distribution composed of two generalized linear models (GLMs): one for low catches (i.e. solitary individuals) and one for ECEs (i.e. schools). These models can incorporate 

spatial covariates within both GLMs, and can select a parsimonious model using Akaike’s information criterion. Bayesian 

hierarchical analysis can also be applied to multispecies data to estimate the distribution of differences in density between 

schooling and solitary individuals among rockfish. Preliminary exploration shows that mixture distributions often fit catch 

data better than single-distribution GLMs. Bayesian hierarchical analysis can also determine the ratio of densities among 

solitary and schooling individuals and this information may be especially valuable for infrequently encountered species. Use 

of mixture-GLM methods for positive catch rates will improve existing survey standardization methods by providing results 

that are more robust to the occurrence of ECEs. 

Acoustical-optical surveys of coastal pelagic species, with emphasis on Pacific sardine, using improved 

allocation of effort, multifrequency acoustic methods, and a towed stereo camera system

Juan P. Zwolinski*, George R. Cutter, Jr., and David A. Demer

SWFSC, La Jolla, CA

Acoustic surveys are currently used for wide-scale monitoring of many coastal pelagic species and are the primary source of 

fisheries-independent information used in their assessments. The recent decreasing trend in the abundance of Pacific sardine 

stock in the California Current Ecosystem (CCE) triggered the need for detailed monitoring of its spatial distribution 

and demography. In 2006, the Southwest Fisheries Science Center initiated a series of coast-wide acoustic-trawl surveys in 
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the CCE, and the preliminary results were encouragingly similar to those from relevant stock assessments. To improve the 

efficiencies of the acoustic surveys, and the accuracies and precisions of their estimates of fish distribution and abundance, 

efforts were made to optimize the sampling timing and design based on the remotely-sensed distribution of essential oceanographic habitat for the Pacific sardine. Based on historical information of essential habitat, the survey timing can be selected 

to match the timing of condensed habitat or to include the spatial location of the seasonal commercial fishery to improve 

species classification and the gathering of biological data. Immediately prior to the survey, the track lines are allocated based 

on a remotely-sensed distribution of essential oceanographic habitat for optimal sardine surveying. The echo energy is apportioned to the various species present using a combination of probabilistic classification including a variety of information 

such as essential habitat, acoustic scattering spectra and intensity, and aggregation depth. The classifications are validated 

and the models refined using independent observations from a net, egg pump, and a new towed stereo camera system. The 

foundation for these methods and some example results from recent surveys are presented.

Trawl survey designs for reducing uncertainty in biomass estimates for patchily-distributed species

Paul Spencer1*, Dana H. Hanselman2, and Denise McKelvey1

1

AFSC, Seattle, WA; 2AFSC, Juneau, AK

‘Patchiness’ in the spatial distributions of marine populations such as Alaska rockfish can arise from heterogeneous habitat 

characteristics, and can result in errors in survey biomass estimates when high-density patches are either over-represented or 

under-represented in survey trawls. In this study, we developed a spatial survey simulation model to evaluate the influence of 

spatial aggregation on biomass estimation, and considered alternative trawl survey designs intended to reduce the variability 

of biomass estimates. Variants of double sampling procedures were simulated in which high-density areas identified from 

acoustic data in the first sampling phase were then assigned increased trawl sampling densities in the second sampling phase. 

Geostatistical analyses of hydroacoustic data collected in Alaskan trawl surveys were used to simulate spatial distributions of 

fish populations. Simulated survey biomass estimates and sampling variability were evaluated as functions of several factors, 

including the spatial aggregation of the population and sampling density. When the relationship between the hydroacoustic 

data and fish density was strong, the double sampling procedure resulted in reduced variance in estimated biomass relative 

to simple random sampling with equivalent sample size. However, the variance in estimated biomass from the double sampling design was not substantially reduced when the relationship between hydroacoustic data and fish density was weak. The 

potential improvement in variance when a strong relationship exists between hydroacoustic data and rockfish density offers 

motivation to continue to refine analyses of hydroacoustic data and rockfish spatial patterns.

Theme E: Developing a Comprehensive Approach for Characterizing Uncertainty

Calculating the uncertainty in fishery assessment forecasts

Richard D. Methot, Jr.

Office of Science and Technology, Seattle, WA

Fishery forecasting models are used to project future catch and stock abundance levels expected from a specified harvest 

policy. These projections are central to determination of acceptable biological catch (ABC) for one to several years into the 

future, and to evaluation of longer-term rebuilding plans. The simplest of these projections use a point estimate of the stock 

abundance at the end of the assessment time series and a point estimate of the target fishing mortality rate (F) for the period 

of the forecast. Typically, future recruitment is treated as a random process so a probability distribution of future catch and 

abundance is forecast. More complete implementations also take into account uncertainty around the estimates of current 

abundance and target fishing mortality rates. Where fisheries are managed to achieve a specified target catch, it is important 

to also take into account the fact that future F levels resulting from this catch will depend upon current and future recruitment levels, which are not known at the time of setting the target catch level. There can be a several year time lag between 
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the last year for which recruitment deviations can be estimated and the last year for which an ABC forecast is needed. The 

forecasting approach developed by Shertzer, Williams, and Prager takes this ‘calculate F from catch’ rather than ‘calculate 

catch from F’ approach and also takes into account implementation error in management of the fishery to attain the target 

catch. Here, I show how a comparable procedure can be implemented within the Stock Synthesis assessment model which 

conducts the forecast as a continuous time series process in the final stage of an assessment analysis. In this approach, the 

forecast time period will include annual values for quantities like the probability that F exceeds the overfishing limit and the 

probability that biomass is below the overfished limit.

Some aspects of scientific uncertainty in west coast stock assessments

Stephen Ralston1*, André E. Punt2, and other members of the Pacific Fishery Management Council Scientific and 

Statistical Committee

1

SWFSC, Santa Cruz, CA; 2University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA

The 2006 reauthorized Magnuson-Stevens Fishery Conservation and Management Act requires that the Scientific and Statistical Committees (SSC) of the regional Fishery Management Councils provide acceptable biological catch recommendations, which must account for scientific uncertainty in the estimation of overfishing limits (OFLs). Quantifying scientific 

uncertainty in estimates of OFL is challenging. Multiple sources of error are likely to occur, including measurement error, 

parameter estimation error, model specification error, forecast error, and uncertainty about overall stock productivity. Although many sources of uncertainty exist, the focus of the Pacific Fishery Management Council’s SSC has been on quantification of parameter estimation error and model specification error, particularly the latter. While not all inclusive, the study 

of these two factors is possible using currently available information. We summarize the first order approximate estimates 

of the standard error on terminal biomass from stock assessments, which we term ‘within’ variation. To quantify variation 

‘among’ stock assessments, as a proxy for model specification error, we characterize retrospective variation among multiple 

assessments of the same stock. Results show that for 16 stocks the mean of the coefficient of variation on terminal biomass 

(‘within’ variation) is 0.19 (s.d. = 0.09). In contrast, the average coefficient of variation ascribable to model specification error (i.e. among-assessment variation) is 0.51 (s.d. = 0.19), which is the far greater of the two sources of uncertainty.

Dominant sources of scientific uncertainty in recent Gulf of Mexico stock assessments—implications for 

ACLs

Shannon L. Cass-Calay1* and Joseph Powers2

1

SEFSC, Miami Laboratory, Miami, FL; 2Louisiana State University

The Magnuson-Stevens Fishery Conservation and Management Reauthorization Act of 2006 mandates the use of annual 

catch limits (ACLs) set such that overfishing does not occur, and calls for strong accountability measures to prevent exceeding the ACL. Furthermore, the law assigns enhanced responsibilities to the Scientific and Statistical Committees (SSCs) 

of the regional Fishery Management Councils (FMCs). The SSCs have been charged with reviewing the relevant scientific 

information, considering the scientific uncertainty and recommending appropriate ACLs to the FMCs, who cannot exceed 

the ACL specified by the SSC. The precise methodology for quantifying scientific uncertainty has not been described or 

uniformly applied across FMCs. Sources of scientific uncertainty include, but are not limited to: measurement error, model 

structure, model mis-specification, uncertainty regarding biological parameters, and forecast error. This study will identify 

the dominant sources of scientific uncertainty for several frequently assessed Gulf of Mexico stocks including: king mackerel, gag grouper, and red grouper. This information could be used by the Gulf of Mexico FMC SSC to assist the construction of appropriate buffers to prevent overfishing.
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Estimating scientific uncertainty in ABC control rules for Bering Sea Aleutian Islands (BSAI) crab stocks

Jack Turnock1*, Robert Foy2, Anne B. Hollowed1, André E. Punt3, Lou Rugolo1 and Diana L. Stram4

1

AFSC, Seattle, WA; 2AFSC, Kodiak, AK; 3University of Washington, School of Aquatic and Fishery Sciences, Seattle, 

WA; 4North Pacific Fishery Management Council, Anchorage, AK

A shared management scheme exists for the BSAI crab stocks between the Federal government and the State of Alaska. 

Annual catch limit (ACL) provisions of the Magnuson-Stevens Fishery Conservation and Management Act require that 

ACL control rules be devised that establish a buffer between the overfishing limit (OFL) and an acceptable biological catch 

(ABC) to account for scientific uncertainty in the OFL. Scientific uncertainty arises from several sources, but can be divided 

into two main categories for computing the ABC: 1) uncertainty within a stock assessment that can be quantified using 

standard methods of variance estimation; and 2) sources of uncertainty which cannot be captured in this way. Examples of 

the latter include: a) errors in proxy definitions for FMSY and BMSY; b) errors associated with the values for prespecified parameters of population models (e.g. natural mortality [M] and catchability [q]); c) methodology (e.g. how survey area swept 

estimates are computed); and d) the choice of which data sources are included in assessments. For stocks with functional 

assessment models, within-assessment uncertainty is a standard output while additional uncertainty can be estimated using 

other methods (retrospective analyses, between-year variability in assessment outcomes). In these cases, the relationship between P* (the probability that the ABC exceeds the true OFL) and the buffer between the OFL and ACL can be estimated 

by stock. For stocks without assessment models, the scientific uncertainty associated with OFL can be computed using 

Monte Carlo simulation. For stocks with insufficient biomass data, the OFL is based on historical catch data, and a default 

buffer must be assumed based on informed judgement.

Incorporating uncertainty into ABC control rules for Bering Sea Aleutian Islands (BSAI) crab stocks

Diana L. Stram1*, André E. Punt2, Jack Turnock3, Lou Rugolo3, Robert Foy4, and Anne B. Hollowed3

1

North Pacific Fishery Management Council, Anchorage, AK; 2University of Washington, School of Aquatic and Fishery 

Sciences, Seattle, WA; 3AFSC, Seattle, WA; 4AFSC, Kodiak, AK

The North Pacific Fishery Management Council (NPFMC), the Alaska Fisheries Science Center (AFSC), and the Alaska 

Department of Fish and Game (ADFG) are developing acceptable biological catch (ABC) control rules for BSAI crab stocks 

which explicitly account for scientific uncertainty to meet annual catch limit (ACL) requirements. There are ten crab stocks 

under Federal management in the BSAI, with Federal overfishing limits (OFLs) annually established for each stock. Catch 

levels below the OFL are managed by ADFG under a deferred management agreement; however, the NPFMC must now 

modify its management of these stocks to incorporate annual ACL levels. Alternative ABC control rules which account for 

scientific uncertainty in the OFL are being developed, employing a probability (P*) approach to compute appropriate buffer 

values between ABC and OFL. Crab stocks are annually classified into a 5-tier system based upon availability of assessment 

information, with most stocks in lower tier levels owing to poor data. The OFL control rule is prescribed based on tier level 

and stock status within each tier. P*s are being considered in the range 0.1–<0.5. Depending upon the individual stock (and 

hence the estimated amount of scientific uncertainty) and P*, these translate into a range of buffers below the OFL. Several 

options are considered for incorporating additional uncertainty outside of the assessment itself. Two policy alternatives are 

being considered (by stock or tier): a fixed P* leading to an annually-varying buffer; or a fixed buffer leading to an annuallyvarying P*. The final selection of P* and/or buffer value will be the NPFMC’s policy decision.
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Utilizing environmental information to reduce recruitment uncertainty in the Alaska sablefish stock 

assessment

S. Kalei Shotwell1*, Dana H. Hanselman1, and David G. Foley2

1

AFSC, Ted Stevens Marine Research Institute, Juneau, AK; 2SWFSC, Environmental Research Division, Pacific Grove, 

CA

Alaska sablefish (Anoplopoma fimbria) are a fast-growing, highly valuable commercial groundfish species in the North Pacific. Relatively little is known about their early life history. Spawning takes place at depth in early spring and larvae swim to 

the surface, developing offshore. Juveniles drift inshore in late summer to overwinter and begin offshore movement the following summer. Sablefish are assessed as a single population in an age-structured model and do not fully recruit to the fishery 

or survey until four to five years of age. Therefore, information to estimate recent recruitment is sparse and highly variable. 

Additionally, recruitment appears to be more related to the environment than to spawning biomass. Our objectives are to 

evaluate the various sources of early life history data and explore integration of several environmental time series within the 

sablefish stock assessment model to reduce the uncertainty of recent recruitment estimates. We collected all available early 

life history survey data to describe the spatial distribution of larval and juvenile sablefish. A qualitative comparison with 

model recruitment estimates reveals potential critical spatial pathways during high recruitment years. Following this we 

considered potential mechanisms influencing recruitment and selected environmental indices representing these mechanisms. We considered large-scale climate indices to high resolution satellite-derived regional time series. Preliminary model 

comparisons suggest large-scale changes in climate, freshwater, and cross-shelf transport explain some of the recruitment 

variability of sablefish. Reducing recruitment uncertainty may increase efficiency in harvest decisions, improve geographic 

catch apportionment, and allow for more reliable future harvest projections.

The relationship between MSY fishing rates (FMSY) and productivity indices

Jason M. Cope1*, Wesley S. Patrick2, and Richard D. Methot, Jr.3

1

NWFSC, Fishery Resource Analysis and Monitoring Division, Seattle, WA; 2Office of Sustainable Fisheries, Silver 

Spring, MD; 3Office of Science and Technology, Seattle, WA

The 2009 revision of the National Standard 1 Guidelines describe a hierarchal approach to prescribing precautionary catch 

recommendations (i.e. overfishing limit [OFL] ≥ acceptable biological catch [ABC] ≥ annual catch limit). This presentation focuses on the specification of the ABC, which is the scientific recommendation for a level of catch that would prevent 

overfishing. To do this, it must take into account any scientific knowledge about the stock, and uncertainty in the estimate of 

OFL (where OFL = FMSY * Bcurrent). The FMSY is typically based on proxies and incompletely accounts for all biological factors 

that could influence the true FMSY. It has been proposed that indices of stock productivity, which potentially consider more 

factors than are directly accounted for in FMSY proxy calculations, could contribute to the scaling of the buffer between OFL 

and ABC. In extreme data-poor situations, it is possible that a productivity measure could be the sole source of information with which to set ABC relative to historical catch levels. As a first step, we investigated the strength of the relationship 

between productivity indices and commonly used measures of FMSY. The goal is to determine if productivity measures could 

serve as a proxy for FMSY in data-poor situations and could provide useful supplementary information for scaling ABC relative to OFL even in more data-rich situations. 
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Quantifying the trade off between precaution and yield in fishery reference points

Deborah R. Hart

NEFSC, Woods Hole, MA

There is nearly universal agreement that fishery reference points should be set using a precautionary approach. This means 

that the target fishing mortality should be set below that which is expected to give the greatest yield. However, there has 

been little discussion regarding trade offs between the level of precaution used and the concomitant loss in expected yield. 

Here, I explore this trade off with Monte Carlo simulations. Uncertainties in the input parameters to yield per recruit and 

stock-recruit analysis is first quantified. These uncertainties are then used to estimate the uncertainty in reference points 

such as Fmax and FMSY, the fishing mortalities that produce maximal yield per recruit and fishery yield. At fishing mortalities 

near these reference points, reductions in fishing mortality will substantially reduce the risk of overfishing at little cost of 

lost expected yield. However, at lower fishing mortality rates, further reductions in fishing mortality result in less marginal 

benefits in terms of reduced overfishing risk, and greater losses in expected yield. Less resilient, ‘low steepness’ stocks require 

additional precaution due to the risk of complete population collapse. If implementation uncertainty (i.e. uncertainty in 

actually achieving a given fishing mortality target) is incorporated in the analysis, the risk of overfishing as well the loss of 

yield due to precaution at a given target fishing mortality rate is increased, except possibly at fishing mortalities near or above 

FMSY.

A review of harvest policies: Understanding the relative performance of control rules

Jonathan J. Deroba1* and James R. Bence2

1

NEFSC, Woods Hole, MA; 2Michigan State University, Department of Fisheries and Wildlife, East Lansing, MI

Rational fishery harvest policies use control rules and associated policy parameters to dictate fishing mortality or catch and 

yield levels. Common control rules include constant catch, constant fishing mortality rate, constant escapement, or a few 

variations of these. Selecting the ‘best’ control rules to meet common fishery objectives (e.g. maximizing yield) has been a 

source of controversy and contradiction in the literature. We reviewed relevant literature to compare the ability of control 

rules to meet widely used fishery objectives and identify potential causes for these apparently contradictory results. The relative performance of control rules at meeting common fishery objectives was affected by: 1) whether uncertainty in estimated 

stock sizes is included in analyses; and 2) whether the maximum recruitment level (e.g. the asymptote of a Beverton-Holt 

stock-recruit function) was varied in an autocorrelated fashion over time. Relative performance of control rules also depended on fishery objectives, and the amount of compensation in the stock-recruit relationship. The influence of assessment 

error on the relative performance of control rules depended upon whether policy parameters were fixed using those that 

performed best without errors, or if the best policy parameters were found while including assessment error. More research 

is needed to compare control rules when: 1) accounting for uncertainty in key population parameters; 2) stock-recruitment 

or other population dynamic parameters vary over time; and 3) fisheries have nonyield-based or competing objectives.
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Setting allowable biological catch for stocks with reliable catch data only

Jim Berkson1*, Luiz Barbieri2, Steve Cadrin3, Shannon L. Cass-Calay4, Andy Cooper5, Paul Crone6, Martin Dorn7, Claudia 

Friess8, Don Kobayashi9, Thomas Miller10, Wesley S. Patrick11, Sarah Pautzke12, Stephen Ralston13, and Michael Trianni14

1

SEFSC, RTR Unit at Virginia Tech, Blacksburg, VA; 2Florida Fish and Wildlife Conservation Commission; 3NEFSC; 

4

SEFSC, Miami, FL; 5Simon Fraser University; 6SWFSC, La Jolla, CA; 7AFSC, Seattle, WA; 8Ocean Conservancy; 9

PIFSC, Honolulu, HI; 10University of Maryland, Center for Environmental Science; 11Office of Sustainable Fisheries, 

Silver Spring, MD; 12Western Pacific Fishery Management Council; 13SWFSC, Santa Cruz, CA; 14Commonwealth of the 

Northern Mariana Islands, Division of Fish and Wildlife

For many stocks, reliable catch data are the only data available for assessing population status. For the purpose of this document, only reliable catch stocks will be referred to as ORCS. Without additional data, traditional stock assessment techniques cannot be applied. There have been a number of alternative methods proposed for and applied to develop total 

allowable catch, and now acceptable biological catch (ABC), for ORCS. Participants at the Second National Meeting of 

regional Fishery Management Councils’ Scientific and Statistical Committees (SSCs), held in November of 2009 on St. 

Thomas, USVI, discussed the pressing need to evaluate existing and potential methods for setting ABCs for these stocks. A 

working group was established to identify, share, and evaluate alternative approaches (regional, national, and international) 

for setting ABCs for ORCS. Members of the working group represent seven of the eight SSCs, as well as academic institutions, an NGO, a regional Fishery Management Council, a state agency, and five of the six NMFS Science Centers. This 

talk will present the results of the working group. This information can contribute to a common framework, established 

among regional SSCs, for setting ABCs for these ORCS. Such a framework would need to incorporate flexibility to allow 

for regional differences in risk tolerance and preference of methods, but would provide a common foundation for all Fishery 

Management Councils.

Management uncertainty in the context of annual catch limits

Mark Millikin* and Galen Tromble

Office of Sustainable Fisheries, Silver Spring, MD

NMFS provides in the National Standard 1 (NS1) guidelines that accounting for both scientific and management uncertainty is necessary when setting annual catch limits that prevent/end overfishing. Management uncertainty is the difference between what you plan to catch and what you actually catch for a stock in a fishing year. Catch includes fish that are 

retained for any purpose, as well as mortality of fish that are discarded. Chief sources of management uncertainty include: 

1) inadequate (not timely, or incomplete) catch data; 2) conservation and management measures that do not take advantage 

of available data; and 3) methods or models and/or quality of stock and fishery data used to estimate future catches that 

result in poor estimates of actual catch. Consequences of management uncertainty could include: 1) exceeding the annual 

catch limit (ACL) or even the overfishing limit (OFL) more often; and 2) more difficulty in achieving optimum yield. 

NMFS recommends the use of an annual catch target (ACT) to address management uncertainty. When following the NS1 

guidelines, OFL > ABC, and ABC ≥ ACL. An ACT < ACL would provide separate transparent accounting of management uncertainty with scientific uncertainty accounted for in the difference of OFL > ABC. Use of an ACT is appropriate 

when: 1) past performance shows that a stock’s actual catch has often exceeded its catch quota or limit; or 2) fisheries are 

being managed with annual catch targets and catch limits for the first time when ACLs are first implemented. A Fishery 

Management Council can ask its Scientific and Statistical Committee (SSC) for advice on how to calculate management 

uncertainty based on past fishery performance; still SSCs are not required to recommend ACLs and ACTs. Assigning ACLs 

to data-poor stocks will be very challenging. Data-poor stocks that have catch data have some basis for setting ACLs, even 

if catch per unit effort data and discard mortality is poorly understood. Data-poor stocks without catch data should be considered for assigning to a stock complex/species group if appropriate; otherwise the basis for allowing harvest of the stock 

needs to be carefully evaluated and an ACL is still needed. Improving data should be a high priority. Councils are currently 

considering frameworks for ACLs that include OFL > ABC, ABC = ACL and ACL > ACT, or OFL > ABC, ABC > ACL 
107

and no use of ACT. The former framework is less likely to trigger accountability measures (AMs) for a stock in a subsequent 

fishing year. The latter framework would benefit greatly from precautionary in-season AMs. 

