Report of the Protected Species 

SAIP Tier III Workshop 

7-10 March 2006 

Silver Spring, MD 

Richard Merrick (Chair) 

Ruth Kelty 

Tim Ragen 

Teri Rowles 

Paul Sandifer 

Barbara Schroeder 

Steve Swartz 

Nathalie Valette-Silver 

April 2007 

U. S. DEPARTMENT OF COMMERCE 

National Oceanic and Atmospheric Administration 

National Marine Fisheries Service 

Report of the Protected Species SAIP Tier III Workshop 

7-10 March 2006 

Silver Spring, MD 

Richard Merrick (Chair)1, Ruth Kelty2, Tim Ragen3, Teri Rowles4, 

Paul Sandifer5, Barbara Schroeder4, Steve Swartz4, Nathalie Valette-Silver2

1

National Marine Fisheries Service, 166 Water Street, Woods Hole, Massachusetts 02543 

2

National Ocean Service, 1305 East-West Highway, Silver Spring, Maryland 20910 

3

Marine Mammal Commission, 4340 East-West Highway, Bethesda, Maryland 20814 

4

National Marine Fisheries Service, 1315 East-West Highway, Silver Spring, Maryland 20910 5

National Ocean Service, 331 Fort Johnson Road, Charleston, South Carolina 29412 

April 2007 

NOAA Technical Memorandum NMFS-F/SPO-78 

U.S. DEPARTMENT OF COMMERCE

Carlos M. Gutierrez, Secretary 

National Oceanic and Atmospheric Administration 

Vice Admiral Conrad C. Lautenbacher, Jr., USN (ret.), Under Secretary for Oceans and Atmosphere 

National Marine Fisheries Service 

William T. Hogarth, Assistant Administrator for Fisheries 
This document will initially be issued only online. It will be available at: 

http://www.nefsc.noaa.gov/nefsc/publications/ 

It will be available in PDF format so that a paper copy can be easily printed out. It may subsequently 

be issued on paper as well. If it is issued on paper, then copies would be available from: 

Protected Species Branch 

Northeast Fisheries Science Center 

National Marine Fisheries Service, NOAA 

166 Water St. 

Woods Hole, MA 02543 

This document may be cited as: 

Merrick R (Chair), Kelty R, Ragen T, Rowles T, Sandifer P, Schroeder B, Swartz S, Valette-Silver N. 

2007. Report of the Protected Species SAIP Tier III Workshop, 7-10 March 2006, Silver Spring MD. 

U.S. Dep. Commerce, NOAA Tech. Memo. NMFS-F/SPO-78, 79 p. 
iii

Table of Contents

List of Illustrations ........................................................................................................................ iv 

List of Tables...... ........................................................................................................................ iv 

Executive Summary........................................................................................................................ v

I. Introduction ...... ........................................................................................................................ 1

A. Background....................................................................................................................... 1

B. Workshop Goals................................................................................................................ 3

C. Workshop Format ............................................................................................................. 3 

D. Working Group Terms of Reference ................................................................................ 4

II. Workshop Presentations............................................................................................................. 5

A. Ecosystem Studies with A Protected Species Component ............................................... 5

B. Protected Species Studies with an Ecosystem Component................................................ 6

III. Working Group Reports............................................................................................................ 9

A. Working Group 1: Supporting the NOAA vision of EAM--Ecosystem Studies with a 

protected species component ........................................................................... 9

B. Working Group 2: The Protected Species Vision - Protected Species Studies with an 

Ecosystem component ................................................................................... 14

C. Working Group 3: Ecosystem Based Stock Assessments For Protected Species........... 20

D. Working Group 4: Governance-Incorporating EAM for Protected Species................... 31

IV. Summary and Conclusions ..................................................................................................... 36

A. What characteristics should a region-specific, national program have?......................... 36

B. Are there appropriate experiences worldwide that demonstrate how this theme can 

inform ecosystem-based protected species management?............................. 36

C. What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision 

making?.......................................................................................................... 37

D. What changes in policy, governance, or science administration are required to more 

effectively inform ecosystem approaches to protected species management?

....................................................................................................................... 37

Literature Cited ..............................................................................................................................39 

Acknowledgments..........................................................................................................................42 

Appendix I. Agenda................................................................................................................... 43

Appendix II. List of Participants................................................................................................. 46

Appendix III. Selected Readings In Ecosystem Approaches To Management ........................... 51

Appendix IV. Expanded answer to WG1’s Question 3 – New research, data collection, models 

and data management required to support and EAM .................................... 54

Appendix V. Working Group III’s List of Research Priorities for Incorporating Ecosystem 

Considerations into Protected Resource’s Assessments................................ 63

Appendix VI. Glossary of Terms................................................................................................. 65
iv

List of Illustrations 

Figure 1. Eight regional marine ecosystems defined by NOAA .................................................. 2

Figure 2. General framework for management strategy evaluation (Sainsbury et al. 2000)....... 34 

List of Tables 

Appendix Table 1. Major themes to consider for ecosystem-based decision making relative to 

EAM for Protected Resources ....................................................................... 67 

Appendix Table 2. Types and attributes of stock assessments for protected species................... 69 

Appendix Table 3. Matrix of governance options .........................................................................70 

Appendix Table 4. Summary of Working Group responses to the four questions........................71 
v

Executive Summary 

Early in the development of the National Oceanographic and Atmospheric Administration 

(NOAA) Fisheries Protected Species Stock Assessment Improvement Plan (SAIP), it was clear 

that there were to be two phases in its development. In the first phase, NOAA developed a plan 

to address the basic marine mammal and turtle assessment mandates of the Endangered Species 

Act (ESA) and Marine Mammal Protection Act (MMPA). After long discussions within NOAA 

and with NOAA’s partners, a two-tiered plan was developed: Tier I - Improve Stock Assessments 

Using Existing Data Collection Resources, and Tier II – Elevate Stock Assessments to New 

National Standards of Excellence. This phase culminated in publication of the protected 

resources SAIP report (NMFS 2004). 

Agency scientists recognized that current methods would not provide all the information needed 

by a changing NOAA. The evolving information needs of NOAA and its partners will require a 

host of data items that have not traditionally been collected. These needs are subsumed under 

the second phase of the SAIP development: Tier III - Next Generation Assessments. This phase 

will involve expanding observing and research programs beyond the traditional single-species 

approach towards an ecosystem-based approach, and will complement the current efforts 

underway for improvements in NOAA’s fisheries science as part of NOAA’s Ecosystem Goal 

Program. 

Given the progress in the development of the SAIP and NOAA’s Ecosystem Approaches to 

Management (EAM), NOAA Fisheries Office of Protected Resources determined it was time to 

begin work on the development of a requirements plan to define and provide Tier III information 

for its protected species mission. The first step in this process was a workshop convened by 

NOAA in March 2006 to clarify the vision of EAM for protected species, and scope the data 

collection and research necessary to support Tier III. The Tier III workshop was designed to 

answer a series of key questions that can provide guidance to NOAA staff in their development 

of the Tier III Plan: 

• How do Protected Species fit into NOAA’s EAM? 

• Should NOAA's focus be “Ecosystem Studies with A Protected Species Component,” 

“Protected Species Studies with An Ecosystem Component,” or both? 

• Can we develop an ecosystem approach for protected species stock assessments (e.g., can 

PBR be further developed to provide an ecosystem based assessment?) 

• How should NOAA deal with the governance issues related to EAM for protected species? 

That is, how can EAM be used by NOAA managers to meet their ESA/MMPA mandates? 

The workshop was held over a four-day period (7-10 March 2006) in Silver Spring, MD, and 

included a diverse group of scientists and managers from NOAA, academia, and other 

government offices. The first day and a half of the four-day workshop was a plenary session 

providing case studies of what an EAM could be for protected species. The remainder of the 

workshop focused on four working groups’ (WG) discussions: 

• WG 1 – Supporting the NOAA vision of EAM - Ecosystem Studies with A Protected Species 

Component 
vi

• WG 2 – The Protected Resources Vision - Protected Species Studies with An Ecosystem 

Component 

• WG 3 – Assessments –Ecosystem Based Stock Assessments for Protected Species 

• WG 4 – Governance – Incorporating EAM into Management of Protected Species 

Each WG was tasked to develop a conceptual strategy for a national and regional program 

supporting their theme. 

What characteristics should a region-specific, national program have? 

The WG’s suggested that a national program to support EAM with explicit protected species 

components should be based on a clearly stated national mission or vision, flexible enough to 

adapt to regional needs, and with goals, objectives and performance measures which are 

responsive to broader ecosystem information. The program should fulfill the ecosystem 

mandates under the Magnusson-Stevens Fishery Conservation and Management Act, the Marine 

Mammal Protection Act, and the Endangered Species Act. Such a program should involve 

coordination and collaboration, transparency in decision making, and precautionary approaches 

to management in a place-based fashion, focusing on issues/threats to ecosystem, rather than on 

species-specific management. 

 

The scientific program should focus on the eight regional ecosystems, while recognizing the 

nested and cross-boundary nature of many protected species. Science-based decisions are made 

using multidisciplinary information. This program should establish a standardized evaluation 

process, be as exhaustive and inclusive as feasible of all ecosystem components, and ultimately 

support an ecosystem based management model. Products of the program should be reference 

documents describing each ecosystem, long term monitoring of the eight regional ecosystems, 

and sustained, coordinated funding for ecosystem research and research platforms. 

Are there appropriate experiences worldwide that can inform NOAA’s ecosystem-based 

protected species management? 

Key examples provided by the WGs included the developing Aleutian Islands Fishery Ecosystem 

Plan, the Convention for the Conservation of Antarctic Marine Living Resources (CCAMLR), 

the International Whaling Commission (IWC), Northwest salmon recovery efforts (including the 

Puget Sound Restoration Plan and the Puget Sound Collective Process), and various Northern 

European efforts, including BORMICON, MULTISPEC, Barents, North, and Baltic Sea 

multispecies models. 

What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision making? 

Guidance varied among the WGs based on their group theme. For example, WG1 (Ecosystem 

Studies) identified six broad themes for which tools are needed: trophodynamics, acoustics, 

health, climate, habitat, and social science. WG3 (Protected Species Assessments) suggested that 

EAM assessments should include traditional single-species scientific advice, but also include 

ecosystem considerations. An “ensemble approach” to assessment using multiple model types 
vii

may be an appropriate framework. Assessment models enhanced by ecosystem considerations 

need to result in clearly defined control rules to inform management decisions. WG4 

(Governance), on the other hand, identified the need for a better Decision Support system to 

provide a framework for incorporating ecosystem science into management decision-making. 