 

Joint Session of the National Stock and Habitat Assessment Workshops

Theme F: Incorporating Habitat Information into Stock Assessments

A framework for incorporating climate impacts on pelagic ocean habitats into stock assessments

Anne B. Hollowed*, Angie Greig, Libby Logerwell, and Chris Wilson

AFSC, Seattle, WA

The volume of suitable pelagic ocean habitat can influence the dynamics of recruitment and growth of marine fish. In the 

case of recruitment, habitat volume influences survival through its role in governing the overlap of predators and prey and 

through its role in governing competition for limited resources. In the case of juvenile and adult growth, habitat volume 

influences the probability of spatial overlap between predators and prey. We present a framework for quantifying climate 

induced shifts in pelagic ocean habitats and incorporating these shifts into the walleye pollock stock assessment as explanatory variables governing growth and recruitment. In this study acoustic backscatter and oceanographic data collected on the 

east side of Kodiak Island from 2001–2006 is used to demonstrate the analytical approach. In most years, dominant pelagic 

fish species are walleye pollock and capelin. These species exhibit niche partitioning in most years and patterns of habitat 

association are used to identify proxies for essential foraging habitats for capelin and pollock. The volume of suitable habitat 

for the western central Gulf of Alaska is estimated by applying these habitat definitions using geographic information system 

software. The role of habitat volume is compared to time trends in size at age and reproductive success to establish functional 

relationships between habitat volume and key life history parameters. These estimates are incorporated into stock assessments to assess the influence of these factors on the resource. 

Incorporating the effects of an environmental regime shift in an assessment of Atlantic menhaden population 

dynamics 

John A. Quinlan1*, Amy M. Schueller2, and Douglas S. Vaughan2

1

SEFSC, Miami, FL; 2SEFSC, Beaufort Laboratory, Beaufort, NC

Large-scale environmental processes may result in alteration of stock productivity. Incorporating such environmental shifts 

into stock assessments should provide a better understanding of the status of a stock and the levels of fishing that fall within 

acceptable levels. Beginning in the mid 1990s Atlantic menhaden began to experience what has been termed a ‘recruitment 

failure’ which coincided temporally with a shift in the Atlantic Multidecadal Oscillation (AMO; an index of sea surface 

temperature in the North Atlantic) and a shift in the North Atlantic Oscillation. An analysis of available data indicated that 

menhaden recruitment success, cohort growth rates, and indices of larval and juvenile abundance in the Mid-Atlantic Bight 

all appeared to vary with the AMO. This suggests that sea surface temperatures, as indexed by the AMO, played a role in 

determining spawning habitat use, vital rates, and stock productivity. Working under the hypothesis that menhaden exhibit 

an AMO-linked two-state productivity regime we constructed a size- and age-structured forward-projection model using 

Stock Synthesis. The model was designed to allow for important temperature-modulated life history characteristics, such as 

time varying growth and recruitment processes, identified in the previous analysis. Although focused on menhaden, varying 

habitat use and vital rate shifts are common features in many fisheries and we offer an example of how these processes can be 

pragmatically included in working stock assessment modeling. 
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Insights for stock assessment and empirical prerecruit indices from an environmentally forced individualbased model of early life history stages for west coast rockfishes

Eric Bjorkstedt1,2* and Stephen Ralston3

1

SWFSC, Fisheries Ecology Division, Trinidad, CA; 2Humboldt State University, Department of Fisheries Biology; 3

SWFSC, Fisheries Ecology Division, Santa Cruz, CA

Recruitment variability to populations of winter-spawning rockfish derives primarily from highly variable survival through 

the larval stage, presumably as a consequence of environmental and ecological conditions affecting early life history stages. 

Existing studies relate recruitment success to mean environmental conditions over (biologically) arbitrarily defined periods 

spanning one or more months, yet environmental processes thought to be critical to productivity (hence larval survival) 

vary substantially at shorter time scales, and spawning does not occur with uniform intensity over protracted periods. We 

have developed and continue to extend a modeling framework in which individual-based models for larval and juvenile 

rockfish are used to integrate the effects of wind-forced cross-shelf circulation and production in a coastal upwelling system 

on growth, transport, and survival. Predictions of recruitment success are obtained by integrating the joint probability of: 1) 

survival conditional on birth date; and 2) entering the plankton on a given date, where the latter is based on the distribution 

of spawning over time. Comparison to recruitment indices taken from stock assessments indicates that the model performs 

best for spawning seasons matching those reported in the literature. In contrast, recruitment indices based on fixed-time 

surveys (e.g. oceanographic surveys, diver surveys, and seabird diets) are best predicted for (hypothetical) spawning seasons 

consistently centered in March, regardless of species, which suggests that, for some rockfish species, such indices are a biased 

measure of reproductive success. 

A habitat-specific approach for incorporating environmental variation into stock forecasting models

Correigh Greene1*, Jason Hall1, Eric Beamer2, and George Pess1

1

NWFSC, Seattle, WA; 2Skagit River System Cooperative, LaConner, WA

Habitat conditions for pelagic species are known to vary widely in time and place, creating challenges for accurately predicting the productivity of fishery stocks. We discuss a conceptual approach incorporating habitat transitions to improve the 

forecasting power of fishery stocks using environmental predictors. We tested this conceptual approach in Puget Sound 

Chinook salmon populations. On one hand, empirical estimation of population size and productivity is relatively simple 

compared to marine fish stocks due to the anadromous and semelparous life history of salmon, yet these same characteristics 

often result in large fluctuations in abundance, and low predictive power for standard stock forecasting approaches that assume static juvenile mortality across years. We conceptualized the Chinook salmon life cycle into four habitat-specific life 

stages (freshwater, tidal delta, bay, and ocean), and developed environmental predictors that coincided with the periods of 

residency in these habitats. The best predictors of recruitment in two populations included a combination of freshwater and 

marine predictors and an estimate of egg production. Our models explained 75–95% of the variation in return rate, had 

very high forecasting precision, and outperformed model forecasts that assumed natural mortality of each age class was fixed 

among cohorts. Our results suggest that an environmental-based forecasting approach that utilizes the concept of life stage 

specific variation tied to habitats offers a way to surmount the challenge of incorporating highly variable natural juvenile 

mortality in some pelagic stocks. 
109

Integrating habitat change and population dynamics: Using the Shiraz framework to evaluate salmon 

recovery efforts

Jeff Jorgensen

NWFSC, Seattle, WA

Few tools are available to evaluate changes in habitat condition and the associated effects on population dynamics. The quality and quantity of available habitat can have large impacts on populations. We describe a modeling framework, developed 

for anadromous salmonids, that focuses on freshwater habitat influences in a spatially explicit life stage-specific manner. Survival is estimated via multiple Beverton-Holt spawner-recruit functions that estimate survival at life stage transition points, 

from egg through spawning adult. Freshwater spawning and rearing habitat can vary by spatial subunits, and fish movement 

and survival depend on habitat conditions within the subunits. We recently applied this framework to Wenatchee River basin spring-run Chinook salmon to evaluate alternative states of freshwater habitat condition as a consequence of restoration 

actions. Relationships were established between landscape-scale attributes (forest cover, road density, precipitation, etc.) 

and fish habitat characteristics (stream temperature and substrate features). The habitat values were inputs for the population dynamics model. Thus, populations responded to habitat changes as a consequence of alterations to the landscape. 

Considerable flexibility allows the framework’s focus to be directed toward other factors affecting survival, such as changes 

in ocean conditions, climate, harvest policies, genetic and ecological impacts from hatcheries, and alternative operations of 

the Columbia River hydropower system. They can be investigated discretely, as we did with habitat, and scenarios can be 

developed where factors can be evaluated collectively to understand the sensitivity of populations to changes across a host 

of factors affecting survival.

Can habitat-based densities predict stock status in a heavily fished Caribbean gastropod?

Ronald L. Hill1*, Kevin McCarthy2, Richard S. Appeldoorn3

1

SEFSC, Galveston, TX; 2SEFSC, Miami, FL; 3University of Puerto Rico-Mayagüez, Department of Marine Sciences, 

Mayagüez, PR

During a recent stock assessment of Queen conch (Strombus gigas) in the U.S. Caribbean, the lack of adequate data negated 

attempts to use traditional stock assessment models. The nature of the fishery, with recreational (subsistence), commercial, 

and artisanal components, makes it especially difficult to quantify all the segment’s landings and effort. An alternative approach was attempted using fishery-independent survey data in a geographic information system with benthic mapping to 

estimate population size and size structure across the fishable depths of the insular shelves of the U.S. Virgin Islands (USVI). 

These characteristics were compared with densities reported from other fished areas where conch stocks are known to range 

from healthy to severely overfished. Using this metric for comparison, stocks in the USVI were judged to be mildly overfished but showing some signs of recovery. Comparison surveys in the Virgin Islands and Puerto Rico (e.g. Southeast Area 

Monitoring and Assessment Program-Caribbean) suggested similar temporal trends. Subsequent peer-review of the alternative method for examining stock status did not fully endorse the approach but the exercise offered suggestions for the way 

forward. Recommendations for incorporating habitat-based survey data into future conch assessments and alternate models 

are presented.
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Can we use habitat information to derive prior distributions for virgin biomass of deepwater groupers and 

tilefish?

John F. Walter1*, Melissa Cook2, Brian Linton1, Linda Lombardi2, and John A. Quinlan1

1

SEFSC, Miami, FL; 2SEFSC, Panama City, FL

Yellowedge grouper and tilefish are relatively sedentary, long-lived fish and occupy burrows, pits, and trenches in discrete 

habitats along a narrow fringe of the continental shelf break in the Gulf of Mexico. Both species are targets of fisheries with 

relatively consistent landings of approximately 400 and 180 metric tons, respectively, with little trend in catch per unit of effort (CPUE) since inception of the fishery in the late 1970s. Particularly with uninformative CPUE and constant landings, 

assessment models have little ability to differentiate between whether near constant landings result from sustainable harvest 

of a large or productive population or represent unsustainable depletion of a declining population. This is problematic for 

sedentary, low productivity species for which serial depletion can lead to hyperstable CPUE and landings, while overall biomass and reproductive potential is ‘mined’. Bayesian priors can often assist in distinguishing between two otherwise equally 

likely hypotheses. We examine the potential to use habitat maps from the marine substrate geodatabase, scientific survey 

data and burrow estimates derived from early 1980s vintage submersible video surveys to develop prior distributions for 

virgin recruitment as input to Stock Synthesis 3 (SS3). We first use a logistic regression to map the area of potential habitat. 

Then we multiply this habitat area by estimates of burrow densities, numbers of fish per burrow and percent burrow occupancy to obtain initial numbers of animals per square kilometer of habitat. From these, we back calculate numbers of age-1 

fish under a stable age distribution and then examine the performance and implications of the SS3 models with the derived 

priors for virgin recruitment. 

Using statistical modeling and Ocean Observing Systems to identify fish habitat at broad scales: Potential 

applications for spatial planning, estimation of natural mortality, and reducing fisheries bycatch

John P. Manderson1*, Josh Kohut2, Laura Palamara2, Steven Grey2, and Matt Oliver3

1

NEFSC, Ecosystems Processes Division, James J. Howard Marine Sciences Laboratory, Highlands, NJ; 2Rutgers 

University, Institute of Marine and Coastal Science, New Brunswick, NJ; 3University of Delaware, College of Marine and 

Earth Studies, Lewes, DE

Pelagic habitat processes are at least as important as benthic processes in regulating the recruitment of marine species. However, the absence of data describing pelagic processes at broad spatial but fine time scales has made it difficult to consider 

these processes in habitat assessments. Ocean Observing Systems (OOS) now sample pelagic processes at ecologically relevant space-time scales. As a first step toward integration of OOS data into fish habitat assessment, we use generalized additive modeling to evaluate the power of OOS to explain abundance variation in two pelagic (longfin inshore squid and 

butterfish) and two demersal (summer flounder and spiny dogfish) species which interact on the northwest Atlantic continental shelf. Regardless of species lifestyle, OOS data (e.g. ocean color, surface advection velocity, and divergence potential) 

increased the power of models by 20–30% above models that considered only traditional benthic and pelagic variables (e.g. 

sediment grain size, bottom rugosity, depth, bottom temperature, and salinity). We also show how OOS-informed habitat models may be used to: 1) refine single species habitat designations for spatial management; 2) model habitat specific 

encounter probabilities of predators and prey for estimation of natural mortality rates; and 3) model the co-occurrence of 

target and bycatch species to provide fishers with tactical advice to reduce bycatch.
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Theme G: Improving Calibration and Precision of Resource Surveys with Habitat 

Information

Incorporating satellite-derived environmental data with Gulf of Mexico pelagic longline observer data for the 

evaluation of bluefin tuna relative abundance and distribution patterns 

Craig Brown1*, Karina Ramírez López2, and John A. Quinlan1

1

SEFSC, Miami, FL; 2Instituto Nacional de Pesca, DGIPA Veracruz, Veracruz, Mexico

In the Gulf of Mexico, bluefin tuna are captured as bycatch in the prosecution of the yellowfin tuna longline fisheries of both 

the United States and Mexico. Analyses of catch rates for this fishery can provide indices of abundance that can be used in 

stock assessments of these commercially and recreationally important species. Data on individual set catch and effort have 

been collected through the scientific observer programs of each country, beginning in 1992 for the United States and in 

1993 for Mexico, and have been combined through an ongoing cooperative program into a database providing complete 

coverage of the Gulf of Mexico. Information is recorded on gear configuration, bait, timing, and location, permitting the 

standardization of catch rates accounting for changes in these factors. Catch rate standardization, however, is incomplete 

because tuna are known to respond to hydrographic features in their environment and the observer records contain little 

environmental data, making it impossible to disentangle habitat effects from abundance trends. This may be particularly 

important in the case of bluefin tuna, which are more sparsely distributed in the catches than yellowfin. The use of satellite 

measures of sea surface temperature, ocean color, and sea surface height may enable standardization of the longline data and 

the development of improved indices of abundance for bluefin and yellowfin tuna. In this paper, we present the results of 

our efforts to overlay longline monitoring records on satellite-derived measures of the environment in the Gulf of Mexico to 

develop a standardized catch per unit of effort index. 

Expansion of Atlantic croaker (Micropogonias undulatus) larval habitat on the Northeast U.S. continental 

shelf

Harvey J. Walsh1*, David E. Richardson1, Jonathan A. Hare1, and Katrin E. Marancik2

1

NEFSC, Narragansett, RI; 2NEFSC/SEFSC, Narragansett, RI

Climate change has the potential to affect the abundance and distribution of marine fish species. The Northeast Fisheries 

Science Center has conducted larval sampling programs along the Northeast U.S. continental shelf since the early 1970s. 

Two programs, Marine Resources Monitoring, Assessment and Prediction (1977 to 1988) and Ecosystem Monitoring 

(1999 to present), provide shelf-wide data from Cape Hatteras, NC, to southern New England. These data were used to 

identify changes in abundance and distribution of larval croaker over a 30 year period. Atlantic croaker larval distribution 

expanded northward from the 1980s to present. A nonlinear least squares larval index indicates an increase in larval croaker 

abundance concomitant with the expansion in distribution. Analysis of larval habitat use (i.e. water temperature, salinity, 

and water depth) indicates preferred larval habitats have not changed over the same time periods. Together, these analyses 

suggest Atlantic croaker larval habitat has expanded on the northeast U.S. shelf, potentially contributing to the increase in 

abundance. Atlantic croaker provides an example of how habitat modeling of long-term abundance and environmental data 

already in existence can be used to identify habitat changes on the shelf. In addition, combining larval indices and larval 

habitat models will improve the data available for stock assessments. 
112

Habitat-specific survey methods to improve assessments of rockfishes off California and Alaska

Mary M. Yoklavich1* and Victoria O’Connell2,3

1

SWFSC, Santa Cruz, CA; 2Alaska Department of Fish and Game; 3Coastal Marine Research, Sitka, AK (current)

Many fish stocks have strong affinities to specific habitats, resulting in patchy spatial distributions in abundance. Sample 

stratification or otherwise explicitly incorporating habitats into survey design can increase precision and accuracy of estimated densities of these stocks. Several economically valuable rockfish species off Alaska and the west coast of North 

America occur in rugged rocky terrain, making them impossible to accurately survey using such conventional methods as 

bottom trawl gear. We have developed direct count, habitat-specific methods to improve stock assessments of a number of 

these species in the Gulf of Alaska and California. Seafloor maps of substratum type and bathymetry are used to identify 

and quantify rockfish habitats on a large spatial scale, providing the frame within which to distribute sampling effort. Fish 

surveys, distributed by habitat, are conducted from a human-occupied research submersible. Abundance and biomass are 

estimated from fish density, size composition, and area of the habitat. These habitat-specific visual survey methods not only 

contribute to improved assessments of rockfish stocks, but also are necessary for an ecosystem approach to the management 

of diverse communities on rocky areas of shelf and slope. Additionally, we are using these methods to characterize fish and 

habitat associations to improve identification of essential fish habitats, to design and monitor marine protected areas, and to 

understand the significance of deep sea coral habitats.

Integrating benthic community structure data into a stratified random sampling design to improve reef fish 

abundance estimates in the Northwestern Hawaiian Islands

Jason Helyer* and Ivor D. Williams

Joint Institute for Marine and Atmospheric Research, University of Hawaii, Honolulu, HI; PIFSC, Coral Reef Ecosystem 

Division, Honolulu, HI

From 2007 to 2009, the Pacific Islands Fisheries Science Center Coral Reef Ecosystem Division participated in a pilot 

study to assess the feasibility of a stratified random survey design (StRS) aimed at collecting fishery independent data on 

the spatial distribution, abundance, size composition, and habitats of coral reef fishes in the Northwestern Hawaiian Islands 

(NWHI). The sampling design used a combination of reef zone (forereef, lagoon, and backreef ) and depth categories (shallow: 0–6 m; moderate: 6–18 m; and deep: 18–33 m) to partition the survey domain into strata. Concurrent with a subset 

of fish surveys, benthic cover and coral population (density and size structure) data were collected. Analysis of benthic cover 

and coral abundance data revealed high spatial heterogeneity within habitat strata; therefore, we post-stratified the survey 

domain to incorporate the two predominant wave regimes in the NWHI (northwest swell and trade wind swell) which 

previous studies have shown greatly influence benthic community structure. Post-stratification results indicate an increase 

in precision of domain wide estimates of benthic cover and coral abundance compared to the original StRS design as well 

as improved precision of abundance estimates for eight candidate fish species. Variability of benthic habitats within several 

‘post strata’ suggests that further refinement of habitat maps could improve performance of fish stock assessments in the 

NWHI. We recommend an approach to improving habitat maps based on higher resolution wave exposure data. 
113

Collaborative Optically-assisted Acoustical Survey Technique (COAST) for surveying the distributions, 

abundances, and lengths of demersal fishes, by species

David A. Demer, John Butler, George R. Cutter, Jr., Kevin Stierhoff*, Kyle Byers, David Murfin, Josiah Renfree, Scott 

Mau, and Thomas S. Sessions

SWFSC, La Jolla, CA

The Collaborative Optically-assisted Acoustical Survey Technique (COAST) was developed at the Southwest Fisheries Science Center to survey rockfish dispersions and abundances, by species, throughout the Southern California Bight (SCB). 

The technique uses historical fishing maps to initially define the survey sites; active acoustics to map the dispersion and abundance of rockfish; and video and still images to estimate the mixture of species and their sizes. The cameras are deployed from 

a remotely-operated vehicle. The physical oceanographic habitat is sampled using a conductivity, temperature, and depth 

sensor with a dissolved oxygen sensor and an acoustic Doppler current profiler, and the seafloor is imaged and classified using new multifrequency biplanar interferometric techniques. Automated data processing algorithms will be explained, and 

some results will be presented from the 2004–2005 and 2007–2008 surveys of 44 sites distributed throughout the SCB.

Using mesohabitat information to improve abundance estimates for west coast groundfish: A test case at 

Heceta Bank, OR

W. Waldo Wakefield1*, Julia E.R. Clemons1, Ian J. Stewart2, and Curt E. Whitmire1

1

NWFSC, Newport, OR; 2NWFSC, Seattle, WA

Historical in situ observations of benthic fishes and invertebrates represent an opportunity for establishing fishery-independent benchmark estimates of abundance from specific time points and in both trawlable and untrawlable habitats. Depending on the original intended purpose of a given study, the direct count data may be nonrandom in nature. The objective of 

this talk is to show how a new method for treating such data was used by combining in situ fish observation data and a habitat map to estimate fish abundance. We evaluated whether increased resolution of habitat information could improve the 

precision of population estimates. For this study we used an existing and previously published data set from Heceta Bank, 

OR. Heceta Bank is one of the largest rocky banks along the U.S. west coast containing a diverse array of habitats supporting 

numerous species of commercially important groundfish, including a diverse assemblage of rockfishes (Sebastes spp.). We 

looked at fish observations relative to the variables of habitat type, depth, backscatter intensity and relative elevation (i.e. 

topographic position index) and post-stratified the data according to levels of sampling effort. We also looked at two levels 

of habitat detail: four habitat types, and ‘hard’ vs. ‘soft’ substrate. We then calculated the density and variance of fish species for each habitat type and then estimated fish abundance for a select group of groundfish species. Based on these results 

it appears that improved precision of more geographically comprehensive abundance estimates may be achieved through 

presurvey stratification based on currently available habitat information. 

Modeling habitat relationships for rockfish to improve fishery-independent survey biomass estimates

Chris Rooper*, Michael Martin, and Paul Spencer

AFSC, Seattle, WA

Rockfish species are notoriously difficult to assess using multispecies bottom trawl survey methodology. Typically, biomass 

estimates have high coefficients of variation and can fluctuate outside the bounds of biological reality from year to year. 

This is thought to be due in part to their patchy distribution related to very specific habitat preferences. We modeled the 

distribution of 12 commercially important and abundant rockfish species including Pacific ocean perch (Sebastes alutus) and 

shortspine thornyhead (Sebastolobus alascanus) in the Gulf of Alaska. The Pacific ocean perch trawl survey biomass estimate 
114

has had coefficients of variation of ~35% in recent years, while the shortspine thornyhead coefficients of variation have been 

~20%. A two-stage modeling method (modeling both presence/absence and abundance) and a collection of important 

habitat variables were used to predict bottom trawl survey catch per unit of effort. The resulting models explained ~35% of 

the variation in Pacific ocean perch distribution and 72% of the variation in shortspine thornyhead distribution. The models were largely driven by depth, seafloor slope, bottom temperature, and measures of ecosystem productivity. The residuals 

of these models were assumed to reflect interannual variability and used as an index of the time series of abundance. The 

trajectories of both population indices were similar to the existing estimates of biomass. However, the habitat-based indices 

exhibited less interannual variability and lower error estimates. These indices may provide stock assessment models a more 

stable alternative to current biomass estimates produced by the multispecies bottom trawl survey in the Gulf of Alaska.

Advances in conducting spatially-explicit, fishery-independent, ecosystem-based reef fish and habitat 

assessments

James A. Bohnsack* and Benjamin Ruttenberg 

SEFSC, Miami, FL

Successful marine spatial planning requires measuring impacts of management interventions at small and large, ecosystemlevel, spatial scales. In a collaborative effort, NOAA (Southeast Fisheries Science Center and Florida Keys National Marine 

Sanctuary, National Ocean Service), the Florida Wildlife Research Institute, the University of Miami, and the National Park 

Service have adopted a single standardized, nondestructive, fishery-independent visual approach using stationary circular 

plots to assess coral reef habitats in southern Florida and the Florida Keys. Data collected include habitat metrics and reef 

fish species composition, total abundance, size distributions, and habitat usage. This approach is optimized by using twostage, random stratification based on depth, habitat type, management zone, and region. By combining efforts, agencies get 

more data, increase their efficiency, and provide significantly more precise estimates of population abundance and other 

parameters than previously possible. These data can be used to assess individual species, communities, and management 

impacts at multiple spatial scales. Monitoring in the Florida Keys and Dry Tortugas over the last decade shows highly significant increased population abundance and size of exploited species in no take reserves. Impacts of marine reserves, hurricane 

disturbance, and fishery regulations on reef fish communities and dynamics were also detected. 

Poster Session

Essential fish habitat three year strategic implementation plan: Priority habitats and data needs for improving 

EFH protection

Karen Abrams, Terra Lederhouse, and Kara Meckley

Office of Habitat Conservation, Silver Spring, MD

A three year strategic implementation plan is under development for the essential fish habitat (EFH) protection program to 

identify more strategic, focused, and transparent national EFH protection priorities. Key objectives of the plan are to implement more efficient and effective approaches for protecting EFH from priority threats, improve EFH program planning, 

and improve the communication of EFH program priorities and accomplishments to internal and external partners. EFH 

priorities were identified by each Regional Office and the Office of Habitat Conservation. Comparisons and discussions of 

these regional priorities led to the selection of four national priority EFH focus areas: submerged aquatic vegetation, tidal 

wetlands and associated shallow water habitats, coral and marine live bottom aggregations, and riverine spawning and migratory habitat. A simplified logic model was utilized to articulate a strategy for achieving specific outcomes for each of the 

four EFH habitat focus areas. Key outcomes identified by the plan include increased knowledge of spatial distribution of 

these habitats, increased knowledge of the linkage between these habitats and managed fish species, and increased ecosystem 

functioning. Specific products requiring Science Center support will be identified through the plan, which will contribute 
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to the broader discussion of habitat research needs.

Prioritizing data collection for assessments based on a cost-benefit analysis

Kate I. Andrews and Linda Lombardi

SEFSC, Panama City Laboratory, Panama City, FL

All stock assessment scientists are aware that uncertainties are unavoidable in fishery science. We do our best to identify 

uncertainties and fully describe them using the best modeling approaches available. Our models are only as good as our data, 

and ‘gather more data’ always seems to be a research recommendation. The question is left: What kind of data? We cannot 

have more of all types of data when we are working on a budget, so how do we make an intelligent recommendation of which 

type of data to prioritize? The cost of data collection varies widely depending on the type of data. It costs about $1,200 per 

sea day for observer coverage in the Southeast United States whether or not data are collected. Each otolith costs approximately $20–$32 to age. Each recreational angler intercept survey runs $35–$40 depending on the season, and it costs $70 

per successful phone interview. The research fishery vessel is the most expensive and variable at $6,000–$22,000 for a day 

of sampling. In our study, we explore the impacts of improving data collection of various data types on the stock assessment 

of a simulated population of fish. We couple those simulations with a cost-benefit analysis to determine if there is one type 

of data that is best to fund. Through this heuristic experiment, we hope to fuel the discussion of which data to collect with 

a little more applied information. 

A spatially-explicit assessment of the adverse effects of fishing on benthic habitats in the Northeast United 

States: The Swept Area Seabed Impact model

Michelle Bachman1, Chad Demarest2, Steve Eayrs3, Jonathan Grabowski3, Bradley Harris4, Vincent Malkoski5, David Packer2

, David K. Stevenson6

1

New England Fishery Management Council, Newburyport, MA; 2NEFSC, Woods Hole, MA; 3Gulf of Maine Research 

Institute, Portland, ME; 4University of Massachusetts Dartmouth, New Bedford, MA; 5Massachusetts Division of Marine 

Fisheries, New Bedford, MA; 6NERO, Gloucester, MA

The Magnuson-Stevens Fishery Conservation and Management Act requires fishery management plans to minimize to the 

extent practicable the adverse effects of fishing on fish habitats. To meet this requirement, fishery managers would ideally be 

able to quantify such effects and visualize their distributions across space and time. The Swept Area Seabed Impact (SASI) 

model provides such a framework, enabling managers to better understand: 1) the nature of fishing gear impacts on benthic 

habitats; 2) the spatial distribution of benthic habitat vulnerability to particular fishing gears; and 3) the spatial and temporal distribution of realized adverse effects from fishing activities on benthic habitats. The model combines fishing effort data 

with substrate data and benthic boundary water flow estimates in a georeferenced, geographic information system compatible environment. Quality-adjusted area swept, our measure of the adverse effect from a unit of fishing on fish habitat, is 

calculated by conditioning a nominal area swept value by the nature of the fishing gear impact, the susceptibility of benthic 

habitats likely to be impacted, and the time required for those habitats to return to their pre-impact functional value. SASI 

increases the utility of habitat science to fishery managers by translating susceptibility and recovery information into a 

quantitative evaluation of fishing impacts on fish habitat. It is currently being used in New England to design and evaluate 

anticipated impacts of fishery management alternatives.
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The value of habitat information at different life stages in refining white shrimp stock assessments in the Gulf 

of Mexico

Ron Baker1, Tom Minello1, and Phil Levin2

1

SEFSC, Galveston Laboratory, Galveston, TX; 2NWFSC, Seattle, WA

Stock assessments of white shrimp in the northern Gulf of Mexico generally provide reasonable predictions of stock size. 

However, the considerable noise in the stock-recruit relationship implies that processes acting on early life stages are important in regulating the population. We developed a stage-based matrix population model for white shrimp to explore the 

effects of variability in vital rates of each life stage on overall population growth rate (λ). The model indicates that λ is orders 

of magnitude more sensitive to variability in early life stage survival rates than it is to variability in vital rates of the fished 

stock. Changing adult survival in the model between scenarios with zero and maximum fishing mortality has relatively little 

effect on λ and stock size. In contrast, changing juvenile survival to account for variability in mortality rates regulated by 

tidal flooding and access to the protective marsh surface had large effects on λ. While white shrimp stock assessments should 

clearly benefit from the incorporation of information on variability in juvenile mortality, the regulation of vital rates in early 

life stages involves a complex interplay between a range of processes that are highly variable and difficult to measure. For 

example, juvenile mortality may be strongly influenced by unpredictable pulse events that create significant bottlenecks in 

the life cycle. Deriving a simple metric or parameter to incorporate habitat processes into stock assessment models currently 

appears unrealistic, but our modeling approach emphasizes the importance of research into environmental and biological 

processes that regulate juvenile shrimp mortality.

The Species Information System: Tracking the success of the Stock Assessment Improvement Plan

Kristan Blackhart and Richard D. Methot, Jr.

Office of Science and Technology, Seattle, WA

The Species Information System (SIS) is a web-enabled database developed and managed by the Office of Science and 

Technology that provides NMFS scientists, resource managers, and policy coordinators with user-friendly applications for 

data entry, retrieval, and report generation. SIS acts as a central repository to collect and manage regional and national data 

across NMFS program offices. The data housed within SIS includes the most up to date information on the status of managed stocks and stock assessment results, as well as a growing collection of historical records and other important associated 

information. This information is necessary to support services NMFS provides to fisheries conservation and management 

efforts, as mandated by the Magnuson-Stevens Fishery Conservation and Management Act. SIS directly supports a number 

of agency reporting requirements, including the Office of Sustainable Fisheries’ Annual Report to Congress on the Status of 

U.S. Fisheries and performance measures under the Government Performance and Results Act, and has significantly reduced 

the number of data calls passed to Science Center representatives. Soon, the database will begin tracking basic catch data and 

annual catch limits, and expand to include protected resources. Development is also underway for a public web site linked 

to the database that will offer value-added data products based on current stock information. 
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The Advanced Sampling Technology Working Group’s recent efforts in improving NMFS’ stock and habitat 

assessment science 

Eric Breuer1, Dezhang Chu2, George R. Cutter, Jr.3, David A. Demer3, Joseph Godlewski4, Scott Ferguson5, Brad Hanson2, 

Michael Jech4, Frank Parrish5, Joseph E. Serafy6, David Somerton7, Charles H. Thompson8, and Chris Wilson7

1

Office of Science and Technology, Silver Spring, MD; 2NWFSC, Seattle, WA; 3SWFSC, La Jolla, CA; 4NEFSC, Woods 

Hole, MA; 5PIFSC, Honolulu, HI; 6SEFSC, Miami, FL; 7AFSC, Seattle, WA; 8SEFSC, Pascagoula, MS

With increasing demands for accurate, precise, and timely information upon which to base assessments of living marine 

resources (LMRs) and their habitats, the NMFS Science Board established the Advanced Sampling Technology Working 

Group (ASTWG) to lead the ongoing process of improving the quality of assessments through development, evaluation, 

and implementation of innovative sampling technology. The ASTWG fosters communication and collaboration among 

experts in sampling technology at the six Science Centers, facilitating increased technical staff capabilities and expedited 

development of sampling technologies through synergy in research endeavors. The thrust of the ASTWG mission is to 

improve the accuracy, precision, and efficiency of living marine resource assessments. The ASTWG principally focuses on 

acoustics, optics, electronic tagging, and other relevant technologies, recognizing that the agency has other working groups 

addressing different research areas (e.g. Biotechnology, Bycatch Reduction Engineering). Key to this strategy is the involvement of quantitative scientists involved in LMR stock assessments. The Science Centers will identify and prioritize gaps 

or constraining levels of uncertainty in stock assessments and habitat inventories for each region and identify candidate 

technologies to reduce uncertainty and fill the gaps. This information will be used to solicit proposals to address sources of 

uncertainty and information gaps in population assessments. Recent projects funded by ASTWG include: 1) evaluation of 

bioelectrical impedance analysis to measure fish energy density and reproductive potential for stock assessment (Northeast 

and Southeast Fisheries Science Centers); 2) autonomous gliders for real-time passive acoustic remote sensing (Northeast 

Fisheries Science Center); 3) automated feature detection, shape estimation, and identification using disparity and spectral 

information in stereo imagery (Southwest Fisheries Science Center); 4) estimating abundance of krill-dependent penguin 

and seal populations breeding on inaccessible islands in Antarctica using vertical take off and landing craft equipped with 

cameras (SWFSC); 5) improving visual survey methods for groundfish and reef fish using the Seabed autonomous underwater vehicle (Northwest and Pacific Islands Fisheries Science Centers); 6) advancing remote marine mammal stock assessment 

with passive acoustic gliders (Pacific Islands Fisheries Science Center); 7) development of an optical sampling trawl for use 

in groundtruthing species and size composition of acoustic backscatter (Alaska Fisheries Science Center); and 8) modifications to a stereo video camera for improved fish measurements (Alaska Fisheries Science Center).

R MAPS: R Mapping and Plotting Scripts for stock assessment

Elizabeth Brooks and Chris Legault

NEFSC, Woods Hole, MA

Visualization tools such as maps are one way of understanding the spatial-temporal nature of your data. They can highlight 

data gaps, sparseness of coverage, or important patterns that may provide insight into fish or fishery behavior. The patterns 

that emerge could reflect a response to environmental features, such as depth or season, or to management actions, such as 

closed areas or fishing seasons. Understanding these data nuances can be helpful in deciding whether the data are appropriate for inclusion in your stock assessment, and if so, how that data should be treated. We have developed scripts in R that 

work with existing geographic information system shape files to create maps of typical fisheries data (landings, discards, and 

observer coverage) and fisheries-independent data (surveys and tagging studies). Mapping in R has several advantages. First, 

the images can be produced with a very small file size, which reduces the overall file size (and enhances the portability) of assessment documents. Second, the ability to automate the scripts to quickly produce many maps where only the year (or gear 

or species) is changing makes it simple and fast to create many plots from within a single script. Additionally, the capability 

to directly import raw data, and to analyze and summarize the data prior to plotting, makes for flexible, ‘one stop shopping’. 

We illustrate some insights gained from recent applications of the mapping scripts, and illustrate the general technique of 
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incorporating shape files into R plots. 

Pilot habitat assessment of a mesohaline embayment of the Chesapeake Bay

David Bruce1, Jay Lazar1, Steve Giordano1, and Ward Slacum2

1

NOAA Chesapeake Bay Office, Annapolis, MD; 2Versar, Inc.

Acoustic habitat mapping and fish census techniques were integrated in an attempt to quantify the ecological importance of 

oyster shell habitats in the Chesapeake Bay. 41 km2 of seabed was mapped at the confluence of the Rhode, South, and West 

rivers in Maryland. A side scan sonar system provided two dimensional textural imagery and a single beam echosounder 

collected bathymetric and seabed classification data. Cover maps were derived from the integration of all three acoustic data 

sets and grab sample data. Benthic habitat classifications were Clay/Silt, Sand, Silt/Sand, Patchy 3-D Oyster Shell with Mud, 

2-D Oyster Shell with Mud, and 2-D Oyster Shell with Sand. An otter trawl was used to collect organisms present within 

geographic information system derived habitat polygons. We used generalized linear models to assess the relationship between fish community metrics and a suite of habitat variables. Dependent variables were abundance of pooled fish species 

(number/m2), the Shannon-Wiener diversity index, and abundance of the five most frequently observed fish taxa. Independent variables were benthic habitat type, season, a habitat type*season interaction, bottom salinity, bottom dissolved oxygen, bottom temperature, and trawl start depth. Benthic habitat type, followed by the habitat type*season interaction term, 

was the most significant factors contributing to variation in fish community metrics. One-way analyses identified significant 

variation in pooled abundance and species abundance relative to habitat type alone. Diversity did not vary significantly with 

habitat type. Contrary to expectations, abundance was generally greatest on Clay/Silt, Silt/Sand, and Oyster Shell with 

Mud bottoms; abundance was lowest on Sand bottoms.

On the road to extinction? Monitoring population trends of the endangered white abalone, Haliotis sorenseni

John Butler1, Kevin Stierhoff1, and Melissa Neuman2

1

SWFSC, La Jolla, CA; 2SWRO, Long Beach, CA

White abalone (Haliotis sorenseni) became the first marine invertebrate to be listed as endangered under the Endangered 

Species Act in 2001. Low densities and recruitment failure due to Allee effects were identified as being the major threats 

to the species’ existence. Beginning in 2002, the Benthic Resources Group at the Southwest Fisheries Science Center has 

conducted fine-scale habitat mapping using multibeam sonar and visual transect surveys using a remotely-operated vehicle 

to monitor the status of white abalone populations at Tanner Bank, an offshore bank in southern California. Results of surveys conducted since the listing indicate continuing declines in total numbers and densities (39–63%, depending on depth) 

at Tanner Bank between 2002 and 2004. Between 2004 and 2008, white abalone populations appear to have remained 

relatively stable. Changes in the size distribution over this same time period indicate a population that is growing larger 

(and older) with no small individuals recruiting to the population. Only five ‘pairs’ of white abalone were sighted in the 

2008 survey (compared to nine pairs and one group of five individuals in 2002, and two pairs in 2004), which suggests that 

the likelihood of reproductive success of this population remains very low. Continued monitoring is needed to determine 

whether rebuilding, however slight, may be occurring. More ‘active’ rebuilding measures (e.g. captive breeding and stock 

enhancement) may be necessary to reverse the present trend toward extinction.
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The effect of contaminant exposure on the behavior and growth of young of the year bluefish, Pomatomus 

saltatrix

Allison Candelmo1,2, Ashok Deshpande2, and Judith S. Weis3

1

Rutgers University, Graduate Program in Ecology and Evolution, and Department of Ecology, Evolution, and Natural 

Resources, New Brunswick, NJ; 2NEFSC, James J. Howard Marine Sciences Laboratory, Highlands, NJ; 3Rutgers 

University, Department of Biological Sciences, Newark, NJ

Certain populations of young of the year (YOY) bluefish (Pomatomus saltatrix) may utilize the habitats and prey resources 

of contaminated estuaries of the mid-Atlantic bight during their early life history. YOY bluefish from the Tuckerton, NJ 

area of Great Bay (TK) were fed daily in a laboratory with common prey fish, menhaden and mummichog, from two sites: 

TK (reference) or Hackensack River (HR) (contaminated). Hackensack-fed lab bluefish, HR-field collected bluefish, HR 

prey fish, and stomach contents from HR bluefish all had significantly elevated concentrations of PCBs, DDT and mercury. 

Hackensack-fed bluefish had reduced feeding, activity, and growth. Furthermore, the percentage of HR-field bluefish caught 

with food in the stomach was low (29%) compared to YOY bluefish reported from other regions, suggesting reduced feeding behavior. The size of HR-field bluefish was also significantly less than the TK-field bluefish. In addition, contaminant 

concentrations in prey fish from the stomachs of the HR bluefish were higher than those in the field-caught specimens. Prey 

with higher body burdens may be slower and easier to capture due to adverse neurotoxic effects. If bluefish are preferentially 

foraging on such prey, greater amounts of contaminants can be trophically transferred. Decreased feeding, activity level and 

growth in the exposed YOY bluefish may make them more vulnerable to predation and starvation and have detrimental effects on their overwinter survival and recruitment success. The inclusion of the contaminated fish in catch per unit of effort 

surveys may produce misleadingly inflated year class estimates. These findings substantiate the importance of the integration 

of habitat quality information into stock assessments. 

A mesohaline submerged aquatic vegetation survey of the U.S. Gulf of Mexico coast

Jacoby Carter1, Joy Merino2, and Sergio Merino3

1

U.S. Geological Survey, National Wetlands Research Center, Lafayette, LA; 2SEFSC, Lafayette, LA; 3IAP World Services, 

Lafayette, LA

Submerged aquatic vegetation (SAV) is important habitat for fish and decapods. We conducted a survey of SAV along the 

northern Gulf of Mexico coast to determine species distributions and characterize estuarine SAV communities. We visited 

276 SAV beds in the states of Florida, Alabama, Mississippi, Louisiana, and Texas in 2001–2002 in oligohaline to polyhaline 

salinities. A total of 20 species were identified and habitat characteristics such as salinity, water depth, pH, conductivity, 

turbidity, dissolved oxygen, and sediment composition were collected. Fourteen aquatic macrophytes occurred two or more 

times in our samples. Ruppia maritima occurred most frequently (n = 148). The next most common species were Eleocharis 

sp. (n = 47 characterized with an emergent growth form), and Halodule wrightii (n = 36). The invasive SAV species Myriophyllum spicatum (n = 31) and Hydrilla verticillata (n = 6) were collected in fresh water. We analyzed species occurrence and 

environmental characteristics using Canononical Correspondence Analysis and Two-Way Indicator Species Analysis, which 

indicated five species assemblages distinguished primarily by salinity and depth.
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The role of the thermal habitat niche on mortality and recruitment in summer flounder, Paralichthys dentatus

R. Christopher Chambers 

NEFSC, James J. Howard Marine Sciences Laboratory, Highlands, NJ

A predictive understanding of how the environment, and the thermal regime in particular, might affect the survival and 

duration of prerecruit life stages is fundamental to habitat use and to quantifying habitat quality. Summer flounder presents 

an intriguing example of a fish whose habitat in early life varies dramatically depending on when and where adults spawn. 

Most summer flounder spawn in continental shelf waters in autumn as adults egress from inshore summer habitats. When 

and where spawning occurs is likely to influence whether offspring reach metamorphic competency, ingress, and settle in 

embayments in the autumn or the following spring. We provide evidence of the duration of presettlement life stages under 

experimental scenarios designed to mimic variations in season and latitude at spawning. We use these data to predict the 

likelihood of ingress prior to winter and to estimate the sizes at ingress as a function of larval habitat. Offspring of adults that 

spawn at thermal regimes typical of southern latitudes or of early autumn at northern ones are likely to initiate metamorphosis, ingress, and settle before water temperatures drop too low to support further development. Offspring of adults that 

spawn in thermal regimes characteristic of the autumn at northern latitudes are unlikely to reach metamorphic competency 

in autumn, and therefore not ingress until spring warming albeit at a significantly larger body size. Data such as these can be 

used to estimate the volume and quality of larval habitats, to illuminate mechanisms underlying changes in larval indices, 

and to inform survey designs.