What changes in policy, governance, or science administration are required to more 

effectively inform ecosystem approaches to protected species management? 

The WGs agreed that the existing NOAA mandates under the ESA, MMPA, NEPA,MSFCMA, 

and other legislative drivers provided ample statutory authority for the NMFS to proceed with 

implementation of EAM. Actual governance remains a thorny issue, however. The WGs 

suggested that perhaps the establishment of a new regional governance body (e.g., a Marine 

Ecosystem Council) could fill this role. The Puget Sound Collective may provide a model for 

such a body. In the short term, the authority of existing governance structures (e.g., Fishery 

Management Councils, Take Reduction Teams) should be expanded so that they have broader 

stewardship responsibilities and wider spectrum of stakeholder participation. 

There was also general agreement that NOAA Science needs to be better integrated across taxa 

and disciplines and this may require the establishment of integrated national and regional marine 

science groups. This will further require a clear mandate from NMFS HQ to the field that the 

Centers and Regions conduct ecosystem/integrative research and management. 

1

I. Introduction 

A. Background 

The NOAA Fisheries’ Protected Species Stock Assessment Improvement Plan (NMFS 2004) 

was crafted in two phases. In the first phase, NOAA developed a Plan to address the basic 

marine mammal and turtle assessment mandates of the ESA and MMPA. After long discussions 

within NOAA, and with NOAA’s partners, about basic information requirements, a two-tiered 

plan was completed: 

 

• Tier I – Improve Stock Assessments Using Existing Data Collection Resources: This tier 

maintains the status quo with no new assessment efforts. 

• Tier II – Elevate Stock Assessments to New National Standards of Excellence: At this Tier 

the quality of all stock assessments should achieve a level commensurate with ESA and 

MMPA mandates. 

This phase culminated in publication of the Protected Resources SAIP Report (NMFS 2004). 

Development of the requirements plan through Tiers I and II represented a simple evolution of 

past practices; however, agency scientists recognized that current methods would not provide all 

the information needed by a changing NOAA. The evolving information needs of NOAA and its 

partners require a host of data that have not traditionally been collected. 

These themes and needs are addressed in the second phase of the SAIP development, “Tier III - 

Next Generation Assessments:” 

• Collection of detailed data on ecology, habitat, behavior, and health of “Ecosystem Indicator 

Species” to provide a better understanding of how marine mammals and marine turtles 

function within their respective ecosystems 

• Ecosystem-based approach to assessments 

 

This phase in the development of NOAA Protected Species requirements plan involves 

expanding observing and research programs beyond the traditional single-species approach 

towards an ecosystem-based approach. This complements the similar efforts already underway 

for improvements in NOAA Fisheries science. For a few key protected species (i.e., “Ecosystem 

Indicator Species”) the second phase involves the collection of a basic suite of data under all data 

categories discussed previously. For all species, the second phase requirements mean that stock 

assessments will be conducted with processes and models not previously used. 

While the SAIP was under development, NOAA Fisheries made considerable progress in 

defining an Ecosystem Approach to Management (EAM), and the concept of EAM is now firmly 

a part of NOAA’s Planning Programming, Budgeting, and Execution System. Initial guidance 

for the agency’s approach to EAM is provided in the report to Congress by the Ecosystem 

Principles Advisory Panel (http://www.st.nmfs.gov/st2/Eco-bas-fis-man.pdf). NOAA managers 

and scientists are now implementing the EAM process, with pilot EAM projects initiating in 

FY07 in a limited number of ecosystems. NOAA scientists and managers met in Charleston, SC 

in late summer 2004 to (1) discuss the delineation of large ecosystems on the basis of natural 
2

science (not political boundaries), and (2) discuss how these ecosystems might be broken down 

into sub-areas, again, based on natural science criteria. As a result of the workshop, NOAA 

defined 10 ecosystems based on the Large Marine Ecosystem (LME) model. These ecosystem 

regions extend from coastal areas to the seaward boundaries of continental shelves and to the 

outer margins of the major current systems. These were later reduced to eight regional 

ecosystems: Alaska Ecosystem Complex, California Current, Caribbean Sea, Great Lakes, Gulf 

of Mexico, Northeast Shelf, Pacific Islands Ecosystem Complex, and Southeast Shelf (Fig. 1). A 

subsequent workshop was held in Key Largo, FL in February 2005 to discuss “Ecosystem-Based 

Decision Support Tools for Fisheries Management: 

http://www.st.nmfs.noaa.gov/st7/ecosystem/workshop/2005/index.html

Figure 1. Eight regional marine ecosystems defined by NOAA. 

 

Given the progress, in both the development of the SAIP and in EAM, NOAA Fisheries initiated 

work to develop a requirements plan to define and provide Tier III information for its protected 

species mission, and complement the existing Protected Species SAIP. The first step involved a 

workshop convened by NOAA in March 2006 to clarify the vision of EAM for protected species, 

and scope the data collection and research necessary to support Tier III. This workshop is to be 

followed by additional discussions within NOAA to prepare a Tier III Requirements Plan, and 

will culminate in an expanded version of the SAIP report to be completed in spring 2007. 
3

B. Workshop Goals 

The Tier III workshop was designed to address four key questions: 

• How do Protected Species fit into NOAA’s EAM? 