Proposing a framework for integrating habitat science and management

Louis A. Chiarella

NERO, Habitat Conservation Division, Gloucester, MA

The NMFS Habitat Program has been engaged in habitat protection activities for over 25 years. The early efforts within 

this program focused mainly on traditional coastal development projects regulated by the Army Corps of Engineers. Today, 

the Habitat Program works with a wide variety of stakeholders to protect and restore habitat that supports living marine 

resources. However, the implementation of the Habitat Program is still mostly reactionary as opposed to strategic. A framework is being proposed that will allow managers to better utilize science in the implementation of the Habitat Program. In 

addition, this framework guides the science that needs to be undertaken for management purposes. The principals of this 

framework have been adopted from the 2006 National Fish Habitat Action Plan which specifies that a plan should: 1) be 

strategic rather than merely opportunistic; 2) address the causes of and processes behind fish habitat decline, rather than the 

symptoms; 3) provide increased and sustained investment to allow for long-term success; 4) monitor and be accountable 

for scientifically sound and measurable results; and 5) share information and knowledge at all levels from local communities 

to Congress. Utilizing these principals, the proposed framework is supported by a strong science-based foundation. Existing and emerging science-based tools must be used to target priority areas and implement appropriate strategies within the 

management program. In order to accomplish this it is proposed that the Science Centers initiate comprehensive regional 

fish habitat assessments. Initial assessments would be undertaken utilizing existing data and supplemented with new data 

where needed. Habitat identification, characterization and mapping would be an integral part of this effort. Once the assessments are completed, priority fish habitats and their threats could be identified and utilized by the Habitat Program to 

develop regional habitat protection and restoration plans. Implementation of these regional habitat plans will yield strategic, 

comprehensive and coordinated efforts to protect and restore fish habitats required by living marine resources. Results on 

the effectiveness of this program would be monitored in a scientifically sound manner by the Science Centers. Monitoring 

results and trends would be reported on a periodic basis in the form of a Fish Habitat Report Card. Results of the report card 

would be utilized to assess the efficacy of the Habitat Program, which would influence development of new strategic plans. 

Gaps in assessment information as well as other scientific needs can be addressed through targeted research projects conducted by the Science Centers. The results of such studies would feed directly back into this management framework. The 

integration of science and management in this type of framework insures that: the science that is being produced is relevant 
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to management; management is utilizing the best available science to implement strategic programs; mechanisms exist to 

feed new science into the process; and management results are being measured in a scientifically sound manner.

AUV (autonomous underwater vehicle) for monitoring fish and their habitat on the U.S. west coast

M. Elizabeth Clarke1, Erica Fruh2, Curt E. Whitmire2, and Hanumant Singh3

1

NWFSC, Seattle, WA; 2NWFSC, Newport, OR; 3Woods Hole Oceanographic Institution, Woods Hole, MA

The Northwest and Pacific Islands Fisheries Science Centers have worked with researchers at Woods Hole Oceanographic 

Institution (WHOI) to redesign the Seabed AUV to overcome the difficulty of monitoring fish populations and habitat 

in rocky areas. Traditional fish monitoring techniques such as bottom trawl surveys have some limitations for assessing 

groundfish populations and their habitat throughout their range because of the abundance of rugged terrain. Hover-capable 

bottom tracking AUVs, on the other hand, offer a unique tool that is appropriate for work in such areas. The Seabed AUV 

developed by Hanumant Singh at WHOI is a multihull hover-capable vehicle that unlike traditional torpedo shaped AUVs 

is capable of working extremely close to the seafloor while maintaining very precise altitude and navigation control. Its small 

footprint coupled with its 2000 meter depth rating makes it an ideal platform for conducting surveys off the continental 

shelf on ships ranging from standard oceanographic vessels to smaller fishing vessels. Key modifications have been made to 

the AUV to simultaneously obtain forward- and downward-looking bottom imagery. In addition, a multibeam echosounder 

is mounted on the AUV to collect very high resolution bathymetry that is coregistered with digital photographs. Use of the 

Seabed AUV will allow the development of nonextractive surveys to monitor groundfish and their habitats in previously 

unassessed rocky habitats. The Seabed AUV is expected to provide better monitoring of groundfish communities in untrawlable habitats and increased resolution and positional accuracy of seafloor imagery, while simultaneously reducing ship time 

requirements.

Interactive habitat database for the Pacific Coast Ocean Observing System (PaCOOS): An ecosystem 

observing tool for the California Current

M. Elizabeth Clarke1, Chris G. Romsos2, Chris Goldfinger2, Bob Gref1, W. Waldo Wakefield3, and Marlene Bellman1

1

NWFSC, Seattle, WA; 2Oregon State University, College of Oceanic and Atmospheric Sciences, Corvallis, OR; 3NWFSC, 

Newport, OR

Building on databases assembled for the development of an Essential Fish Habitat Environmental Impact Statement for west 

coast groundfish, we have developed a data portal that links several remote servers and delivers a variety of habitat relevant 

data including benthic, biological and oceanographic data, and allows multilayer query and reporting and query comparisons (http://pacoos.coas.oregonstate.edu/). This data server is part of Pacific Coast Ocean Observing System (PaCOOS), 

whose long-term objective is to develop and maintain an integrated distributed data access, transport, and analysis system 

serving data and products and meeting research and management needs for multiple users in the California Current Ecosystem. The habitat data portal provides for data discovery, direct client access to data, custom/interactive view environments, 

as well as developing integrated decision support tools for ecosystem-based management. Specific examples of data available 

via the portal are: seafloor habitat data, bottom trawl survey data, nonconfidential observer and fishing activity information, 

cold water coral locations and management areas and boundaries. These data are linked to a habitat utilization database for 

west coast groundfish (> 90 species). Our immediate goal is to provide a portal that allows data exploration by experts as well 

as by managers and stakeholders to support decision making for such things as spatial management. Our long-term goal is 

to bring the 2-D geospatial world and the 4-D oceanographic world closer to seamless exploration by examining interoperability between these two inherently different data structures.
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Estimating biomass from in situ counts of demersal fishes—the challenge in creating a random sample from 

data collected nonrandomly 

Julia E.R. Clemons, W. Waldo Wakefield, Ian J. Stewart, and Curt E. Whitmire

NWFSC, Newport, OR

The objective of this poster is to provide a detailed layout of the methodology for a statistically sound and organized approach for combining nonrandomly collected in situ direct count fish observation data with a habitat map to estimate fish 

biomass. Specifically, how does one treat a nonrandom data set that was collected with potentially different objectives in 

mind, in this case, fixed station and geological reconnaissance? For this study we used an existing and previously published 

upon data set from Heceta Bank, Oregon. Heceta Bank is one of the largest rocky banks along the U.S. west coast containing 

a wide range of habitats supporting numerous species of commercially important groundfish, including a diverse assemblage 

of rockfishes (Sebastes spp.). We used high resolution bathymetry and backscatter imagery of the bank collected with a Simrad EM 300 multibeam echo sounder, and strip transect video surveys of habitat and demersal fishes, using a remotely-operated vehicle. We examined fish observations relative to the habitat variables of depth, sediment type, backscatter intensity 

and relative elevation (i.e. topographic position index). We post-stratified the data to address sampling bias toward shallower 

water (along the top of the bank) and present abundance estimates for select species of groundfish to illustrate the method. 

This type of approach could be evaluated for nonrandomly collected data wherever the most important habitat information 

dictating fish abundance is available. 

Demographics by depth: Spatially-explicit densities and life history dynamics of hogfish (Lachnolaimus 

maximus) in the eastern Gulf of Mexico

Angela B. Collins1 and Richard S. McBride2

1

Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL; 2NEFSC, 

Woods Hole, MA

A combined approach of SCUBA observations and life history analyses revealed spatially-specific demographic patterns of 

hogfish (Lachnolaimus maximus) in the eastern Gulf of Mexico. Hogfish (64–774 mm fork length and 0–19 years old) were 

widespread, existing in harems year round over multiple habitat types, in depths from 1 to 69 m. As depth increased, density 

decreased but size and age increased, demonstrating a cross-shelf ontogenetic migration. Size at age was smaller in nearshore 

(< 30 m) habitats, suggesting that faster-growing fish migrate offshore sooner. A strong red tide, occurring the year before 

sampling began, likely affected hogfish in nearshore waters, at least partially influencing demographic structure. Specifically, 

maximum size and age was smaller and younger in nearshore waters. Fishing pressure is also presumably higher nearshore 

and presents a confounding source of increased mortality. Size and age at sex change of nearshore hogfish were half that of 

offshore hogfish and were coincident with the minimum size limit, which indicated effective, selective harvesting. These 

spatial patterns were not evident prior to this research because this stock component was previously assessed in aggregate. 

Despite evidence of fishing effects, persistent escapement of fish to offshore habitats indicates that the aggregate status of 

this stock component is still stable.

Integrated habitat restoration monitoring for program planning and project implementation

Mathias J. Collins1 and Bryan DeAngelis2

1

NOAA Restoration Center, Gloucester, MA; 2NOAA Restoration Center, Narragansett, RI

The NOAA Restoration Center has recently improved project monitoring for stream barrier removals. This has been accomplished through two distinct, yet related efforts: 1) development and publication of the Gulf of Maine Council’s Stream 
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Barrier Removal Monitoring Guide; and 2) development and nascent implementation of the Open Rivers Initiative Stream 

Barrier Removal Performance Measures and Project Monitoring. These efforts built upon an earlier improvement of salt 

marsh restoration monitoring through the development, publication, and implementation of the Gulf of Maine Salt Marsh 

Monitoring Protocol. Similar to the experience with salt marsh monitoring, improved stream barrier removal monitoring 

at the site-scale does not necessarily translate to information that facilitates regional-scale analyses suitable for program 

planning. To have restoration project monitoring that produces usable, planning-level feedback requires a network of sites 

carefully chosen to illuminate broad-scale questions. Also needed are: systematic data capture, storage and management; 

project- and regional-level data analyses by project type; and mechanisms for adaptive management that allow information learned from project monitoring to affect program priorities, project selection, and/or technique selection. We report 

on our recent experience in the northeast United States to develop a network of stream barrier removal monitoring sites 

explicitly selected to facilitate regional analyses and program planning by representing the range of habitat types and scales 

typically used by NOAA trust resources in the region. We also describe our efforts to generalize this experience to inform 

restoration monitoring of all project types and to develop systematic data handling, analyses, and feedbacks for program 

planning and project implementation.

Estimating total spawning abundance from index area counts using a GIS-based habitat intrinsic potential 

model

Thomas D. Cooney1, Damon Holzer2, and Rich Carmichael3

1

NWFSC, Portland, OR; 2NWFSC, Seattle, WA; 3Oregon Department of Fish and Wildlife

Counts in selected stream sections (index reaches) have been used to monitor trends in steelhead (Oncorhynchus mykiss) 

abundance in several mid-Columbia River tributaries. Index reaches are visited one or more times during the spawning season to generate an estimate of the number of steelhead redds (spawning nests). Index areas were selected based on a number 

of criteria including accessibility and the relative potential to observe spawning under a range of relative abundance levels. 

As a result, while index area counts may reflect year to year patterns in abundance, expansions based on the ratio of habitat 

area within index reaches to the total available for spawning are likely biased. We applied a geographic information system 

(GIS) based habitat intrinsic potential model that uses empirically derived relationships to assign a spawning potential rating to stream reaches based on physical characteristics. The model was used to expand from annual index redd counts to total 

population spawning abundance estimates for several mid-Columbia steelhead populations. Comparisons to abundance estimates based on alternative methods (e.g. weir counts or randomized sampling) indicate that expansions from index counts 

to total abundance based on habitat intrinsic potential outperformed expansions based on linear stream miles. 

Multifrequency biplanar interferometric imaging for ultra high resolution three-dimensional imaging of 

seabed habitat

George R. Cutter, Jr. and David A. Demer

SWFSC, La Jolla, CA

The resolution of 3-D seabed imaging is greatly improved using a new multifrequency biplanar interferometry (MBI) 

technique. Using data from a multifrequency acoustic pulse-echo system (e.g. Simrad EK60 or ME70), ranges to coherent 

targets, estimated from propagation delays, and the phase differences between echoes received with four quadrants of a 

split-aperture array are converted to Cartesian distances, and transformed into Earth coordinates. The collective data set is 

interpolated to create a surface closely approximating the target’s image. The resolution of the resulting image is improved 

orders of magnitude relative to those created with measures based on echo intensity or single frequency uniplanar interferometry. The MBI method allows estimation of seabed slope and surface scattering as a function of incidence angle for seabed 

characterization on a sub-beam basis. We present results from MBI applied to data from split single (EK60) and multibeam 

(ME70) echosounders.
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Under what circumstances, if any, do we need to post-stratify species/habitat data?

Doug DeVries, Chris Gardner, John Brusher, and Gary Fitzhugh

SEFSC, Panama City, FL

 

To optimize survey resources and develop abundance estimators for a given species, a sampling protocol incorporating prestratification by habitat type would certainly improve efficiency and is deemed important in survey design. But the issue 

becomes complex when we consider the numbers of species needing assessment and the diversity of habitats. Of necessity 

there may be a need to post-stratify collection records, perhaps censoring many records depending on the species. It is no 

secret that the heavily exploited reef fishes (mostly serranids and lutjanids) in the northeastern Gulf of Mexico are closely 

tied to hard/live bottom habitat most or all of their lives. Cross-shelf multibeam and side scan mapping and remotely-operated vehicle and stationary drop camera video surveys conducted by the Southeast Fisheries Science Center revealed not 

only that such habitat is widespread and quite extensive across the West Florida shelf off northwest Florida; but also that it 

varies widely in vertical relief, rugosity, morphology, density, area, and in density and composition of sessile invertebrate and 

algal cover. Not surprisingly, these different forms of habitats tend to hold different suites and densities of reef fishes; and the 

demographics within species may also vary. Variability related to depth and zoogeographic boundaries is also common. We 

will present some species-habitat-location examples and will welcome feedback regarding the need and means to objectively 

post-stratify fishery-independent survey results.

The role of socio-economics in habitat conservation

Peter E.T. Edwards

Office of Habitat Conservation, Silver Spring, MD

Ecosystem services are the benefits people obtain from ecosystems. Examples include services such as water purification, 

flood protection, recreation, aesthetics, and climate regulation. Improving habitat conservation will require resource managers to have better information about how ecosystems contribute to society’s well being and how management actions might 

affect those contributions. Valuation of ecological systems may sometimes be required for national rulemaking. For example, 

legislative and executive orders often require that cost-benefit analyses be part of the decision making process. Additionally, 

ecosystem service valuation (ESV) can play an important role in setting program priorities and in assisting governmental 

and nongovernmental organizations in choosing among environmental options and communicating the importance of their 

actions to the public. ESV utilizes an integrated methodological approach and requires collaboration among a wide range of 

disciplines, including ecologists, economists, and other social and behavioral scientists, at each step of the valuation process. 

Social sciences and economic valuation have a role to play in habitat conservation. These methods can assist in measuring the 

social outcomes of the results of habitat conservation. Socio-economic data can improve the decision making process, assist 

in prioritization and support and justify the need for conservation funding. Socio-economic data can be very important to 

the consultation process and should be central when applying a cost-benefit analytical approach for decision making. Data 

collected using social science approaches can improve habitat managers’ understanding of the public’s preferences for conservation and therefore assist with public relations and education.
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Identification and monitoring of dynamic habitat in the changing ocean 

David G. Foley

SWFSC, Environmental Research Division, Pacific Grove, CA; Joint Institute for Marine and Atmospheric Research, 

University of Hawaii, Honolulu, HI

There is an increasing emphasis on the employment of ecosystem-based management towards the stewardship of living 

marine resources. This inherently includes a requirement for the accessibility of timely descriptions of the aspects of marine 

environment that are relevant to a given ecosystem. In the past decade there has been a proliferation of publicly available 

oceanographic data sets derived from a variety of platforms and sensors. National, provincial, and municipal researchers and 

managers who are not necessarily expert in the production and distribution of oceanographic satellite data often face a bewildering, and seemingly contradictory, array of options when choosing data for use in their applications. We offer examples 

of applications, including several client-side tools designed to extract environmental data within the spatial-temporal locus 

of a given animal track, and to then import this data directly into the working environment with which a given research or 

managerial team is comfortable. Additionally, we present sample applications employed along the North American Pacific 

coast in the support of management of both fisheries and protected species. These examples utilize highly-derived products 

that fully integrate data provided by electronic tags placed on Chinook salmon (Oncorhynchus tshawytscha) and more traditional cetacean surveys with environmental data derived from remotely sensed and in situ data, and model output using the 

various dissemination systems discussed. Such integrated data suites will allow for improvement of the identification and 

monitoring of essential habitat over a broad range of spatial and temporal scales.

Mapping hard bottom reef fisheries habitat off northwest Florida—needs, methods, and status

Chris Gardner1, Doug DeVries1, and David Naar2

1

SEFSC, Panama City, FL; 2University of South Florida

The west Florida shelf (WFS) supports some of the most valuable reef fish fisheries in the U.S. Gulf of Mexico. However, 

very little of its area has been mapped with enough resolution to accurately locate and quantify the hard/live bottom habitat 

these fisheries are so strongly tied to. Such maps are essential for designing an efficient fishery-independent survey of reef 

fishes, enabling prestratification by habitat, and thereby minimizing variance and optimizing survey resources. Accurate 

habitat maps will also be critical for ecosystem-based fisheries management and marine spatial planning. In support of a 

recently expanded fishery-independent reef fish survey, the SEFSC began mapping cross-shelf transects on the northern 

WFS using multibeam and side scan sonar. Two transects ~1.5–2.5 x 30 nautical miles (n.mi.) were mapped with a 300kHz 

multibeam sonar and seven single swath cross-shelf transects ~20–30 n.mi. x 150 m were mapped using a 600 kHz side scan 

sonar. An inexpensive live video drop camera and occasionally an remotely-operated vehicle were used for visual ground 

truthing. Although the multibeam provided bathymetry and backscatter data at very high resolution, the side scan hardware 

and software was much more user friendly and provided data on which hard/live bottom habitat could, after a very short 

learning curve, be easily identified. Given the scale of most interest for fisheries-related needs, the 600 kHz side scan sonar 

may be the most cost-effective tool for our purposes.
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Growth variability of the splitnose rockfish (Sebastes diploproa) in the northeast Pacific Ocean: Pattern 

revisited

Vladlena V. Gertseva1, Jason M. Cope2, Sean E. Matson3

1

NWFSC, Fishery Resource Analysis and Monitoring Division, Newport, OR; 2NWFSC, Fishery Resource Analysis and 

Monitoring Division, Seattle, WA; 3Oregon State University, Department of Animal Sciences

Understanding patterns of somatic growth within populations greatly contributes to fisheries stock assessment and helps 

determine the proper model structure. Splitnose rockfish was reported as having a striking pattern of latitudinal growth variability from studies conducted in the 1980s. We investigated variation in growth parameters of splitnose rockfish by latitude 

using recent data from the NMFS Groundfish Survey (2003–2008), current ageing techniques and advanced modeling and 

statistical methods to provide an updated understanding of growth along this species’ latitudinal range. Age data generated from sectioned otoliths was fit to a von Bertalanffy growth function incorporating ageing error. Growth parameters 

were estimated for each of five International North Pacific Fisheries Commission (INPFC) areas along the U.S. west coast. 

Generalized linear models and Akaike’s Information Criteria were used to evaluate hypotheses for growth parameter relationship with latitude. We found that splitnose rockfish exhibited a cline in asymptotic length (L∞) with L∞ increasing with 

rising latitude. We also found that although the growth coefficient (k) was smallest in the Conception INPFC area, there 

was no apparent cline along the coast; a northward cline in k has previously been reported in the literature. We propose that 

differences in fishing intensity could be responsible for cline in L∞, as higher fishing pressure in the south could skew the 

size distribution of the population in that region, and reduce southern L∞ estimates. We also attribute slower growth in the 

Conception area to the oceanographic characteristics and low productivity of the area south of Point Conception.