• Should NOAA's focus be “Ecosystem Studies with A Protected Species Component”, 

“Protected Species Studies with An Ecosystem Component,” or both? 

• Can NOAA develop an ecosystem approach for protected species stock assessments (e.g., 

can PBR be further developed to provide an ecosystem based assessment) ? 

• How should NOAA deal with the governance issues related to EAM for protected species? 

That is, how can EAM be used by NOAA managers to meet ESA/MMPA mandates? 

Other topics addressed included how the NOAA Ocean and Human Health Initiative fits into 

EAM, and how EAM can assist NOAA and its partners in meeting Tier III information needs. 

These questions were addressed largely from the perspective of marine mammal, marine turtle, 

and salmonid conservation. However, the results of these discussions are applicable to other 

NOAA protected marine species. 

Finally, results of the workshop, including the speaker and working group reports are available at 

https://reefshark.nmfs.noaa.gov/pr/saip/. 

C. Workshop Format 

The first day and a half of the four-day workshop was a plenary session (See Appendix I for the 

workshop agenda). The morning session of the first day was used to review current activities 

within NOAA is at this time with respect to EAM and SAIP development. The afternoon of the 

first day and the morning of the second day involved formal presentations and discussion of 

elements of EAM by invited speakers. Case studies were provided to generate discussion of 

what an EAM would be for protected species. The remainder of day 2, as well as most of day 3, 

focused on working group discussions designed to develop conceptual approaches to EAM for 

Protected Species. 

The workshop included a diverse group of scientists and managers (see Appendix II): 

• NOAA Fisheries staff representing Headquarters Office (F/PR, F/SF, and F/ST), and at least 

1 representative from each of the Science Centers and Regional Offices 

• NOAA NOS staff including staff from relevant NCCOS, Sanctuaries, NERR sites, and 

Ocean and Human Health 

• DOI representatives from USFWS 

• Marine Mammal Commission staff 

• Selected scientists from outside of the US Government 

• Selected scientists from other nations (e.g., Canada, UK) 

The workshop was held over 7-10 March 2006 at the Hilton Silver Spring in Silver Spring, MD. 

NOAA provided full funding support for invited speakers and partial support for invited 
4

participants. This meeting was open to the public but did not include formal public comment 

sessions. 

D. Working Group Terms of Reference 

Plenary sessions of the meeting were chaired by Dr. Richard Merrick. Each working group had a 

facilitator and science/management chair working in tandem to move the discussions along. 

Rapporteurs were provided for each working group. Each working group produced a written 

report included later in this report. 

Separate working groups were used to pursue four themes: 

• WG 1 – Supporting the NOAA vision of EAM - Ecosystem Studies with A Protected 

Species Component: What protected species information needs should be included in a 

national strategy to support EAM? Note that this ecosystem modeling is meant to include 

not only multispecies fishery assessments with predation explicitly included, but also 

ecosystem based acoustic analyses, ocean and human health, etc. 

• WG 2 – The Protected Resources Vision - Protected Species Studies with An Ecosystem 

Component: What should a national strategy for ecosystem based protected species studies 

encompass? 

• WG 3 – Assessments –Ecosystem Based Stock Assessments for Protected Species: Can 

traditional single-species protected species assessments (e.g., PBR) be made multi-species? 

• WG 4 – Governance – Incorporating EAM into Management of Protected Species: 

How can NOAA implement ecosystem based management of protected species under 

MMPA and ESA? 

Each WG was tasked to develop a conceptual strategy for a national and regional program 

supporting their theme, and to prepare a brief (~5 page) report on the outcome of the discussion. 

Each of the reports addressed, at a minimum, the following questions: 

• What characteristics should a region-specific, national program have for this EAM theme? 

• Are there appropriate experiences worldwide that demonstrate how this theme can inform 

ecosystem-based protected species management (include appropriate references)? 

• What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision making? 

• Based on the above, what changes in policy, governance, or science administration are 

required to more effectively inform ecosystem approaches to protected species management? 

Participants were assigned to Working Groups generally based on their interests, although some 

balancing was done to assure roughly equivalent participation in each WG. 
5

II. Workshop Presentations 

A. Ecosystem Studies with A Protected Species Component 

Disease and Ecosystems – Dr. Andy Dobson, Princeton University - Pathogens are a major 

component of biodiversity. In a healthy ecosystem, consideration of parasites may double the 

number of species. Absence of parasites is beneficial to invasive species. Shared pathogens and 

spillover create serious health problems for humans and endangered species. Biodiversity creates 

an important disease buffer, particularly against vector transmitted pathogens. 

ICES Ecosystem Assessment WG – Dr. Jake Rice, Canadian Department of Fisheries and 

Oceans (DFO) - Jurisdictions around the world are facing many of the challenges to be 

addressed by Tier III assessments. The International Council for Exploration of the Sea (ICES), 

as the main provider of scientific advice to the European Community Director General for Fish 

and Environment, and to the fisheries and environmental commissions in the Northeast Atlantic, 

has been revising its Working Group structure and refocusing the activities of its Science and 

Advisory Committees to build capacity for integrated ecosystem assessments, and for provision 

of advice to management agencies which integrates fisheries issues, environmental quality, and 

species covered under the Species and Habitat Directive of the European Community. In 

Canada, the adoption of Canada's Oceans Strategy in 2002 and coming into force of the Species 

at Risk Act (SARA) in 2003 have required a similar restructuring of the approaches to 

assessments and provision of science advice. Ecosystem Assessments and a focus on recovery 

potential of species listed under SARA have taken a central place in DFO Science advisory tasks. 

CCAMLR/SCAR – Dr. Christian Reiss, NMFS (SWFSC) - CCAMLR is an international 

body addressing living marine resource use and conservation in the Antarctic Ecosystem. Many 

of the assessment models for targeted and protected species are in some form linked to lower 

trophic level production, particularly of krill. Management decision criteria are developed in a 

precautionary manner, including “set asides” for krill. These can vary by species, but all are 

generally adaptive and coordinated. 

EMAX – Dr. Jason Link, NMFS (NEFSC) - Energy Modeling and Analysis eXercise (EMAX) 

is a focused ecosystem study being conducted by the NEFSC. It is a network analysis model 

(aka a more nuanced energy budget) of the entire food web. It includes the entire Northeast US 

continental shelf, broken into 4 subregions, 34 network “nodes” or biomass state variables across 

a broad range of biology. The emphasis is on the role of small pelagics, with some pseudodynamic scenarios possible. Interactions with protected species are explicitly included. 

Ocean and Human Health Initiative – Dr. Teri Rowles, NMFS/NOS - The OHHI seeks to 

understand the nature of interactions between human health and ocean processes, and to provide 

useful information to policy and decision makers. Focus areas include marine toxins and 

infectious diseases, chemical pollutants, coastal water quality and beach safety, seafood quality, 

and sentinel species as indicators of both potential human health risks and of human impact on 

marine systems. Importantly, the OHHI also focuses on the positive benefits of the sea such as 

the ecologically sound discovery of curative agents and marine natural products. 
6

B. Protected Species Studies with an Ecosystem Component 

Amphibian (and other species) epizootics – Dr. Andrew Cunningham, Zoological Society of 

London - Without coordinated disease surveillance with collaborative, multi-disciplinary (often 

multi-national) investigations, important diseases which threaten biodiversity and, in some cases, 

economic activities and human health, would remain unrecognized and undiagnosed. The more 

you look, the more you find; disease surveillance is an essential component of ecosystem 

management, and there is a need to establish base-line parameters wherever and whenever 

possible. There is more to disease threats than just pathogens causing mass mortality events. 

Ecopath/Ecosim model for green turtles in the Caribbean -- Colette Wabnitz, University of 

British Columbia - The roles of sea turtles as major consumers in many marine ecosystems 

have only recently been recognized. Green turtle (Chelonia mydas) biomass levels required to 

maintain “healthy” sea grass beds within the Caribbean were explored using a quantitative 

ecosystem model, Ecopath with Ecosim. 

The Ecopath model was designed as a “snapshot” estimation of turtle density for the Puerto 

Rico/Virgin Island shelf region, and extrapolated to the Caribbean. Thus, the Ecopath result is an 

estimate of turtle biomass per km2

 of sea grass, given a number of trophic considerations. These 

biomass estimates were then evaluated over a range of conditions (e.g. competitive interactions) 

to determine turtle biomass levels needed to maintain a productive system. The Ecosim module 

allowed predicting changes in community structure under varying levels of turtle impact given 

fine-tuning of trophic mediations built into the system (e.g. impact of shorter sea grass canopy on 

refuge role afforded to juvenile fish populations). Important assumptions underlying the 

exploration of such interactions are that: i) shoot density is independent of blade length, thus an 

increase in sea grass biomass can be equated with longer blade length; and ii) an increase in 

biomass is coupled with a decrease in productivity:biomass ratios, which have been validated by 

simulated grazing experiments in the Bahamas. These explorations combined with apparent 

changes in community structure are used to characterize carrying capacity of green turtles for the 

Caribbean. Moreover, preliminary results highlight gaps in our understanding of sea grass 

ecosystem dynamics and allow us to draw up hypothetical scenarios of management decisions.

Canadian Research on Cod-Seal Interactions – Dr. Garry Stenson, Canadian Department 

of Fisheries and Oceans - The collapse of the Northwest Atlantic cod fishery has become a 

metaphor for ecological catastrophe and is universally cited as an example of failed management 

of a natural resource. Various hypotheses have been advanced for the demise of these once 

abundant stocks. One is that physical changes in habitat have led to the decline. Cold water, 

reduced salinity, and other environmental parameters have been posited as components of the 

problem by reputable researchers. Another hypothesis is that the decline resulted from 

overfishing of cod stocks, and a statistically significant relationship has been demonstrated 

between the decline of cod and commercial harvests (Hutchings and Myers 1994). A third 

alternative hypothesis is that harp seal (or grey seal) predation on cod has contributed to the 

decline of cod stocks and/or to the lack of recovery. Over the past decade(s) scientists at the 

Canadian DFO have studied the interaction between seals and cod in an attempt to explore this 

hypothesis. Work has focused on building accurate consumption models derived from the 

considerable data collected on seal population dynamics, physiology, prey consumption, and 
7

movements. These consumption models can then be incorporated into cod assessment models to 

evaluate seal impacts on cod stocks. 