Mapping marine benthic habitats along the U.S. west coast: Current status, future plans and applications 

Chris Goldfinger1, H. Gary Greene2,3, Rikk G. Kvitek4, Guy R. Cochrane5, Samuel Y. Johnson5, W. Waldo Wakefield6, 

Mary M. Yoklavich7, M. Elizabeth Clarke8, and Crescent Moegling9

1

Oregon State University, College of Oceanic and Atmospheric Sciences, Corvallis, OR; 2Tombolo Institute, Eastsound, 

WA; 3Friday Harbor Laboratories, Friday Harbor, WA; 4California State University, Monterey Bay, Seafloor Mapping Lab, 

Seaside, CA; 5U.S. Geological Survey, Pacific Science Center, Santa Cruz, CA; 6NWFSC, Newport, OR; 7SWFSC, Santa 

Cruz, CA; 8NWFSC, Seattle, WA; 9National Ocean Service, Office of Coast Survey, Seattle, WA

Seafloor mapping serves a variety of needs for habitat scientists and resource managers. Maps of marine benthic habitats are 

a fundamental part of any habitat assessment and are clearly useful for marine spatial planning. Many fish stocks have strong 

affinities for specific habitat characteristics, resulting in patchy spatial distributions of abundance. Incorporating habitat 

characteristics into survey designs and stock assessments could increase their accuracy and precision while potentially reducing field effort, resulting in improved identification and conservation of essential fish habitat (EFH). Working with academic and agency partners in 2003, NMFS developed the first comprehensive seafloor habitat map for the west coast as part 

of a habitat assessment of EFH for west coast groundfish. Although useful, the effort clearly illustrated gaps in the knowledge base for west coast benthic habitats. Since 2003, there has been a major increase in both coverage of high resolution 

swath mapping and habitat interpretations concentrated in the state waters of Oregon, California and Washington (Puget 

Sound) and at select deep water sites. Significant areas of the continental shelf and slope have not been mapped. Within the 

past several years, in part stimulated by the Action Plan of the West Coast Governors Agreement on Ocean Health, the three 

states have conducted seafloor mapping workshops to document the status of habitat assessments, identify seafloor mapping 

priorities and develop strategies to obtain funding. This presentation identifies initiatives and gains in mapping west coast 

marine benthic habitats over the past six years and presents plans and expectations for the future.
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Biotopes in a fisheries ‘habitat hot spot’: Investigating Georges Bank patch complexes in the larger context of 

habitat assessment

Vincent G. Guida1 and Page C. Valentine2

1

NEFSC, James J. Howard Marine Sciences Laboratory, Highlands, NJ; 2U.S. Geological Survey, Woods Hole Science 

Center, Woods Hole, MA

We explored the occurrence of individual fisheries species and the distribution of seabed characteristics on the northern 

edge of Georges Bank in August 2009 using visual imagery obtained by the U.S. Geological Survey Seaboss vehicle and 

water column temperature profiles. Demersal and benthic stocks occur in a complex physical and biological setting where 

movement of a strong tidal front causes bottom temperatures at a location to vary from < 1 ̊ to 7 ̊ C during a semidiurnal 

tidal cycle. Distributions of geological, hydrological, and biostructural factors create small scale (i.e. hundreds of meters) 

habitat patches, each with a potentially different value to various resource species. Preliminary analysis shows habitat areas 

defined by the occurrence of individual species do not correspond precisely with habitats defined by sediment types, topography, hydrology, and epifauna. Sea scallop habitats of sand and gravel partly overlapped, but were not identical, with similar 

habitats occupied by haddock, cod, and silver hake. Bottom water warmer than 14 ̊ C, associated with the invasive colonial tunicate Didemnum vexillum, rarely overlapped the occurrence of juvenile cod. Gravel habitat characterized by dense 

benthic epifauna dominated by the erect bryozoan Eucratia loricata supported cod and haddock but not silver hake, which 

were observed on adjacent mobile sand substrate. We suggest that in such complex areas the roles of habitats in species’ life 

histories need to be modeled on a fine scale based on real data to complement coarser scale modeling appropriate for more 

spatially homogeneous regions.

Patterns and processes underlying Pacific hake (Merluccius productus) migrations: Progress on developing 

forecast tools to predict distribution and density 

Melissa A. Haltuch1, Carrie Holt2, André E. Punt3, and M. Elizabeth Clarke1

1

NWFSC, Seattle, WA; 2Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC; 3University of 

Washington, School of Aquatic and Fishery Sciences, Seattle, WA

The spatial distribution of Pacific hake (Merluccius productus) exhibits strong environmentally-driven interannual variation 

during the stock’s annual northerly migration, impacting monitoring, assessment, and management of this species. Spawning and rearing habitat temperatures and strength of alongshore currents are hypothesized drivers of that variation, both of 

which may be impacted by global climate change. Prediction of hake distribution is important for long-term planning under 

future climate scenarios, and short-term decisions. Specifically, hake management would be enhanced via optimized survey 

design and planning from improved estimates of hake distribution and density. Given the ability to predict the distribution and density of hake prior to a survey, survey effort could be distributed to minimize (expected) variance. Substantial 

benefits, in terms of more precise estimates of abundance, could be possible for the hake survey off the west coast of North 

America which forms the basis for stock assessment and management advice. This presentation discusses the development 

of a forecast tool for predicting hake distribution and abundance based on fitting spatial time series models with environmental covariates. Previous studies have modeled hake distribution and density. However the covariates for this project are 

derived from real time satellite data and short-term ocean model forecasts, and hence have the potential for a more spatially 

explicit and extensive predictive tool than previous efforts. While these forecasts focus on time scales from weeks to seasons, 

developing the ability to produce reliable short-term forecasts for hake is a precursor to forecasting the longer-term impacts 

of global climate change on the hake stock.
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Application of an adaptive acoustic/trawl survey to reduce uncertainty in rockfish biomass estimates

Dana H. Hanselman1, Paul Spencer2, Denise McKelvey2, and Michael Martin2

1

AFSC, Ted Stevens Marine Research Institute, Juneau, AK; 2AFSC, Seattle, WA

Survey biomass estimates of several Alaskan rockfish species have shown large interannual variations that are not consistent 

with their longevity. This variability reflects the ‘patchiness’ of the spatial distribution of the population. This study evaluates 

an experimental survey design to reduce the variability in estimated biomass for Pacific ocean perch (POP). The design is a 

variant of adaptive sampling and uses acoustic information to distinguish strata of different densities. In addition to planned 

trawl stations, additional trawl tows are conducted in the high density fish areas identified during the cruise. The rationale of 

the design is to reduce sampling variability by allocating more sampling effort in the areas of higher fish density. Reducing 

the uncertainty of biomass estimates for patchily distributed rockfish has been identified as an assessment and management 

priority. We analyzed historic echosign data to delineate patch strength and size. In August 2009, we conducted a 12 day 

pilot survey on the F/V Sea Storm near Yakutat, AK to test the design. A total of 59 trawl hauls were completed, with 19 

‘patch’ stations and 40 background stations. Catch of all species was 30.1 tons with 55% of the catch comprised of POP. 

Mean catch per unit effort of POP in the ‘patch’ stations was 42,540 kg/km2 and 7,540 kg/km2 in background stations. We 

compare the hybrid estimates from the study to simple random sampling and stratified random sampling in terms of precision and efficiency. We also compare the results to the NMFS trawl survey conducted weeks earlier.

Gulf of Mexico pink shrimp stock assessment model recalibration and model migration to Stock Synthesis 

Rick A. Hart and James M. Nance

SEFSC, Galveston Laboratory, Galveston, TX

The Southeast Fisheries Science Center pink shrimp stock assessments currently use only fisheries-dependent data, including landings, port agent interviews, and electronic logbooks estimating fishing effort. The Gulf of Mexico pink shrimp 

stocks were deemed undergoing overfishing in 2008. This designation was made because the SEFSC virtual population 

analysis (VPA) model results indicated the spawning stocks fell below overfishing limits. However, because other fishery 

indicators (e.g. catch per unit of effort [CPUE]) did not corroborate this finding, SEFSC staff recommended maintaining 

the current stock status designation until the VPA model could be reviewed to determine if this designation should be supported. In June 2009 an internal NMFS review panel was convened to critically review the VPA. The panel concluded the 

presently used VPA is not suitable for making a status determination for the Gulf pink shrimp stocks. In addition the panel 

stated new fisheries models should be investigated for future assessments. In light of these findings, we have migrated our 

pink shrimp assessment data into Stock Synthesis (SS3). We tested the applicability of SS3 to the commercial pink shrimp 

data using a preliminary model setup of just one random year of data (1976). In this test configuration, SS3 was able to fit 

both the weight and age composition data. Subsequent full time series runs in SS3 illustrated the model’s ability to fit the 

expected and observed values of CPUE, revealing the applicability of this model to these data. In these full time series runs, 

spawning biomass, numbers of recruits, as well as the CPUE estimates, were also generated. Upon completion of the model 

calibration with commercial shrimp data, we hope to incorporate fishery-independent surveys of shrimp abundance, as well 

as environmental data into future models. We believe environmental factors are of primary importance in regulating pink 

shrimp populations in the Gulf of Mexico. 
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Delay-difference, age-structured, and state-space models: Are hyphenated models useful for assessing stocks 

of orange roughy?

Allan Hicks 

NWFSC, Seattle, WA; University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA

Age-structured models are commonly used to assess orange roughy stocks, but many of the life history parameters are assumed known and a deterministic biomass trajectory (no recruitment variability) is often estimated. A simpler model is 

the delay-difference model, which can capture much of the same dynamics as an age-structured model without keeping 

track of individual ages. However, the assumptions made in these deterministic models may result in biased estimates and 

underestimate the true uncertainty. Through simulation, this study compares the ability and the usefulness of three models 

to estimate a biomass trajectory and catchability parameters that mimic a stochastic orange roughy population depleted to 

three different levels. The three models are a delay-difference model with observation error, an age-structured model with 

observation error, and a state-space delay-difference model with both process and observation error. Results showed that 

estimates of depletion were biased with the state-space model showing the least bias. Estimates of virgin biomass from the 

state-space model, however, were highly variable and showed a large positive bias. This was related to the amount of process 

error and the bias was reduced with some prior information on virgin biomass or catchability from one or more surveys. The 

deterministic delay-difference and age-structured models performed similarly under these assumptions and the inclusion 

of process error in the state-space model resulted in less biased estimates of depletion but much more variable estimates of 

virgin biomass.

Recent findings and accomplishments of NOAA’s Fisheries and the Environment (FATE) program

Anne B. Hollowed1, Steven Bograd2, Elizabeth Brooks3, Melissa A. Haltuch4, Jonathan A. Hare5, Roger Hewitt6, Evan 

Howell7, John Lamkin8, Kenric Osgood9, Jeffrey Polovina7, and Michael J. Schirripa8

1

AFSC, Seattle, WA; 2SWFSC, Pacific Grove, CA; 3NEFSC, Woods Hole, MA; 4NWFSC, Seattle, WA; 5NEFSC, 

Narragansett, RI; 6SWFSC, La Jolla, CA; 7PIFSC, Honolulu, HI; 8SEFSC, Miami, FL; 9Office of Science and 

Technology, Silver Spring, MD

The goal of the Fisheries and the Environment (FATE) program is to provide the information necessary to effectively forecast these changes to evaluate management strategies needed to sustain fisheries while preserving ecosystem structure and 

function. In support of this goal, the FATE program was developed to accelerate the development of next generation forecasting tools. The FATE program provides leading indicators of ecological and oceanographic change at the population and 

ecosystem level and local to ocean basin scales. FATE supports research on the functional relationships between environmental forcing, competition for prey, or predation on the growth, distribution or reproductive success of managed species. 

This presentation provides highlights and results from projects funded in 2007 and 2008. These examples demonstrate that 

FATE research projects are now being incorporated into population dynamics models used to inform managers of the implications of their actions on the current and future status of marine resources. In some regions, FATE indices provide early 

warnings of major shifts in the productivity or distribution of key stocks. While the program is based on an ecosystem approach, it targets a suite of commercially important species including groundfish, coastal pelagics, Pacific salmon and highly 

migratory fishes as well as protected species. 
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The Deep Sea Coral Research and Technology Program: Assessing deep sea habitats

Thomas F. Hourigan1, M. Elizabeth Clarke2, Andrew David3, Dan Dorfman4, Maile Sullivan1, John Tomczuk5, and Fan 

Tsao1

1

Office of Habitat Conservation, Silver Spring, MD; 2NWFSC, Seattle, WA; 3SEFSC, Panama City, FL; 4National Ocean 

Service, National Centers for Coastal Ocean Science, Silver Spring, MD; 5Office of Oceanic and Atmospheric Research, 

Ocean Exploration and Research, Silver Spring, MD

Deep sea corals and sponges can form complex biogenic habitats of astonishing biological diversity. In several regions, such 

biogenic habitats have been identified as essential fish habitat by regional Fishery Management Councils. Before most areas 

have even been surveyed, however, these deep sea communities are threatened by damage from fishing gear and other activities. In 2009, the NOAA launched the Deep Sea Coral Research and Technology Program, called for in the reauthorization 

of the Magnuson-Stevens Fishery Conservation and Management Act. The program conducts targeted field expeditions 

using state of the art mapping and research technologies, and analyzes and integrates existing information on the deep sea 

coral ecosystems and human activities that may impact them. Initial program priorities are to identify and map deep sea 

coral habitats and understand their relationship to managed fisheries species. In its first year, new mapping and exploration 

in deeper waters off Florida identified new coral-rich areas that informed the final boundaries in the South Atlantic Fishery 

Management Council’s historic efforts to enhance protection for over 23,000 square miles of complex deepwater coral habitats located off the coasts of the Carolinas, Georgia, and eastern Florida. In 2010, the Deep Sea Coral Research and Technology Program is expanding new field research to the U.S. west coast, in partnership with the region’s five National Marine 

Sanctuaries and the Pacific Fishery Management Council. This poster summarizes the program’s first year of activities and 

identifies future plans that will inform NOAA’s fisheries habitat assessments. 

Incorporating the negative impacts of chemical habitat quality into stock assessments

John Incardona, Nathaniel Scholz, and Tracy Collier 

NWFSC, Environmental Conservation Division, Seattle, WA

Emerging science indicates a need for incorporating information on the impact of pollution (or ‘chemical habitat quality’) 

on fish stocks. In the past, there was little focus on this area, because toxicology emphasized acutely lethal effects of chemical contaminants, occurring at high concentrations rarely achieved in open water. Using more sophisticated techniques 

adopted from biomedical research, recent NOAA ecotoxicological research has identified sublethal and indirect effects on 

fish at different life history stages that can produce population level impacts. These findings represent key impacts of coastal 

development and nonpoint source pollution on fresh water, estuarine, and other nearshore habitat that support early life 

history stages and food webs required for ecologically and commercially important fish species. Coastal development and 

population growth are only expected to be an increasing threat to nearshore habitats nationwide. Four broad areas relating 

to habitat and stock assessment would benefit strongly from an increased focus on chemical habitat quality: 1) overall ecological considerations, particularly those relating to the conservation and recovery of threatened or endangered species, or 

those that are otherwise imperiled by overfishing or habitat loss, including indirect effects on fish stocks through food web 

impacts; 2) the potential for maritime accidents or natural disasters to impact commercially important species, highlighted 

by the potential effects of oil spills on the herring fisheries of Prince William Sound and San Francisco Bay; 3) the potential for bioaccumulative contaminants to impair seafood safety; and 4) the potential loss of tourism revenue due to coastal 

habitat degradation.
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Adding ecological context to essential fish habitat models using groundtruthing technologies 

Steven Intelmann1, Keith Smith1, Bob McConnaughey1, and Yuri Rzhanov2

1

AFSC, Seattle, WA; 2University of New Hampshire, Center for Coastal and Ocean Mapping, Durham, NH 

Variable absorption and reflection by geological and biological materials affect the acoustic returns from seafloor mapping sonars. Subsequent groundtruthing enables ecological interpretations of the acoustic information, and can be a useful 

component of seafloor characterization. In order to improve our understanding of the seafloor as an element of essential 

fish habitat (EFH), we use three different devices to groundtruth acoustic backscatter: 1) a Free Fall Cone Penetrometer 

(FFCPT); 2) a SEABed Observation and Sampling System (SEABOSS); and 3) a Towed Auto-Compensating Optical 

System (TACOS). The FFCPT is a probe designed to free fall through the water column and can penetrate the seabed to 3 

meters depth. Measurements of both acceleration and pressure allow a profile of sediment types to be determined. The SEABOSS allows us to observe surficial sediment properties and acquire physical seabed characteristics using a single instrument 

deployment. Digital still and video cameras are configured to image the seafloor surface while simultaneously obtaining a 

physical sample with a van Veen grab. The TACOS design provides the ability to capture downward-looking video streams 

in a towed application. An industrial machine vision camera provides overlapping video frames that can be mosaicked into 

a seamless picture providing greater spatial context of seabed composition and biological attributes than is possible through 

single image exposures. These devices provide complementary information on seafloor characteristics and generate a multifaceted view of the physical and biological components of habitat. Such views improve our understanding of ecological 

relationships and guide the formulation of our quantitative EFH models.

Can fishery policies for the U.S. west coast simultaneously sustain habitat, target species, and ecosystem 

health?

Isaac Kaplan and Peter Horne

NWFSC, Seattle, WA

Fishery managers need tools to evaluate how alternative management actions will simultaneously impact target stocks, habitat, and other components of the ecosystem. In this context, here we use an Atlantis ecosystem model to test five broad options for managing fishing impacts on the U.S. west coast, both coast-wide and then specifically in central California. These 

five management scenarios include a mix of spatial planning and shifts to alternate gears. We score the scenarios relative to 

metrics based on economics, target species management, and ecosystem considerations. Ecosystem metrics include bycatch 

and truncation of rockfish (Sebastes spp.) age structure, the abundance of protected species, and damage to habitat. We 

quantify the impact of fishing gear on habitat very simply, by measuring the footprint of each fleet in each scenario, scaled 

by the habitat types and sensitivity indices presented in the 2005 Pacific Coast Groundfish Essential Fish Habitat Environmental Impact Statement. The results suggest that scenarios that shift to alternate (non-trawl) gears perform the best in 

terms of reducing both bycatch and habitat destruction. Spatial management scenarios lead to more mature age structure 

for rockfish, but intermediate overall biomasses. The scenarios illustrate strong trade offs between economic objectives and 

ecological objectives related to habitat and fish populations. On the other hand, economic yield is more compatible with the 

abundance of protected species such as birds and mammals. The strategic application of Atlantis to screen policy scenarios is 

one of the modeling approaches useful within NOAA’s Integrated Ecosystem Assessment framework. 
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A multispecies bioeconomic model with biological and harvesting interactions using a surplus production 

model of stock dynamics

Stephen Kasperski 

AFSC, Seattle, WA

This paper develops a multispecies bioeconomic model that incorporates biological and harvesting interactions to determine 

the optimal effort and stock size for each species. A surplus production model of each population including the interactions 

between species is estimated and explores how the inferences drawn from the single species bioeconomic model may differ 

from inferences drawn from the multispecies bioeconomic model. The model also separates fishing effort by target species 

and allows for bycatch and combined harvesting of multiple species to differ by target species. The empirical application uses 

the pollock, Pacific cod, and arrowtooth flounder populations in the Bering Sea/Aleutian Islands region of Alaska as a case 

study. Between 1990 and 2008 in the Bering Sea/Aleutian Islands region, estimates of the pollock and Pacific cod population have declined by 46% and 39% respectively, while estimates of the arrowtooth flounder population have increased by 

105% over the same time period. As arrowtooth flounder are a low value species which preys on pollock and competes with 

Pacific cod for resources, it is possible that increases in the arrowtooth flounder population reduce the value of this multispecies fishery. This paper also explores the value of these relatively simple bioeconomic models in relation to more complex 

biological and economic models. 

Developing an essential fish habitat geodatabase, workflow and data model

Charles Keith

NEFSC, Woods Hole, MA

The NEFSC has been tasked to create up to date essential fish habitat (EFH) map products for use by fisheries managers and 

regional Fishery Management Councils for selected commercial species inhabiting the eastern U.S. continental shelf. Maps, 

in conjunction with detailed written descriptions, represent the full extent of a species’ EFH as required by the MagnusonStevens Fishery Conservation and Management Act. EFH maps were previously developed using separate computer programs to analyze data sets, and then compiled in a piecemeal standalone geographic information system (GIS). Currently, 

a geodatabase has been created to store the necessary building blocks, which through geoprocessing steps and calculations 

creates EFH features and surfaces. Within the geodatabase, relationships and behavior rules can be created to accurately 

represent the spatial relationships of EFH feature classes, tables, and raster data sets. The workflow and data model diagrams 

create a road map of how EFH representations were created, allowing the data products to be easily replicated. Accurate 

metadata can be easily generated as well. The data model can be updated and changed as new data sets are developed and 

EFH geoprocessing methodologies advance. Help files can guide the GIS analyst in creating new or updating existing EFH. 

Ideally, future work will result in a web-published geodatabase and mapping application for public access and downloading. 

Assessment of geomorphological characteristics and reef fish utilization of reported reef fish aggregation sites 

in the Florida Keys, USA

G.T. Kellison1, A.C.R. Gleason2, and J.C. Taylor3

1

SEFSC, Beaufort, NC; 2University of Miami, Physics Department, Coral Gables, FL; 3National Ocean Service, National 

Centers for Coastal Ocean Science, Beaufort, NC

Fish spawning aggregations (FSAs) are a vital part of the life cycle of many reef fish species. In many cases, a lack of knowledge of the location of FSA sites prohibits their protection and effective management, and practical approaches to identify 
133

those sites and assess their utilization by aggregating species are needed. We are using acoustic technologies at reported FSA 

sites in the Florida Keys to accomplish two objectives: 1) assess whether reported FSA sites are characterized by similar 

habitat characteristics, with a focus on geomorphological features; and 2) determine whether sites reported to have been 

‘fished out’ in previous decades are currently utilized by remnant or recovering aggregations. For the habitat component, 

preliminary results from the upper Florida Keys indicate that drowned, margin-parallel, rocky ridges, known locally as outlier reefs, are features found in proximity to all FSA sites studied. In particular, three geomorphic characteristics were consistently observed: a steep slope of the landward boundary of the upper-slope terrace; an exposed outlier reef forming the 

seaward boundary of the upper-slope terrace; and at least one other exposed outlier reef on the upper-slope terrace. For the 

fish utilization component, initial surveys indicate positive signs of aggregating fish during predicted aggregation periods, 

but true spawning aggregations have not been observed. From a management perspective, the results suggest the benefit of 

using acoustic and habitat approaches to identify critical sites for fisheries monitoring and management focus.

Multivariate models to predict distribution of structure-forming benthic invertebrates

Lisa Krigsman1, Mary M. Yoklavich1, and Guy R. Cochrane2

1

SWFSC, Santa Cruz, CA; 2U.S. Geological Survey, Pacific Science Center, Santa Cruz, CA

The California Seafloor Mapping Project (CSMP) is a collaborative venture designed to create comprehensive maps of the 

seafloor, which are derived from high resolution multibeam echo sounder data collected within state waters (shoreline to 

three nautical miles). CSMP will result in a suite of maps detailing seafloor morphology and geology, and characterizing 

potential benthic habitats. Groundtruthing these seafloor data and surveying biological components of benthic habitats are 

a major part of CSMP. We are using a towed camera sled to collect presence/absence data of macro-invertebrates associated 

with specific sediment types, depth, and latitude. We have developed multivariate models using logistic regression to predict 

the distribution of key species (including some deep sea coral species), and couple these results with spatial information on 

sediments and depth to map the probability of occurrence of these important components of seafloor communities on a 

coast-wide scale. These maps will provide managers, policy makers, and the public with information that can be used in the 

conservation and management of sustainable marine resources. We will demonstrate this approach using data from southern 

California. 