Ecosystem-scale analyses in support of management in Puget Sound – Dr. Mary 

Ruckelshaus and Dr. Michelle McClure, NMFS (NWFSC) - The Puget Sound ecosystem 

contains over 40 species currently listed on state and federal imperiled species lists, dead zones 

within certain embayments, and over a dozen Superfund sites within the Sound. These insults to 

the ecosystem impair the services that it provides—hindering not only recreational enjoyment of 

the region, but also human health, fishing and other economic pursuits. Scientific analyses in 

support of recovering and rebuilding species within the Puget Sound led inexorably towards 

ecosystem approaches to management. Ecosystem-scale scientific analyses have been used to 

develop a regional salmon recovery plan and are now being conducted to support regional efforts 

in ecosystem-scale management. The salmon recovery plans are based on restoring landscapes 

and habitat-forming processes in terrestrial, estuarine and marine environments. Recovery 

planners designed landscape restoration strategies based on models of the combined effects of 

habitat, hatchery and harvest management, and how alternative future climate scenarios impacted 

the predicted success of their proposed strategies. Given recent Orca listings, the strong food 

web interactions in marine waters, and water quality degradation in Puget Sound, it was 

recognized that a more scientifically explicit ecosystem framework was needed within which 

species and their habitats could be managed. In conjunction with a Puget Sound-wide ecosystem 

management initiative launched by Governor Christine Gregoire, there is a scientific effort to 

develop a collaborative 'state of the science' document. The document is authored by scientists 

from multiple agencies and universities, and provides a common vision of what is known about 

how the Puget Sound ecosystem functions, the ecosystem services it provides, key threats to 

those services, and socio-economic values. The document also contains a decision support 

framework illustrating how natural and social sciences will inform an eventual EAM plan for the 

Sound. Preliminary analyses are presented for several components of the ecosystem-scale 

modeling in Puget Sound. 

 

Eastern Tropical Pacific (ETP) Dolphin Studies – Dr. Lisa Ballance, NMFS (SWFSC) - 

Incidental mortality of dolphins in the eastern tropical Pacific yellow fin tuna purse-seine fishery 

has been historically high. That mortality has dropped to values close to 0 since 1990. However, 

depleted populations of dolphins have not recovered as expected and the natural question is why? 

We posit four possible causes: time lag, fishery effects, a change in carrying capacity of the 

system, or some other factor. A major climate shift occurred in the North Pacific in the late 

1970’s. Evidence of ecosystem change in the ETP associated with this shift is equivocal. It is 

conceivable that environmental change at this time affected spotted and spinner dolphins, 

although it is unlikely to have caused the apparent 3- to 5-fold decrease in carrying capacity 

needed to explain the lack of recovery. 

Linkages Between North Atlantic Right Whales and their Habitat – Dr. Andrew Pershing, 

Cornell University - Oceanographers and atmospheric scientists have done a good job 

describing the average, or climatological, conditions over the Earth, and in understanding the 

major processes that account for these conditions. There is now much interest in understanding 

what causes one year (or decade, or century...) to be different from another. Cornell researchers 

have conducted several studies of the changes in physical conditions in the Gulf of Maine since 
8

the 1950s and how these changes have impacted zooplankton populations. One current project 

uses this knowledge to develop predictive indices for physical and biological conditions in the 

Gulf of Maine. This is of particular importance in understanding survival and recruitment of 

North Atlantic right whales. With only a few hundred animals left, the North Atlantic right 

whale is one of the most endangered marine species. Cornell scientists have investigated the 

impact of interannual variability in copepods (e.g., Calanus finmarchicus) on right whale 

reproduction, and are currently studying factors which can be used to predict aggregations of 

right whales based on the distribution of their prey. 

Ecosystem-Based Approaches to the Management of Coral Reefs – Dr. John Ogden, 

University of Florida - Over the past 50 years, global coral reefs have precipitously declined 

from synergistic combinations of three major human disturbances: fishing; land-based pollution; 

and global climate change. Reefs are biologically diverse and characterized by the diversity and 

strength of interactions between species, for example, in larval dispersal and recruitment, 

competition, predation, and herbivory. Reefs rapidly lose resilience with disturbances to key 

functional groups and with physical stresses, particularly temperature. Any coral reef ecosystem 

is the product of its geography and history and is dependent upon other coastal ecosystems, 

including sea grasses, mangroves, and adjacent land masses. These considerations argue for 

ecosystem-based approaches to management to preserve and restore ecosystem structure and 

function, to reduce stresses, and to separate conflicting and damaging human activities. The 

ecosystem approach is based upon mapping, assessment, monitoring, and modeling and is 

dependent upon stakeholder involvement and gap-filling research. The coral reef ecosystem is 

defined as the area of concern at a variety of geographic scales depending upon the scientific and 

social considerations central to any management plan. As with any place-based management, 

zoning is a critical tool-- applied with a precautionary strategy and adjusted adaptively with 

increasing knowledge. 
9

III. Working Group Reports 

A. Working Group 1: Supporting the NOAA vision of EAM--Ecosystem Studies with a 

protected species component 

1. What characteristics should a region-specific, national program have for this EAM 

theme? 