Successes and challenges in displaying essential fish habitat spatial data through the EFH Mapper 

Terra Lederhouse, Mike Onzay, Karen Abrams, and Kara Meckley

Office of Habitat Conservation, Silver Spring, MD

The Essential Fish Habitat (EFH) Mapper is a web-based tool that is the first of its kind to display essential fish habitat 

data and maps nationally. The interactive Mapper enables users to query information from multiple Fishery Management 

Plans at once to view habitat maps and species lists for a specific location. The Mapper uses a customized ArcIMS HTML 

viewer to create a platform for distributing spatial habitat data, providing a user-friendly and highly interactive upgrade to 

the static maps of the past. The Mapper provides a coordinated interactive map service that houses EFH data for regions 

that do not have geographic information system (GIS) applications on the internet while connecting users to those existing 

systems operated by Regional Offices and regional Fishery Management Councils. Key challenges include the limited ability 

of the Mapper to accurately host and display EFH designations for each life stage of each managed species. The spatial data 

necessary to depict individual designations in a GIS format varies in quality and availability by region. Improving the spatial 

description of EFH designations and the resolution of regional EFH data will allow users to perform more accurate location-specific queries, thereby improving the functionality of the Mapper for the public and resource managers. The mapper 

may be found at: http://www.nmfs.noaa.gov/habitat/habitatprotection/efh/index_GIS.htm.
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Predicting the distribution of anadromous fish in fresh water using habitat models

Steve Lindley

SWFSC, Fisheries Ecology Division, Santa Cruz, CA

Effective management of anadromous species under the Endangered Species Act is facilitated by a comprehensive understanding of historical distribution. Elevation, climate and hydrologic data can be used with a number of modeling approaches to predict species distributions for large areas. In this paper I review methods based on bioclimatic envelopes, multivariate 

distance metrics, and literature-derived habitat preferences and applications to green sturgeon, coho salmon and steelhead. 

Output from these models has been influential in designating management units, critical habitat, and recovery goals for 

anadromous species inhabiting the U.S. west coast. 

Deciphering environmental patterns and effects from messy data

Sandra A. Lowe and Jim N. Ianelli

AFSC, Seattle, WA

Alaska Atka mackerel (Pleurogrammus monopterygius) are an important component of the Aleutian Islands ecosystem and 

support a large commercial fishery. Sustainability of this population has been dependent on highly variable recruitment 

and the consistent appearance of strong year classes. Interestingly, strong year classes of Aleutian Islands Atka mackerel have 

occurred in years of hypothesized climate regime shifts 1977, 1988, and 1999, as indicated by indices such as the Pacific 

Decadal Oscillation. El Nino Southern Oscillation (ENSO) events are another source of climate forcing that influences the 

North Pacific. Preliminary analyses have not indicated a relationship between strong year classes of Aleutian Atka mackerel 

and ENSO events. We reexamine this relationship in light of significant recent recruitment events. Quantitative observations about the ENSO effects on fishes can be difficult, and as such we also examine anomalies of weight at age tracked by 

cohort to decipher potential patterns that may reflect environmental influences. We suggest ways that environmental indicators of growth patterns may be incorporated into the stock assessment.

The role of SEAMAP plankton surveys in monitoring the pelagic habitats of early life stages of fishes in the 

Gulf of Mexico

Joanne Lyczkowski-Shultz, David S. Hanisko, Glenn Zapfe, Katrin E. Marancik, and Christina Schobernd

SEFSC, Mississippi Laboratories, Pascagoula, MS 

Plankton samples and associated environmental data have been collected during annual Southeast Area Monitoring and 

Assessment Program (SEAMAP) surveys in the Gulf of Mexico since 1982. This time series of observations has produced 

an extensive database on the early life stages (ELS) of fishes and their pelagic habitats. The associated environmental (hydrographic) data have not undergone the same rigorous scrutiny as plankton sample data and, therefore, their value is not 

fully realized. In recent years, habitat-related data collection has been expanded to include: fluorometric chlorophyll a measurements; quantification of net-collected Sargassum and gelatinous zooplankton; and continuous surface zooplankton 

sampling with corresponding environmental measurements. The vertical dimension of larval fish habitat is also now being 

described through discrete depth sampling during SEAMAP surveys on an ‘as time permits’ basis. These new data on pelagic habitats along with recent analysis of archived hydrographic data reveal the importance of considering habitat when 

interpreting survey-generated occurrence and abundance data for gray triggerfish, snappers and groupers. This set of georeferenced observations describes the physical and environmental characteristics of habitats where larvae of fishery species 

have been consistently found over the past three decades. These depictions of essential ELS habitat represent baselines for 

future habitat assessments and marine spatial planning. They also provide guidance for improving SEAMAP survey design 
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and alternate means of predicting/identifying locations of spawning habitat.

Large decline in resource species accompanied by a changing habitat in southern New England and New York 

since the mid 1980s

Clyde L. MacKenzie, Jr.

NEFSC, James J. Howard Marine Science Laboratory, Highlands, NJ

In the estuaries and coastal zones of southern New England, CT to Cape Cod, and Long Island, NY, the water temperature 

has risen about 1 ̊ C and concentrations of pollutants, mainly nitrates, have risen and eutrophication has prevailed since 

the mid 1980s. Over this time, the abundances of some commercially-important resource species, such as winter flounders 

and some other demersal fishes, oysters, softshell clams, bay scallops, and lobsters, have declined sharply. Surfclams have also 

become scarce off coastal New Jersey. The reasons for the declines may be due to changes in foods for the larvae and juveniles, 

higher predation rates, and increased metabolic rates while the animals grow. Eelgrass meadows, an important component 

of estuarine habitats, also have become scarcer. The abundances of two types of species that prey on important mollusks 

have also changed sharply. Crabs have become more abundant while starfish have become scarce. A scarcity of starfish in 

Connecticut may be the reason for a large increase in abundance and commercial landings of hardclams in that state, the rise 

in clam abundance there being an exception among the mollusks. Similar abundance declines had occurred in the 1930s, a 

decade when temperatures were unusually warm. There was a return to higher abundances when the waters became cooler 

during the 1940s to early 1980s. 

A Coastal and Marine Ecological Classification Standard (CMECS)

G.F. Mayer1, R.J. Allee2, G. Cicchetti3, M.A. Finkbeiner2, K.L. Goodin4, L.R. Handley6, C. J. Madden4, C.S. Moses6, and J. 

Soule3

1

Office of Habitat Conservation, Silver Spring, MD; 2National Ocean Service, Coastal Services Center, Charleston, SC; 3

U.S. Environmental Protection Agency, Atlantic Ecology Division, Narragansett, RI; 4NatureServe, Rosslyn, VA; 5U.S. 

Geological Service, Lafayette, LA; 6Florida International University, Department of Earth Sciences, Miami, FL

The Coastal and Marine Ecological Classification Standard (CMECS) provides a uniform approach for identifying, characterizing and naming ecological units in coastal and marine systems. It is intended to facilitate the study, monitoring, protection, restoration and management of habitats supporting commercially- and recreationally-important species, vital habitats 

for protected species, unique biotic assemblages, and key ecosystem features. CMECS describes standards for classifying 

ecological units in the benthic, sub-benthic, geological, and water column regimes and proposes unit definitions for inventorying, sampling, and mapping activities. CMECS is intended to create a comprehensive ecological classification, build on 

existing work, be easily compatible with mapping, document terminology, and allow for dynamic content. It is the product 

of development, testing and validation by experts from multiple Federal and state agencies, academia and nongovernmental organizations, led by NOAA and NatureServe. It is designed for use in North American marine, estuarine, and Great 

Lakes ecosystems, but is applicable world-wide. In April 2010, CMECS was submitted to the Federal Geographic Data 

Committee’s Standards Working Group. This is the first official step in vetting the proposed standard prior to its publication 

for public comment in the Federal Register. The CMECS team is interested in receiving comments from NMFS scientists on 

the proposed standard. It also encourages pilot projects and crosswalks with approaches presently in use to test and enhance 

the compatibility and applicability of CMECS. 
136

Mapping environmental variables to produce essential fish habitat models 

Bob McConnaughey, Steve Syrjala, Cynthia Yeung, and Keith Smith

AFSC, Seattle, WA

We are developing quantitative models to explain the distribution and abundance of fish on the continental shelf of the 

eastern Bering Sea (EBS). This effort addresses the essential fish habitat (EFH) mandate that applies to all life stages of all 

Federally managed species. The large number of species, their considerable value, and the enormity of the U.S. Exclusive Economic Zone dictate a descriptive approach that is both rigorous and efficient. In practice, we use systematic trawl survey data 

to identify EFH as those areas supporting high relative abundance. This approach presumes that density data reflect habitat 

utilization, and the degree to which a particular habitat is utilized is considered to be indicative of habitat quality. When 

the trawl data are combined with existing environmental data, preliminary models can be developed that spatially link fish 

abundance with relevant physical and biological variables. By this empirical method, habitat quality is judged ‘through the 

eyes of fish’ (rather than through those of the scientist). Unfortunately, only limited environmental data are available for this 

purpose and development of new variables is required for model improvements. For example, pilot studies with historical 

data demonstrate that surficial sediments are useful for characterizing EFH in the EBS. However, these data are sparse and 

additional sampling with grabs and cores would be prohibitively inefficient. For this reason, we are investigating more costeffective methods such as acoustic seabed mapping. Ecological interpretation of these habitat measurements is based on 

diverse groundtruthing information.

Using acoustics to characterize sediments for essential fish habitat models

Bob McConnaughey1, Lloyd Huff2, Cynthia Yeung1, Steve Syrjala1, Steven Intelmann1, and Meghan McGovern1

1

AFSC, Seattle, WA; 2University of New Hampshire, Center for Coastal and Ocean Mapping, Durham, NH 

The importance and broad scope of the essential fish habitat (EFH) mandate requires a rigorous and efficient process for describing and mapping the habitats of Federally managed species. To this end, we are developing quantitative habitat models 

for eastern Bering Sea (EBS) species, using density estimates from annual bottom trawl surveys and synoptic environmental 

data. Previous research with sparse historical data indicates that surficial sediments affect the distribution and abundance of 

EBS groundfish. Traditional sampling with grabs and cores is, however, impractical over large areas. Acoustic tools, on the 

other hand, are suitable for large-scale surveying but it is unknown whether they measure the relevant properties of sediments. Pilot studies with a split-beam echosounder (38 kHz) and a side scan sonar (455 kHz) were used to examine marginal 

contributions of acoustic data for explaining fish and invertebrate abundance in our habitat models. After processing with 

proprietary software (QTCView and Sideview, Quester Tangent Corporation, Sidney, BC), statistical analyses indicate 

relatively minor contributions from the echosounder data (2–13%) as compared to the side scan sonar predictors (9–54%). 

Based on these findings, a definitive experiment is being conducted in the EBS to compare the statistical value of normalized 

backscatter data from several different hull-mounted and towed systems, including a prototype long-range side scan sonar. 

Ultimately, the most cost-effective system will be deployed in the EBS for acquiring data to improve our shelf-scale continuous-valued habitat models.
137

Science support needs for east coast diadromous fish protection and restoration: Addressing management 

priorities

Sean McDermott1, Pace Wilber2, Louis A. Chiarella1, Prescott Brownell2, Jason Link3, Kevin Friedland3, Brian E. Smith3, 

and Tim Sheehan3

1

NERO, Gloucester, MA; 2SERO, Charleston, SC; 3NEFSC, Woods Hole, MA

NMFS is responsible for protecting and restoring diadromous fishes and their habitat under the Magnuson-Stevens Fishery 

Conservation and Management Act, Fish and Wildlife Coordination Act, Federal Power Act, and Endangered Species 

Act. These regulatory efforts are based on the best available science. The Northeast Regional Office (NERO) and Southeast 

Regional Office (SERO) have identified limited technical expertise in the Regional Offices and limited Science Center 

research support as key challenges facing effective hydropower relicensing and diadromous fish habitat restoration. NERO 

and SERO organized a joint hydropower program planning, capacity building and research coordination workshop. A 

primary component of this workshop identified priority east coast diadromous fish science and technical expertise needs, 

and outlined proposals for addressing these needs. The workshop was an opportunity for the Regional Offices to share these 

needs and strategies with relevant Science Center and Office of Science and Technology representatives. As an example of 

how science and management are currently working together, NERO is undertaking a study looking at the link between 

diadromous fishes and Federally managed fish predators in support of the NERO hydropower program. The results of this 

study could have far reaching benefits for other NMFS offices engaged in habitat conservation activities as well as influencing fisheries management actions. This study is a model for how science and management can work together to insure the 

science being produced is relevant to management and that management is utilizing the best available science. 

Determination of best scientific information available for acceptable biological catch and other fishery 

conservation and management measures

William L. Michaels1, Manoj Shivlani2, and Stephen K. Brown1

1

Office of Science and Technology, Silver Spring, MD; 2Center for Independent Experts, Northern Taiga Ventures, Inc., 

Miami, FL

Fishery conservation and management measures, such as acceptable biological catch (ABC), should be determined using 

the best scientific information available (BSIA) as stated in the Magnuson-Stevens Fishery Conservation and Management 

Act (MSA) Section 301(a)(2). Fishery stock assessments and other pertinent science undergo a series of evaluations and 

review processes involving internal workshops conducted by NMFS, external peer reviews, and evaluation by the Scientific 

and Statistical Committees (SSC) for the purpose of providing ABC recommendations and other advice to their regional 

Fishery Management Council (FMC). Scientific peer review plays an important role in ensuring the credibility and reliability of the science, and peer review processes are established and utilized in each region. Examples include the Southeast 

Data Assessment Review (SEDAR), Stock Assessment Review Committee (SARC), West Coast Stock Assessment Review 

(STAR), and Western Pacific Stock Assessment Review (WPSAR). Peer reviews frequently include both regional and external expertise to balance perspectives, and reviewers from the Center for Independent Experts (CIE) are often contracted 

to ensure high standards for expertise and independence without perceived conflicts of interest. The NMFS, CIE, and SSC 

partnership in the determination of BSIA is an iterative process because the goal is to continuously develop and improve the 

science required for the FMC’s fishery management decisions to achieve sustainable living marine resources and conserve 

their essential habitats. Presently, NMFS is proposing to revise the MSA Section 301(a)(2) provision, referred to as National 

Standard 2 (CR 600.315), to provide national guidelines on BSIA, peer review standards, the SSC’s role in the review of 

scientific information, and requirements for Stock Assessment and Fishery Evaluation reports (Federal Register Doc. E9-

29556, Filed 12/10/09). 
138

Merging abundance and habitat modeling: A predictive spatial approach

Paula Moreno1,2,3 and Michael Mathews4

1

SEFSC, Mississippi Laboratories, Pascagoula, MS; 2University of Southern Mississippi, 3Texas A&M University at 

Galveston; 4Flat Earth GIS Solutions

Ecosystem approaches to fisheries management require a solid understanding of species habitat, biological and environmental conditions that influence managed populations. Marine mammals are long-lived, apex predators and have been used as 

good indicators of complex ecosystem changes. The bottlenose dolphin, the most prevalent coastal marine mammal in the 

Gulf of Mexico (GOM), interacts with the highly valuable shrimp fishery. Identifying prime habitat of bottlenose dolphins 

on the GOM shelf can help reduce uncertainty in fisheries stock assessments by accounting for predation by dolphins as a 

fish mortality source. Also, dolphins can be used as indicators of high productivity areas for fisheries. We developed a finescale (20 x 20 km) predictive, spatial abundance model for bottlenose dolphins on the GOM continental shelf. Combining 

GIS, Density Surface and Generalized Additive Modeling techniques, we accounted for imperfect detection of dolphins 

and evaluated relevant environmental predictors of abundance, including oceanographic and topographic conditions, chlorophyll and oil platform density. Dolphin responses to environmental gradients were nonlinear. Dolphins were more abundant at about 650 km from the Mississippi River in water approximately 25 m deep. To identify mutually important habitat 

for dolphins and fisheries, we will use a summer scenario to compare the degree of overlap of high abundance of dolphins, 

shrimp fishery effort and red snapper catches. The latter are based on commercial and fisheries-independent data. A similar 

approach can be used for other key species to build spatially-explicit ecosystem models.

Where should they spawn? An assessment of the oceanic habitat of larval brown shrimp using dynamic 

linkages between offshore waters and estuarine nursery grounds

Redwood W. Nero1, Dong S. Ko2, and Ian McCoy3

1

SEFSC, Stennis Space Center, MS; 2Naval Research Laboratory; 3SEFSC, Pascagoula, MS

Several commercially important fish and Crustacea in the northern Gulf of Mexico migrate as larvae from offshore spawning grounds to coastal estuarine nurseries. For most species this oceanic phase is poorly known but likely contributes to 

yearly variability in recruitment. A behaviorally cued Lagrangian particle tracking model was used to determine the intrinsic 

oceanographic linkages between the continental shelf and coastal estuaries for larval brown shrimp, Farfantepenaeus aztecus. 

This was accomplished by running the tracking model over several years of high resolution oceanographic nowcast data from 

the northern Gulf of Mexico Nowcast Forecast System to derive ensemble averages of thousands of migration paths. Initially, several migration models were compared to select the best possible combination of behaviorally based environmental 

cues linking larval age and growth to the dynamic ocean environment. The resultant winning model was used in the final 

shelf-wide assessment. The migration paths demonstrate strong spatial fidelity of larvae and estuaries with most successful 

larvae likely recruiting from a 30–60 nautical mile distance. Some regions of the shelf are likely spawning hot spots, with a 

high chance of recruitment of propagules into local estuaries while other regions are of low quality, with most propagules 

being lost at sea. An overall shelf-wide oceanographic-based assessment is proposed using larval characters representative 

of many species as a quantitative technique to assess habitat that encompasses the seasonal climate dynamics of the ocean 

environment.
139

River response to dam removal: The Souhegan River and the Merrimack Village Dam, Merrimack, NH

Adam J. Pearson1, Noah P. Snyder1, Mathias J. Collins2, and David Santaniello1

1

Boston College, Department of Geology and Geophysics, Chestnut Hill, MA; 2NOAA Restoration Center, Gloucester, 

MA

The Souhegan River is a tributary of the Merrimack River that drains a 443 km2 watershed in southern New Hampshire. 

The lowermost barrier on the Souhegan River was the ~4 m high Merrimack Village Dam (MVD; ~500 m upstream of 

the confluence with the Merrimack River), which was breached and removed starting on August 6, 2008. The MVD was 

built in 1906 at a location where various dams have existed since the 18th century. Based on a preremoval sediment thickness 

survey, the MVD impounded at least 62,000 m3 of sediment, mostly sand. We use a May 2008 ground penetrating radar 

survey of the impoundment to better constrain this sediment volume and stratigraphy. We also use historical maps and aerial 

photographs to estimate the possible extent of dam-influenced deposition at the site. We use 12 monumented cross sections, 

longitudinal profiles, repeat photography, and sediment samples to document the response of the Souhegan River to the 

removal of the MVD. Our study is part of the first full application of a recently published guide for stream barrier removal 

monitoring. Prior to dam removal, in August 2007 and June 2008, we surveyed the cross sections and longitudinal profile. 

We conducted re-surveys after removal in August and October 2008, and again in July and August 2009. Comparison between pre- and post-removal surveys shows that, in a 495 m reach upstream of the former location of the MVD, the Souhegan River eroded a net 38,100 m3

 (47,900 metric tons) of sediment. This response began with rapid (hours to days) incision 

of a narrow channel, exhuming in some places bedrock and boulders that likely formed the predam riverbed. Over the year 

since dam removal, the channel has widened by bank erosion but this process is limited by root strength and recruitment of 

large woody debris in the riparian zone of the former impoundment. Downstream of the former dam location, during the 

first days after removal, a sand deposit up to 1.0 to 3.5 m thick, or approximately 18,500 m3 (23,500 metric tons), prograded 

almost to the confluence with the Merrimack River. From August 2008 to August 2009, the Souhegan River removed a net 

8,400 m3 (10,700 metric tons) of this sediment leaving 11,100 m3 (14,100 metric tons) from the initial post-removal pulse. 

Over this interval, the unaccounted 27,000 m3 (33,800 metric tons) of sediment eroded from the former impoundment left 

the study reach and discharged into the Merrimack River. The Souhegan River experienced massive change during our two 

year study and continues to evolve as a new channel forms and stabilizes upstream and downstream of the former dam site.

Ocean scale hypoxia-based habitat compression of Atlantic istiophorid billfishes

Eric D. Prince1, Jiangang Luo2, C. Phillip Goodyear3, John P. Hoolihan1, Derke Snodgrass1, Eric S. Orbesen1, Joseph E. 

Serafy1, Mauricio Ortiz1, and Michael J. Schirripa1

1

SEFSC, Miami, FL; 2University of Miami, Rosenstiel School of Marine and Atmospheric Science, Miami, FL; 31214 

North Lakeshore Drive, Niceville, FL 32578

Oxygen minimum zones (OMZs) below near-surface optimums in the eastern tropical seas are among the largest contiguous areas of naturally occurring hypoxia in the world oceans and are predicted to expand and shoal with global warming. In 

the eastern tropical Pacific (ETP), the surface mixed layer is defined by a shallow thermocline above a barrier of cold hypoxic 

water, where dissolved oxygen levels are ≤ 3.5 mL L-1. This thermocline (~25–50 m) constitutes a lower hypoxic habitat 

boundary for high oxygen demand tropical pelagic billfish and tunas (i.e. habitat compression). To evaluate similar oceanographic conditions found in the eastern tropical Atlantic (ETA), we compared vertical habitat use of 32 sailfish (Istiophorus 

platypterus) and 47 blue marlin (Makaira nigricans) monitored with pop-up satellite archival tags in the ETA and western 

North Atlantic (WNA). Both species spent significantly greater proportions of their time in near surface waters when inside the ETA compared to those in the WNA. We contend that the near surface density of billfish and tunas increases as a 

consequence of the ETA OMZ, therefore increasing their vulnerability to overexploitation by surface gears. Since the ETA 

OMZ encompasses nearly all Atlantic equatorial waters, the potential impacts of overexploitation are a concern. Because 

of the obvious differences in catchability inside and outside the compression zones, it seems essential to standardize these 

catch rates separately in order to minimize inaccuracies in stock assessments for these species. This is especially true in light 
140

of global warming which will likely exacerbate future compression impacts.

Benthic habitat assessment and mapping in the Pacific Islands region

John Rooney, Jonathan Weiss, Emily Donham, Frances Lichowski, and Joyce Miller 

PIFSC, Honolulu, HI; Joint Institute for Marine and Atmospheric Research, University of Hawaii, Honolulu, HI 

Since 2001, the Pacific Islands Fisheries Science Center has been conducting systematic mapping of coral reef ecosystems 

and deeper habitats around the U.S. affiliated islands in the central and western Pacific Ocean. Funding for this work has 

been derived entirely from sources outside of NMFS, mostly from the NOAA Coral Reef Conservation Program (CRCP). 

Mapping has focused on developing a series of map layers of seafloor characteristics with biological significance that are logistically feasible to produce. To date more than 67,400 km2

 of high resolution bathymetry and acoustic backscatter imagery 

have been collected at depths from ~20 to >3000 m. Video and still imagery are also collected, using camera sleds, remotelyoperated vehicles, and more recently, a SeaBED autonomous underwater vehicle, and used to characterize and map benthic 

and demersal communities and provide validation of acoustically delineated habitat characteristics. Optical imagery covering more than 635 linear kilometers of seafloor at depths below ~30 m has been collected. For shallower depths not feasible 

to be mapped acoustically, depths are being estimated from satellite imagery. Several products are standardly derived from 

bathymetric data, including slope, rugosity, and Bathymetric Position Index zones and structures. These bathymetry-derived 

products and optical map data are being used in ENVI® software to generate maps of hard (rock, boulders, and rubble) versus 

soft (sand and mud) substrates to use as the basis for stratification to improve sampling design and efficiency for reef fish 

surveys. Using similar methods, maps predicting fish distributions and algal meadows serving as juvenile fish habitat are also 

being developed. 

Estimates of rockfish habitat utilization and biomass on an isolated rocky ridge using acoustics and stereo 

image analysis

Chris Rooper, Jerry Hoff, and Alex DeRobertis 

AFSC, Seattle, WA

For those marine fish species with specific habitat preferences, a habitat-based assessment may provide an alternative to traditional surveys. We conducted a habitat-based acoustic and stereo camera stock assessment survey for rockfish on a rocky 

ridge habitat in the eastern Bering Sea. Video analysis suggested that juvenile and adult rockfish were more abundant on 

the seafloor in the rocky ridge area than on the surrounding sandy flats. Over the ridges, the distribution of rockfish was 

uniformly low in the water column during night time surveys and higher during daytime surveys. The opposite pattern was 

observed in the video on the seafloor between night (high density) and day (lower density) indicating that fish in the water 

column during the day moved to the seafloor at night. Mean biomass of adult rockfish for the rocky ridges was 15,447 t 

based on acoustic data. The biomass of juvenile fish was estimated to be 916 t. Utilization of similar survey methodologies 

on a larger scale may improve assessment of rockfishes not only in Alaska, but throughout their range where fishery-independent biomass estimates have been difficult to obtain.
141

The effects of bottom fishing on the benthic macrofauna and demersal fish feeding habits of northern Georges 

Bank 

Brian E. Smith1 and Jeremy S. Collie2

1

NEFSC, Woods Hole, MA; 2University of Rhode Island, Graduate School of Oceanography, Narragansett, RI

The impact of mobile bottom fishing gear on marine benthic habitat and demersal communities has been well documented 

for Georges Bank in the northwest Atlantic and elsewhere. However, few studies have examined the effects of bottom fishing on the feeding habits of benthivorous fishes within this shelf region. Here, we quantified the differences in the benthic 

macrofaunal and demersal fish communities between sites with disparate levels of disturbance from mobile bottom fishing 

gear for northern Georges Bank (i.e. the habitat area of particular concern (HAPC) of northern Closed Area II, and a 

contiguous Canadian region). The study compares a suite of benthic macrofaunal and fish diet indices across year and fishing disturbance level as fixed effects. Fishes selected for diet comparisons included winter skate (Leucoraja ocellata), little 

skate (Leucoraja erinacea), Atlantic cod (Gadus morhua), haddock (Melanogrammus aeglefinus), winter flounder (Pseudopleuronectes americanus), and longhorn sculpin (Myoxocephalus octodecemspinosus). Benthic macrofaunal abundance (n/L), 

biomass (g/L), and species richness were generally higher in the nonfished areas, whereas an evenness index was greatest in 

areas disturbed by bottom fishing. Within the HAPC region, the effect of fishing was less pronounced and additional factors were proposed. Nonetheless, marked differences in fish feeding habits were present and predator-prey dynamics were 

shown to be altered by a fishing disturbance effect. In several cases, prey that contributed to the diet dissimilarity between 

sites were taxa most sensitive to the impact of bottom fishing disturbance as shown in the benthic macrofaunal community, 

yet these results were variable on Georges Bank.

An assessment of coastal and nearshore fish habitat for the National Fish Habitat Action Plan

Susan-Marie Stedman1, David Moe Nelson2, Patrick Polte3, Correigh Greene3, and Joe Nohner4

1

Office of Habitat Conservation, Silver Spring, MD; 2National Ocean Service, National Centers for Coastal Ocean 

Science, Silver Spring, MD; 3NWFSC, Seattle, WA; 4Office of Science and Technology, Silver Spring, MD

The National Fish Habitat Action Plan is a multipartner effort to address the loss and degradation of fish habitat by taking 

a science-based regional partnership approach to identifying conservation priorities and leveraging resources to address 

those priorities. As part of this effort, scientists from a number of agencies and academia are working together to produce a 

national assessment of fish habitat. NOAA is responsible for the coastal and nearshore portion of the assessment. This study 

synthesizes existing nation-wide data sets on anthropogenic disturbance and natural drivers affecting coastal and estuarine 

ecosystems, and includes indicators of connectivity, hydrology, benthic complexity, and water quality. A quantitative assessment of habitat components will be nested into a multiscale spatial framework for the coastal Atlantic, Pacific, and Gulf of 

Mexico using NOAA’s Coastal Assessment Framework (CAF). In 2010, indicator values will be assigned to units within the 

CAF and composite habitat condition scores will be assessed using principal component analysis and other data reduction 

methods. Work in 2011 will focus on testing how these scores predict fish species composition and abundance metrics of 

well-studied stocks.

Evaluating the habitat impacts of nonfishing human activities in Federal Fishery Management Plans

David K. Stevenson 

NERO, Habitat Conservation Division, Gloucester, MA

A section of the essential fish habitat (EFH) Final Rule requires that regional Fishery Management Councils (FMCs) ‘identify activities other than fishing that may adversely affect EFH’ and ‘recommend options to avoid, minimize, or compensate 
142

for the adverse effects’ of nonfishing activities on EFH. FMC recommendations could be very persuasive in encouraging 

responsible agencies and organizations to take action that would help to conserve and protect Federally managed fishery 

resources from the detrimental effects of a variety of nonfishing activities, yet they are seldom included in Federal Fishery 

Management Plans (FMPs) because the FMCs have no direct authority to regulate these activities. A fundamental problem has been the scarcity of information required to evaluate ways in which specific human activities can adversely impact 

exploited resource species and populations. This situation is improving with the recent publication of a NOAA Technical 

Memorandum ( Johnson et al., 2008) which describes a range of nonfishing activities that affect marine habitats in the 

northeastern United States and ranks them in terms of their potential impacts. Summary information from this Technical 

Memorandum has been included in a draft of an amendment to the Mid-Atlantic FMC’s Squid, Mackerel, and Butterfish 

FMP and will be presented in this poster to demonstrate what can be done with the available information and what still 

remains to be done to generate information that is specific enough to support effective conservation recommendations. 

More active strategic partnering between the Science Centers, Regional Offices, other government agencies, and academic 

institutions is needed in order to ensure that this information is made available to the FMCs.

Incorporating environmental factors affecting recruitment into the stock assessment for snow crab in the 

Bering Sea

Cody Szuwalski and André E. Punt

University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA

Bering Sea snow crab (Chionoecetes opilio) are currently designated as overfished and are under a rebuilding plan. However, 

the dynamics of snow crab abundance are driven not only by fishery-induced mortality, but also by large fluctuations in recruitment. Fishery management advice is based on the assessment model for this stock, which is sex- and size-structured and 

estimates annual recruitment starting at 25 mm carapace width. In common with many fishery resources, very little of the 

variation in snow crab recruitment can be explained by changes in female spawning biomass, and no significant correlation 

has been found between recruitment estimates for snow crab from the stock assessment and ecosystem-scale environmental 

indices in the past. We outline an approach in which environmental factors can be incorporated directly into the stock assessment to assess whether these factors determine recruitment. This allows the uncertainty associated with any relationship 

between recruitment and environmental covariates to be quantified. We illustrate the approach using cold pool data and 

outline other environmental covariates which quantify plausible environmental drivers of recruitment.

Incorporating food web and habitat interactions in a forage fish stock assessment

Howard Townsend 

NOAA Chesapeake Bay Office, Cooperative Oxford Lab, Oxford, MD

Some researchers have suggested that because of the multiple sources of mortality that forage fish face, fisheries managers 

could use other biological reference points (e.g. total mortality [Z]) as a benchmark for making management decisions. Doing so would require accounting for other sources of natural mortality. In this paper, we outline the potential for using ecosystem and habitat models to estimate natural mortality for forage fish stocks. We use the Chesapeake Bay Fisheries Ecosystem Model (CBFEM) to generate various sets of a time series for predation mortality on Atlantic menhaden. In alternative 

runs of the CBFEM, we use forcing and mediation functions to influence physical factors/species interactions and generate 

additional time series of natural mortality. Then using a simple stock assessment model and the time series generated with 

the CBFEM, we compare the fit of the various formulations (i.e. constant natural mortality, variable natural mortality based 

on trophic effects alone, and variable mortality based on physical factors and trophic interactions) to determine the utility of 

incorporating physical and trophic interactions into stock assessment models. These model scenarios and stock assessment 

approaches are presented to gain insight into the possible responses of menhaden to fishery management and water quality 

management actions.
143

Science needs for coastal and marine spatial planning for offshore renewable energy siting 

Sue Tuxbury and Chris Boelke

NERO, Gloucester, MA

As the implementation of the Ocean Policy Task Force’s Interim Framework on Coastal and Marine Spatial Planning moves 

forward, NOAA will be looked upon to provide critical data for developing regional plans. The use of coastal and marine 

spatial planning for the purpose of siting offshore renewable energy has already rapidly taken off on a state level in New 

England. The Massachusetts Ocean Plan and the Rhode Island Ocean Special Area Management Plan have led the nation in 

coastal and marine spatial planning for offshore wind development. These states have looked to NOAA for data and guidance on information needs for management decisions. Though experiences from Europe have provided some insight, questions remain on how these renewable energy projects may affect marine resources off our coasts. We provide an overview 

of offshore renewable energy planning efforts for New England, information resource managers’ need for review of such 

projects, and science needs to help close the data gaps. Lessons learned from these smaller-scale projects may provide insight 

into information needs for planning on a regional scale. 

Identifying pelagic habitat in Shelikof Strait and the Bering Sea using GIS-based tools for analysis and 

visualization

Tiffany C. Vance1, Sharon M. Mesick2, Annette B. Dougherty1, and Janet Duffy-Anderson1

1

AFSC, Seattle, WA; 2NOAA National Environmental Satellite, Data, and Information Service, National Oceanographic 

Data Center, Stennis Space Center, MS

Healthy habitat is crucial to the survival and recovery of commercially and recreationally important species as well as endangered species. Climate change, environmental variability, and increased anthropogenic modification of the oceans add 

a sense of urgency to the correct identification, monitoring and conservation of essential fish habitat. While marine habitat 

is commonly thought of as the seafloor that supports benthic organisms, there are also marine organisms that occupy a fully 

three-dimensional pelagic habitat. Identifying essential habitat in three dimensions (width, breadth and depth) is the first 

step in being able to set conservation priorities to mitigate changes in the environment caused by any of these drivers. The 

ability to create these types of analyses for pelagic species will also improve our ability to support integrated ecosystem assessments under changing environmental conditions. Geographic information systems (GIS) have been used extensively 

to define and describe benthic habitat. Tools have been developed to integrate a number of environmental variables to 

determine the location and size of optimal benthic habitats. For example, sediment type, depth, rugosity and aspect can be 

integrated to characterize habitat usability for corals in American Samoa (Lundblad et al., 2006). This poster will describe 

HabitatSpace, a tool developed to extend these types of analyses to three-dimensional pelagic habitats. Using a combination 

of ESRI’s ArcGIS software and Unidata’s Integrated Data Viewer, it allows users to load environmental data and specify 

parameters for habitat based upon an organism’s environmental requirements. The tool outputs both 2-D and 3-D visualizations of the volumetric habitat defined by the input parameters. Statistical analyses such as mean center and area of the 

habitat volume can be calculated.
144

Hypoxia: An important component of benthic habitats for U.S. west coast groundfish stocks

W. Waldo Wakefield1, Aimee A. Keller1, Victor Simon1, Keith L. Bosley1, Francis Chan2, John A. Barth3, Dezhang Chu1, 

Stephen Pierce3, and M. Elizabeth Clarke4

1

NWFSC, Newport, OR; 2Oregon State University, Department of Zoology, Corvallis, OR; 3Oregon State University, 

College of Oceanic and Atmospheric Sciences, Corvallis, OR; 4NWFSC, Seattle, WA

Understanding the relationship between environmental variables and fish distribution and abundance has long been a goal of 

fisheries biologists. A recent report prepared by NMFS identified ‘insufficient research on environmental effects’ as a major 

obstacle (among several) to producing and using habitat science in stock assessments and management. Since 2002, hypoxic 

conditions have been observed on the continental shelf off the coast of the Pacific Northwest in a region not previously 

characterized by low bottom oxygen concentrations. Major declines in dissolved oxygen have been observed in the oxygen 

minimum zone (OMZ) of the southern California Current as well as a shoaling of the OMZ. Despite recent increases in the 

frequency, duration and spatial extent of hypoxia and the recognition of hypoxia as a threat to worldwide fish production, 

little is known about its effects on upper trophic levels. In 2007, the Northwest Fisheries Science Center (NWFSC) initiated studies on the extent of hypoxic conditions on the continental shelf and slope and the influence of hypoxia on demersal 

fishes and invertebrates. This project was an extension of the NWFSC Groundfish Bottom Trawl Survey. Studies in 2007 

and 2008 focused on a segment of the Oregon coast—an established area for ongoing interdisciplinary studies on hypoxia. 

In 2009, working with oceanographers at Oregon State University, the NWFSC expanded its hypoxia research by incorporating an oceanographic sensor package into the NMFS coast-wide survey. This poster summarizes the results of ongoing 

research and discusses some implications for stock assessments and management.

Pelagic habitats and ecosystem considerations for salmon and other pelagics of the central coast of California 

Brian Wells 

SWFSC, Fisheries Ecology Division, Santa Cruz, CA

The productivity of salmon and the ecosystem of central coastal California are dependent on upwelling, wind strength, and 

wind structure which respectively determine the degree of enrichment, concentration, and retention of nutrients and prey 

items regionally. To examine the role of these factors on the ecosystem we have developed a hierarchal, mechanistic ecosystem model for estimating productivity of krill, rockfish, and seabirds along central California. Once these relationships 

were quantified we used our findings to explore potential causes of recent poor salmon production. Evidence suggests that 

weak upwelling reduced enrichment and below average wind turbulence led to a shallow mixed layer and diffusion of krill 

(a dominant prey item) southward from the primary habitat of juvenile salmon. Also, increasing winds seaward moved the 

convergent zone, which retains local production and pelagic prey items, offshore and beyond the range of juvenile salmon. 

In total, recent years may have represented a restructuring of the marine habitat whereby krill, pelagic fish prey, and salmon 

were not overlapping which led to reduced survival of juvenile salmon. 

Identifying coral habitat areas that are potentially vulnerable to fishing interactions

Curt E. Whitmire1, M. Elizabeth Clarke2

1

NWFSC, Newport, OR; 2NWFSC, Seattle, WA

Due to their sessile nature and slow growth rates, deep sea corals are vulnerable to a variety of anthropogenic stressors, most 

notably bottom trawling. Off the west coast of the continental United States, corals are encountered during research trawl 

surveys and recorded as bycatch by fishery observers during commercial fishing operations. With the reauthorization of the 

Magnuson-Stevens Fisheries Conservation and Management Act in 2006, NOAA and the regional Fishery Management 
145

Councils were mandated to minimize interactions between corals and fishing gears. In order to minimize interactions, it 

is necessary to first identify areas of coral habitat that are vulnerable to such interactions. One method is to simply overlay 

coral observations onto a map of fishing intensity. Due to confidentiality requirements for commercial fishing information, 

however, intensity data is often aggregated to large blocks (e.g. 10 x 10 km; 10’ latitude x 10’ longitude). Unfortunately, 

mapping of intensity data at such coarse spatial scales precludes any meaningful analysis of risk. For this study, we developed 

a metric of vulnerability defined not only as a factor of fishing intensity, but also relative coral abundance and taxon rarity. 

What makes this metric unique is that vulnerability is defined from the perspective of the coral habitat area, thus preserving 

the confidentiality of commercial fishing information. In other words, vulnerable coral habitats can be identified on a map 

without directly showing the distribution of fishing intensity. Such maps may be used by fishery managers to develop gear 

modifications or regulations that protect these vulnerable habitats from damage by fishing gears.

Catch composition in the NMFS west coast bottom trawl survey as a predictor of habitat complexity

Curt E. Whitmire1, M. Elizabeth Clarke2, James D. Hastie2, Beth Horness2, and Aimee A. Keller2

1

NWFSC, Newport, OR; 2NWFSC, Seattle, WA

For many assessments of west coast fish stocks, an annual bottom trawl survey is the main source of fishery-independent 

information on biomass trends. Unfortunately, these biomass estimates are made under the assumption that densities of fish 

observed in the trawl catches are uniform across all benthic habitats. From in situ habitat studies, we know however that density can vary significantly in relation to various habitat types. The recent availability of coast-wide maps of surficial geologic 

habitat off the west coast has provided the opportunity to explore trawl survey catch rates in the context of seafloor characteristics. For this study, we compared catch per unit effort data for select species of demersal fishes and benthic invertebrates 

to the habitat types encountered during the trawl. These trawls were conducted between 2003 and 2009 by the Northwest 

Fisheries Science Center as part of an annual trawl survey of commercially important groundfishes. The species used in this 

analysis were chosen due to their ubiquitous distributions and strong affinities to certain benthic habitat types—either soft, 

unconsolidated sediments or hard, rocky outcrops. We hypothesize that for trawls that encounter a variety of habitats, the 

catch composition will reflect those changes in habitat type. In other words, for those trawls that cross varying habitats, we 

expect to see a more diverse set of species with varying habitat affinities. If our hypothesis is correct, we hope to develop a 

model using catch composition as a predictor of greater habitat complexity, particularly in areas where habitat information 

is lacking.

Multivariate bathymetry-derived landscape ecology model accurately predicts rockfish distribution in Cordell 

Bank National Marine Sanctuary, CA, USA 

Mary A. Young1, Pat J. Iampietro2, Rikk G. Kvitek2, and Corey D. Garza3

1

University of California, Santa Cruz, Long Marine Lab, Santa Cruz, CA; 2California State University, Monterey Bay, 

Seafloor Mapping Lab, Seaside, CA; 3California State University, Monterey Bay, Marine Landscape Ecology Lab, Seaside, 

CA

Accurate, efficient estimation of actual and potential species distribution is a critical requirement for effective ecosystembased management and marine protected area design. Here we test the applicability of a terrestrial landscape modeling technique in a marine environment for predicting the distribution of ecologically and economically important groundfish, using 

three species of rockfish at Cordell Bank National Marine Sanctuary as a model system. Autoclassification of multibeam 

bathymetry along with georeferenced submersible video transect data of the seafloor and demersal fishes were used to model 

the abundance and distribution of rockfish. Generalized Linear Models were created using habitat classification analyses 

of high resolution (3 m) digital elevation models combined with fish presence/absence observations. Model accuracy was 

assessed using a reserved subset of the observation data. The resulting probability of occurrence models generated at 3 m 

resolution for the entire 120 km2 study area proved most reliable in predicting the distribution of the two species associated 
146

with rocky habitat, Sebastes rosaceus and S. flavidus, with accuracies of 80% and 70%, respectively. The models did not do 

as well for S. elongatus, a species associated with low relief, mixed and sedimentary habitats, and thus not as amenable to 

analysis based solely on bathymetry-derived geomorphology metrics. These results indicate that site- and species-specific 

algorithmic habitat classification applied to high resolution bathymetry data can be used to accurately extrapolate the results 

from in situ video surveys of demersal fishes across broad areas of rocky habitat.
147

Appendix 5: Habitat Science and Management 

Questionnaire Summary

Preceding the National Habitat Assessment Workshop, an 

eight question survey was sent out to National Marine Fisheries Service (NMFS) habitat staff to gather information on 

existing habitat processes and opinions on ways forward. 

The questionnaire was sent to each NMFS Science Center 

(SC), Regional Office (RO), and regional Restoration Center (RC). A total of 33 responses were received, including 

responses from each SC, RO, and RC. Responses are summarized for each of the questions below.

Question 1: What is your existing process for identifying and agreeing upon priorities for habitat science?

a. Near-term priorities (one year)

b. Long-term priorities (two years or longer)

• A majority of regions have no existing formal processes 

in place specific to habitat science. In some cases, there 

are a variety of informal communications and processes 

operating, but in many cases the overall perception is 

that there is no process at all. Some ROs perceive the 

SCs as operating on their own in setting habitat science 

priorities.