NOAA’s vision of EAM explicitly calls for an interdisciplinary, cross-sector approach for 

managing coastal and oceanic resources (Ecosystem Goal Team [EGT], etc.). Thus, in the 

context of protected species, is necessary to consider a broader range of factors than under 

current single species protected resource management strategies. For example, ecosystem 

considerations as diverse as trophodynamics, acoustic environments, water quality, and ocean 

health will merit greater direct consideration in assessments. How these and other ecosystem 

factors directly impact protected species is probably best addressed in a single-species stock 

assessment context. How these ecosystem factors indirectly impact and are impacted by 

protected species, as well as cumulative systemic affects, are best addressed in a broader 

ecosystem context. Thus, a national program to support EAM with explicit protected species 

components should: 

• Address major issues (e.g. trophodynamics, acoustics, water quality, ocean health, climate, 

habitat) by providing germane information required by other NOAA partners and 

stakeholders as well as EGT or Protected Resources (PR). 

• Set national standards but be adaptable to regional needs 

• Be responsive to legislative mandates 

• Have a clearly stated national mission. However, this would need to be operable at the 

regional level. In general terms, we define the mission of this particular program as: 

“Provide protected species information to better understand broader ecosystem dynamics and 

to produce integrated regional assessments.” 

• Coordination and collaboration across line offices and other programs are critical to the 

success of this theme. As such, stakeholders, partners, and end-users need to be clearly 

identified and there needs to be adequate processes for stakeholder input and inclusion. 

Additionally, the program should have the ability to “kill two birds with one stone” from the 

same type of data provided or from coordinated platforms. For example, tissue plugs taken 

from marine mammals might be used to augment other efforts on trophic ecology, ocean 

health, human consumption of fish and sea mammals, and toxin biomagnification. 

• Be as exhaustive and inclusive as feasible of all germane ecosystem factors. This would 

require objectives and performance measures for broader ecosystem information, and also 

require clearly identified processes for review of outputs. But arguably most prominent, the 

Facilitator : Cyr 

Science Chair: Rowles, Link 

Participants: Bigford, Clapham, Collins, Fair, Ford, Gerke, Hall, Hoffman, Lang, 

Lewandowski, McFaddern, Menashes, Norse, Reiss, Roden, Southall, Whaley 
10

national program needs to establish a standardized process to evaluate the most prominent 

factors in each regional ecosystem. 

2. Are there appropriate experiences worldwide that demonstrate how this theme can 

inform ecosystem-based protected species management? 

A prime example can be found in the Convention for the Conservation of Antarctic Marine 

Living Resources (CCAMLR), an international treaty administered in the United States by 

NOAA Fisheries. The CCAMLR approach sets out three broad objectives to the management 

and rational use (harvesting) of krill in the Southern Ocean. These include, a) Prevent decrease in 

size of harvested populations below that necessary for stable recruitment; b) Maintain ecological 

relationships between harvested, dependent and related species; c) Prevent or minimize risk of 

changes not reversible over two or three decades. The scientific input for CCAMLR is based, in 

part, on an age based fishery model; monitoring of krill and predator populations, reproduction 

and feeding ecology, and through development of ecological indicators of ecosystem state. 

Feedback mechanisms in the management arena provide the link between science and the 

fishery. 

Other examples include1

: 

• Southern ocean GLOBEC 

• NAMMCO- Norway/Iceland- BORMICON/MULTSPEC 

• International Whaling Commission working groups 

• Yodzis et al. model from Argentina and Yodzis et al. model from South Africa 

• Ecopath w/Ecosim and marine mammals 

• Australian Dugong management 

• NMFS AKFSC- Steller Sea Lions and groundfish 

• NMFS NEFSC- EMAX 

• Sea otter, kelp interactions and trophic cascades 

• NOAA’s Ocean and Human Health initiative 

• Discovery of toxoplasmosis in sea otters leading to evaluation of run-off from feral and 

domestic cats which may have human health implications 

• Cold-water coral management in the North Atlantic (ICES, NMFS) 

• Australia’s Great Barrier Reef initiative 

Considerable reference material is also available as part of the efforts to conserve Northwest 

salmon. One key research area is the use of habitat and environmental information to inform 

stock assessments or recovery plans (Bartz et al. 2006, Lawson et al. 2004, Logerwell et al. 2003, 

Scheuerell and Williams 2005, Scheuerell et al. 2006. A second area of active research is 

 

1 See: Bogstad et al. 1997, Butterworth and Thompson 1995, Courchamp et al. 1999, Constable 2001, Crooks and 

Soule 1999, Hannon 1973, Hannon and Joiris 1989, Hammond and Fedak 1994, Hedley et al. 1999, Hewit and 

Linen Lowe 2000, IWC 2001, 2002, 2003, Koen Alonso and Yodzis 2005, Leontief 1951, Mangel and Switzer 

1998, McLaren et al. 2002, Mohn and Bowen 1996, Punt and Butterworth 1995, Stefansson and Palsson 1998, 

Thomson et al. 2000, Ulanowicz and Puccia 1990, UNEP 1999, Whipple et al. 2000, Yodzis 1988, 1998. 
11

species interactions (Johnston et al. 2004, Levin and Williams 2002, Levin et al. 2001, Nickelson 

2003, Ruggerone et al. 2005, Ruggerone and Nielsen 2004, Scheuerell et al. 2005) 

3. What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision making? - An 

ecosystem approach to management will require additional information on ecosystem structure 

and function, as well as managed populations. Just as an ecosystem approach will not replace, 

but enhance, existing single-species approaches to management, so too more and better 

ecosystem information will not replace the need for existing basic biological and physical data, 

research and modeling. The recommendations herein are intended as enhancements to existing 

programs. 