• Informal communications between RO and SC staff is 

often for the purposes of information sharing or discussions on emerging issues, ongoing research, essential fish 

habitat (EFH) needs, or consultations. It does not facilitate coordination activities or priority setting. Existing 

communication processes work only to a limited extent 

to provide input on ‘immediate attention’ type tasks, 

and to an even lesser extent for science technical input 

questions/participation (e.g. permit consultation, nonregulatory stewardship forums, or new habitat program 

areas).

• Identifying and discussing priorities does not necessarily 

lead to agreement or a coordinated set of priorities between the RO, SC, and RC. Given current programs and 

resource (staffing and funding) levels, it will be difficult 

to fully meet the needs of all in the near future.

• At many SCs, the availability of funding and staffing may 

drive habitat priorities and can replace a formal process 

for identifying priorities. Outside “soft” funding seems 

to play a large role in establishing SC research priorities. 

However, long-term and emerging management needs 

are considered, and used to focus priorities and attempt 

to generate funding mechanisms. Short-term projects in 

response to urgent policy or management requests may 

temporarily redistribute spending and human resources.

• Long-term research priorities at the SCs are largely 

determined by research needs identified by the principal 

investigators in consultation with resource managers, 

both at the regional and national level. Priorities can be 

driven by both external (changes in the mandates of the 

Magnuson-Stevens Act, output from significant national 

and international working groups) and internal (within 

SC strategic planning, NMFS’ mission) forces. 

• ROs may have a variety of processes in place for identifying habitat science needs, but need to develop more 

defined processes for prioritizing these needs. Near-term 

priorities are generally project specific, short turnaround 

needs for science to support habitat consultations or 

provide technical assistance to other agencies. Establishing long-term priorities, outside of budget planning, 

is based on programmatic requirements but is difficult 

because habitat management needs are usually near-term 

in nature and dependent on the types and numbers of 

projects received.

• When existing research is being conducted, the ROs take 

advantage of SC work for some types of science support, such as development of Fishery Management Plan 

(FMP) amendments and documents associated with 

EFH identifications/descriptions and 5-year reviews. 

However, for other science needs the ROs will sometimes pursue extramural sources of research support. 

Extramural sources can include other parts of NOAA, 

outside agencies, or regional universities.

• The RCs do not have formal processes in place to identify and coordinate priorities. Planning is often focused 

on near-term needs and related to funding availability, 

although many of the RCs are beginning to focus on 

longer-term priorities. However, funding is not set for 

out years and many of the habitat science issues the RC 

focuses on are directly linked to projects with a shorter 

turnaround time, which makes long-term planning difficult.

• There is often a discrepancy in the time scale required to 

complete science projects (longer-term) and information 
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needs from habitat managers (short-term). This discrepancy makes joint priority setting challenging.

Question 2: How do you currently decide which 

habitat research priorities will be funded?

• Decisions are largely driven by the availability (or lack 

thereof ) of funding. Available amounts are applied to 

projects that have been identified as high priority and 

can be served by the available funding amounts.

• There is some use of EFH funds to support habitat 

research, but this is inconsistent across regions. The 

large majority of habitat science currently conducted is 

opportunistic, generally short-term in nature, and takes 

advantage of external, competitive funding sources.

• The ROs and RCs generally do not perceive themselves 

as having a voice in directing priorities for habitat research, while the SCs generally think that they have little 

direct support. No formal, established processes exist 

for ROs and SCs to decide jointly on habitat research 

project funding decisions.

• A key limitation to supporting an ongoing program of 

habitat research in support of regional management 

needs is the limitation of year to year funding. In the 

absence of a stable funding stream, it is difficult to plan 

for and conduct a multiyear research effort, which is a 

key need to develop more information useful for habitat 

management needs.

• Projects in the SCs are funded based on: 1) if targeted 

funding has been made available for a specific activity; 

2) if it has the potential to generate new funding; 3) if 

it supports one of the SC major programs; or 4) if it is 

in response to a critical management need or request. 

Feasibility, in terms of personnel and logistics, are also 

factored in to funding decisions. 

• Because very little direct funding for habitat science is 

available, SCs often have to apply for external funding to 

complete habitat science projects. This process is largely 

opportunistic and can vary depending upon a number of 

factors.

• The ROs for the most part do not make decisions on 

funding habitat research or participate in formal funding 

discussions with the SCs. The exception is annual competition for funds through the Office of Habitat Conservation to fund management or science projects related to 

refining EFH or hydropower. 

• The ROs may sometimes use discretionary funds to fund 

outside research projects in direct response to a critical 

management need. Funding for specific projects may be 

provided to the SC or to outside entities. 

• RCs request funding for projects on an ad hoc basis. 

Securing funds for longer-term questions or priorities is 

difficult unless they are directly linked to a current project or ‘hot topic’. Funding for science and monitoring at 

the RCs is selected at the Headquarters level with leadership looking at all of the available science options and 

preferring those that can be completed within a short 

time frame. Although the RCs advance funding requests 

for specific projects forward to the Headquarters level 

for consideration, the region has little control over the 

selection process. 

Question 3: What is your existing process for 

providing/receiving Science Center input on habitat 

issues related to fishery management (identifying 

EFH, minimizing effects of fishing, etc.)?

• There is some mismatch in how the regional entities view 

their roles with relation to each other. Overall, SCs think 

of themselves as providing habitat science information 

to ROs, but less so to the RCs. However, ROs and RCs 

generally viewed SCs as minor sources of information on 

habitat science in support of fishery management.

• Publication of scientific results in reports and peerreviewed literature is an important component of the 

research process for SC staff. However, scientific papers 

are viewed as a relatively minor method for transferring 

information by the ROs and RCs.

• Consultations on habitat issues between the SC and RO 

or FMC may occur on an informal basis by contacting 

an individual scientist with a question. In some regions 

where SC and RO staff are stationed within the same 

facility, such staff to staff contact is common, quick, and 

easy. However, other regions do not use such informal 

requests as often. This type of informal communication 

only works for small requests. 

• In some cases, ROs may solicit science input from other 

entities (other NOAA Offices, state or other Federal 

agencies) on an informal basis as well. 

• For input that requires more extensive work, formal 

requests to the SC Directorate are required; if approved, responsibilities will be assigned and a response 

assembled. Usually, specific details of the request will be 

discussed with the requestor to better understand information needs and how to best provide data or materials.

• Some SCs have a habitat coordinator that handles infor-
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mation requests and transfer. Habitat coordinators are 

responsible for communication between the SC, the RC, 

the RO, and the Office of Habitat Conservation with 

regard to priority research needs.

• SCs support Fishery Management Councils (FMCs) by 

assigning staff to serve on Plan Development Teams or 

Fisheries Management Action Teams, participating in 

workshops and meetings, assisting in FMP amendment 

development, and through direct interactions with SC 

scientists on an informal basis. An EFH Coordinator 

works with the FMCs and provides information in the 

form of EFH species source documents (NOAA Technical Memorandums).

• Some ROs generally do not request much assistance 

from the SCs because of limited contact. Previous 

limited success in receiving assistance, given other SC 

priorities, also plays a role in this disconnect. Additionally, some ROs may feel that without available funding, 

they cannot request assistance from the SC because SC 

funding dictates effort be placed elsewhere.

• In most cases, communication between the SC and RC 

is limited and priorities are not very connected (RC 

priorities are more closely aligned with the RO). RCs 

would like to interact with SCs to a greater degree on 

restoration issues of shared interest, but have the impression that time and funding limit SC staff ’s ability to 

work with RC staff. Responsiveness to real time needs is 

an issue.

Question 4: What is the Regional Office’s existing 

process for enlisting Science Center input on 

nonfishing impacts to habitat (topical research, 

support for specific EFH consultations or 

restoration projects, etc.)?

• Requests for input on nonfishing impacts generally have 

shorter deadlines because ROs need to respond to the 

applicable regulatory agency on a set schedule. 

• Existing processes for enlisting science input from SC 

staff are poorly defined, if they exist at all. Clarifying 

or developing a process would be useful. Most requests 

are made on an informal, ad hoc basis via staff to staff 

interactions. Some regions are currently discussing ways 

to improve communication and formalize the process.

• Less often, formal requests are transmitted from RO 

managers to SC managers. Some regions show a preference for a less formal process for making and managing 

requests for SC assistance from the RO to the SC.

• Collocation of SC and RO staff helps to facilitate professional communication and assistance.

• Conflicting RO-SC time lines can sometimes be a problem. There is insufficient long-term planning for operations capacity in both the RO and SC. Thus, support for 

emerging needs of project types (e.g. energy, hydro, tools 

development, research survey input, etc.) are insufficient.

• RC staff have only limited interactions with SC staff, often related to ad hoc involvement on projects of mutual 

interest. Interactions are usually informal and may be 

constrained by a lack of communication by SC scientists 

to RC staff on current research activities and results.

• Solicitation of SC participation on projects requiring 

substantial effort is difficult without specific allocation 

of funds to support their time on a project. There is some 

perception that SC research is more geared to outside 

organizations or academic interests rather than addressing the questions and needs of the ROs/RCs.

• In the cases where the ROs/RCs have been able to 

provide funding to support SC participation to address 

specific questions or monitoring/programmatic issues, 

results have sometimes been mixed. ROs need real 

deliverables, often on short time frames, while the SC 

staff may have research interests that are more theoretical 

than the applied questions being addressed at the RO. 

• ROs at times may opt to not utilize the SCs, and instead 

pursue science input from regional universities or other 

entities. 

Question 5: How quickly are you able to provide/

receive habitat science information for short 

deadlines (regarding both fishery management 

issues and nonfishing impacts)?

• Responses are generally timely but depend on the availability of data and the scope of the request. Time frames 

may range from minutes to years depending on the 

complexity of the question. Obtaining qualitative information can be relatively quick and easy, but obtaining 

analysis or data can be very difficult on the constrained 

time frames that the RO operates on. 

• Generally, the time frames for SC help are longer than 

the quick turnaround needed to meet consultation 

deadlines. SC response is tied to the workload and time 

availability of staff scientists involved. Unless there is 

specific funding for a project with a formal work plan 

that includes deliverables and deadlines, there are no 

institutionalized expectations for meeting time frames. 
150

• The lack of a formal process for engagement on habitat 

science issues between ROs and SCs makes receiving SC 

assistance on short notice problematic. Although SCs are 

generally responsive when timing can be appropriately 

anticipated, comment periods are generally too short 

(i.e. 10 to 15 days) to appropriately engage the SC. Time 

requirements depend on the information needs.

• SC responses to information requests are limited by lack 

of staff (both staff time and technical skill) and outdated 

data management systems. Sometimes, despite best efforts, deadlines may not be met because of these limitations.

• SCs may not be able to provide habitat science information for some requests from the ROs/RCs because data 

is not available. Many data gaps exist, hampering the 

ability of SCs to provide habitat science information on 

a reasonable time line. In cases where a proposal needs to 

be developed and a source of funding found to initiate 

a new research project, the time lag is often several years 

before a product can be developed.

• Smaller, informal staff to staff requests that do not 

require higher level tasking and approval generally are 

more successful in getting quick responses. 

• Longer-term or more complex issues provide opportunities for increased communication and collaboration 

between SC and RO staff. Such issues provide opportunities to expand on regional interactions for longer-term 

habitat science research.

• In some cases the usefulness of the information provided 

by the SC depends on the ability of RO staff to understand it—SC staff may provide analyses that RO staff do 

not have the specialized background or training to utilize 

in a meaningful way.

Question 6: Are there any structure or 

organizational changes that you feel would work 

better to support habitat science requirements?

• Lack of staff and funds to support staff are a significant 

limitation, and lack of funds to conduct habitat science 

greatly limits overall understanding.

• To receive the funding and support necessary for habitat 

science requirements to be well supported by SC capabilities, habitat science must be made a priority on par 

with stock assessment. The Habitat Assessment Improvement Plan (HAIP) is a great step towards this.

• Each SC should have a dedicated habitat science program or division, which will require adequate funding 

and administrative support.

• Institutionalized planning and coordination meetings, 

for appropriate personnel, would help to identify and 

agree on science needs and priorities. This could help to 

develop a unified and clear process to select projects for 

research and evaluation.

• A process for joint budget planning would help with 

strategic planning of research needs for management, in 

a way that would be easier for the SCs to manage. 

• A long range science needs plan developed by the ROs 

might serve the SCs in aligning some of their research 

priorities in a more thoughtful, coherent manner, rather 

than responding mainly to ad hoc requests for research 

support.

• SCs and ROs should work to develop, maintain, and 

support a core team of scientists with multidisciplinary 

expertise that could be accessible for consultation with 

the ROs; this would help tremendously to provide better science in support of management both in terms of 

breadth of expertise and rapidness of response. This ‘core 

team’ concept should be viewed as fluid across the SCRO boundary, and include identification of personnel 

who can directly interact to identify critical uncertainties 

that would benefit management to make more informed 

decisions. Separate from this fluid interaction with 

regard to defined areas, there should be a clear division of 

responsibilities between the SC and RO.

• A national online directory cataloging specialized 

habitat-related scientific expertise should be developed. 

While some habitat science issues are regionally-specific, 

others cut across regions and top expertise may reside in 

another SC. NMFS should find ways to establish connections between habitat managers and national habitat 

experts.

• Improved data interpretation for management use is a 

key need. SCs tend to be more interested in analyses that 

necessarily take time and may not provide information 

in a form that lends itself to qualitative interpretation or 

application, while ROs are in need of qualitative and/or 

short-term data that indicate the current state of a habitat area that may be affected by an action. ROs thus need 

to interpret available data within the context of a specific 

consultation or action in response to a short deadline.

• Examine ways to relieve SC scientists of the requirement 

to publish results in order to be competitive for advancement, or to modify the requirement to make it more 

attractive for SC personnel to pursue research that is of 

importance to management (but perhaps not as compelling academically). This might allow SCs to expand 
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roles in developing science-based conservation tools, 

approaches, alternative solutions, etc. to address regional 

habitat threats.

• Determine how, where, and when it may be appropriate 

to pursue other avenues for acquiring research and information support. Some services (e.g. providing literature 

reviews of habitat science) might be better accomplished 

through contracting with a consultant. Non-NMFS 

resources (e.g. the U.S. Geological Survey, NOAA’s 

National Centers for Coastal Ocean Science) might 

be identified as primary providers for specific types of 

research or information for managers.

• A structural change in how the habitat community 

works together may be necessary to facilitate more 

coordinated and strategic interactions among regional 

entities. Each region (RO/SC/RC) should seek to find 

major topics or themes of mutual interest and formulate 

a long-term plan for how respective resources will be 

focused on those issues in a coordinated way. Such an approach would focus regions in a programmatic way that 

would facilitate sustained coordination among different 

agency emphases.

• Perhaps SCs could seek to receive reimbursable funding 

from regulatory agencies (e.g. Army Core of Engineers) 

to help provide data on impacts to fishery resources from 

large project proposals such as port development and 

energy development, enabling the RO to provide credible and scientifically defensible advice in fulfillment of 

its mandates.

• Year to year competitive allocation of funding to the RO 

habitat divisions makes it impossible for the ROs and 

SCs to sustain multiyear research efforts in support of 

habitat management.

Question 7: Aside from more money, if you could 

change one thing (or up to three) about how your 

RO, RC, and SC work to provide science in support 

of habitat management, what would you choose?

• Make habitat science an agency priority on par with 

stock assessment and protected resources.

• Demonstrate the importance of habitat science to the 

stock assessment community by dedicating a staff member to work at the interface of habitat science and stock 

assessment.

• Develop rigorous means to include habitat information in stock assessments. Fostering habitat scientists 

with greater quantitative skills will be an important step 

towards improving communication with population 

modelers.

• Make habitat science in support of management a priority and codify, to the extent practicable, the SCs role in 

providing science information and scientific advice in 

support of habitat management.

• Dedicate a staff position in each region to coordinating between the RO, SC, FMC, and Marine Fisheries 

Commission. This staff member could be instrumental 

in identifying both short- and long-term research needs 

and capabilities among different entities. 

• Common, mutually beneficial priorities with respect to 

NMFS mandates should be used to more closely align 

regional habitat component operations (RO, RC, SC). 

Structural changes that focus the three regional entities 

on more integrated themes that address the most critical 

mutual issues could be a powerful paradigm shift that 

leads to more efficient use of funding and also creates an 

opportunity to build real partnerships.

• Clarify how habitat science should be prioritized in the 

context of additional research needs.

• Conduct regular, periodic regional habitat science 

priority setting exercises to better align science and 

management needs. Outcomes should include joint 

agreements from RO/RC/SC representatives on habitat 

science priorities, identification of potential collaborations, work plans, and funding strategies to address those 

needs. Regional staff should also meet periodically to 

review progress on addressing habitat science needs and 

promote broader dialog about habitat science in support 

of resource management.

• Work to establish more formal communication between 

ROs, RCs, and SCs. This could include joint retreats, 

symposia, planning meetings, and workshops.

• Encourage program managers and staff to contact SC 

staff more frequently to allow direct interchange of needs 

and questions that need to be addressed. 

• Increase communication between SCs and ROs. even 

when funding restrictions prohibit formal meetings, 

increased communication through conference calls, written summaries of current science projects and regional 

needs, and other means, are important to fostering a 

regional habitat science community.

• Establish a habitat program or division in every SC. 

Some have no such program, while others have habitat 

science spread across several divisions.

• Better focus habitat science efforts on agency mandates, 

jurisdictions, and management needs. Go beyond the 
152

primary focus on habitat utilization to encompass 

habitat recovery and the impacts of coastal development. 

Move beyond maps and think about ecological processes.

• Combine empirical and theoretical approaches to help 

NMFS better respond to emerging science needs and 

enable more effective habitat management.

• Better align the habitat research being conducted by SCs 

with the delivery of management needs, information, 

and products. Shift focus away from academic research 

endeavors and more towards habitat characterization, 

mapping, and assessment activities. Work towards providing managers with the information they need to make 

better decisions.

• Reduce the role of personal academic interests in prioritization of habitat science at the SCs.

• Increase accountability in the SC to ensure that the science that is being funded and conducted has direct need 

and benefit back to a NMFS division office.

• Improve communication about current research and 

recent scientific findings to managers so they can better 

utilize existing data and analyses. ROs and SCs should 

work together to identify ways to make data and analyses 

more accessible to RO staff. 

• Better budget management and development training 

for SC staff. 

• Be more efficient about the use of existing money. For 

example, the RC should allocate funds to monitoring 

restoration projects that it funds and ROs might benefit 

from using the SCs as a “preferred consultant” and go 

outside of NMFS for science information only when 

absolutely necessary. 

• Seek long-term reimbursable sources of funding, which 

would allow SCs to provide long-term data sets of 

coastal habitat and take into account seasonal and cyclical variation.

• Additional effort should be placed into technology 

transfer. This would enhance the value of research done 

by NOAA by increasing the awareness (both internally 

and externally) of available work.

• Support and participate in biannual National Habitat 

Assessment Workshops.

Question 8: What one or two core SC functions to 

support habitat management could be enhanced by 

the development of long-term science capability?

• An increased focus is needed on research that can help 

support management decisions, and/or can result in applied products on a short-term time frame of several days 

up to two years.

• The goal of SC habitat programs should be to understand how habitats function to support fishery production. This work entails research on identifying EFH, 

refining definitions of EFH, examining human and 

natural impacts on EFH, developing design criteria for 

habitat restoration, monitoring the success of habitat 

restoration, modeling linkages between habitats and 

fishery production, and developing integrated ecosystem 

assessments. All of these support habitat management 

needs.

• Habitat science programs must have the support necessary to be able to address the full scope of habitat issues, 

beyond species found only in the marine environment. 

Regional management entities have a significant interest 

in and responsibility for the management of nearshore, 

estuarine, and riverine habitats, and the species that 

utilize them.

• A crucial management need is more refined EFH and 

habitat areas of particular concern (HAPC) designations, including the use of Level 3 and 4 information, 

and reduced reliance on trawl survey data. The main 

barrier to speeding up the process to identify, and 

more specifically, to refine, EFH is the lack of scientific 

information and research on basic species and habitat 

functions and relationships within a geographic context. 

A plan should be developed that identifies priorities for 

habitat research that would help refine EFH and define 

the cost of this research over the next five and ten years.

• Better integration of fishery statistics work is needed 

regarding year classes of various species as they recruit 

from one life stage to another with the habitat needs of 

those species and life stages. Such integration would help 

to refine the approach to identifying EFH/HAPCs and 

assist in efforts to protect the habitats that are the most 

critical or sensitive.

• Initiate a long-term habitat assessment and monitoring 

program utilizing specific ecological indicators.

• Identification of habitat impacts and habitats most at 

risk from effects of nonfishing activities, especially in the 

coastal zone.

• There is a need for more and better understanding of 
153

early life history of fishery resources, especially in relation to how nearshore and estuarine habitats are used. 

The emphasis is often on the offshore component, which 

is fine for many species, but does not adequately serve 

the needs of habitat science for estuarine-dependent or 

diadromous species.

• Better ecological data on: 1) fish movements; 2) spatial 

variation in productivity (e.g. survival, growth); and 3) 

mark recapture programs to simultaneously measure 

natural and harvest mortality.

• Analysis/modeling: 1) incorporating habitat or spatial 

variation into stock assessment; and 2) analysis that 

estimates cumulative impacts to a population’s habitats.

• Expertise in estimating ecosystem values from habitat 

restoration projects or habitat protection through regulation. 

• Access to expertise on developing monitoring approaches for various restoration project types (e.g. dam 

removal) and assistance for applicants in identifying 

and following appropriate monitoring protocols is a key 

need. If data from various project types were contributed 

to SC studies on restoration ecology, NMFS could potentially require applicants to follow certain monitoring 

protocols and ensure further data sharing.

• Building more resilient systems should be a key big picture goal, but will require greater understanding of the 

relations between land management and linked water 

quality and coastal resource recovery.

• Measurement of the sensitivity, impact, and recovery of 

disturbed benthic habitat.

• Translating research results into products ready for 

immediate management use needs to a larger focus. Development of tools (e.g. geographic information systems, 

analytical tools, decision support tools) that can facilitate rapid application of research should be a focus.