The Working Group divided its charge into broad themes: trophodynamics, acoustics, ocean 

health, climate, and habitat (Appendix Table 1). For each, the Group identified priorities for new 

work in four areas: research, data collection, models and data management. 

Trophodynamics - Key research questions include: What are the relative removals of and by 

protected species? What is the role of the abundance, distribution and nutritional quality of prey 

to changes in abundance and vital rates of protected species predators? What are the indirect 

effects of changes in prey to protected species? What is the role of competition with and among 

protected species? 

Data to be collected on individuals or populations include: abundance, rate of increase and 

removals; vital rates (survival/mortality, maturity, reproduction); bioenergetic rates (metabolism, 

consumption, respiration); diet composition; foraging behavior; interspecific relationships (niche 

separation, competition, spatial/temporal overlap, dietary overlap); carrying capacity; and 

interactions with fisheries. Many models with which to analyze these data exist already, but 

need to be carefully parameterized and tested against data from ecosystem scenarios with known 

outcomes. A critical review of existing models is essential, and it would be useful to test 

multiple models on the same data sets to assess variability in reliability of output. Different data 

sources exist (many online), and these should be integrated. 

Acoustics - Owing to the physical properties of water, sound is the principal means by which 

information is transferred over any appreciable distance. Sounds associated with marine biota, 

physical forces, and human activities provide detailed information with which both people and 

animals sense the marine environment. Further, sound can be used as an active investigative tool 

for locating objects. Because a wide range of biotic and abiotic information that may be 

obtained, an ecosystem approach to marine research and management should rely strongly on 

acoustic sensing. Specifically, passive acoustic sensors should be integrated into ocean 

observing systems to: 1) detect seasonal presence, activity, and (in some instances) abundance of 

species within ecosystems; 2) provide remote measurements of climatological and geological 

processes (e.g., rain and earthquakes); and 3) assess ecosystem-specific, spatial and temporal 

trends in ambient noise ‘budgets’ from the range of source contributions. Active acoustic 

sensing should be applied and advanced, where appropriate, as a means of identifying specific 

features of marine ecosystems (e.g., temperature, prey abundance, or the presence of specific 

species). 
12

A systematic approach is required for assessing marine ecosystem elements using passive 

acoustics. Specific questions regarding biotic and abiotic contributions to marine ambient noise 

should be identified and relevant sampling regimes specified (e.g., bandwidth, duty cycle, 

directionality) specified. Passive acoustic deployments to date have identified the seasonal 

presence of specific marine species, demonstrated human sound source contributions to marine 

ambient noise, and contributed to meteorological measurements. Further deployments and new 

sampling regimes should have the ability to assess spatial and temporal trends over a range of 

ecosystem features. Comparative ambient noise measurements should be taken across various 

marine ecosystems having variable anthropogenic influences. Acoustic data should be integrated 

with information on habitat and ecological factors to develop predictive ambient noise models. 

These will be distinct from the fairly well-derived sound propagation models for predicting 

received levels from a specified sound source. Ambient noise models would be useful in 

gauging not only estimated baseline conditions against which to assess anthropogenic inputs, but 

also in identifying environmental features relevant for active acoustic deployments. Data 

management should ensure maximal retention of raw data but be amenable to auto-recognition 

and other analyses. 

Ocean and Human Health - Ocean and human health parameters have rarely been included in 

ecosystem models or in ecosystem approaches to management. Under this theme, a hypothesis 

driven research plan should be included to support an ecosystem approach to understanding 

causal relationships between humans, ocean processes, marine ecosystem health, human health, 

and protected species health outcomes. For this effort, ocean health encompasses multiple 

ecosystem stressors and the protected resources within such systems and includes anthropogenic 

persistent and non-persistent organic and inorganic compounds, naturally occurring harmful 

algal blooms and their associated biotoxins, pathogens (including parasites), pharmaceuticals, 

water quality, and nutrients that contribute to hypoxic events. This theme also ties in with the 

Habarca Act, OHHI and Title IV and CCM. In addition risk and hazard communication plans 

should be integrated into the data management plan for this theme. 

Climate - Climatic and environmental data are critical components of any EAM approach to 

management, as they form the background state of the natural world in which protected 

resources reside. Any movement towards EAM with a protected species component will require 

a significant applied research program to support EAM, especially since EAM will naturally be 

adaptive, and region specific. Such a research program must elucidate linkages between 

ecosystem productivity, habitat structure and carrying capacity, as variability in the former two 

components will directly affect the latter. For example, climate variability may alter the 

productivity of the ocean or coastal environments. Such an ecosystem response would likely 

affect the ability to reach current rebuilding goals regardless of the protections afforded to 

species over projected time scales. Thus, research should include development of environmental 

and climate indicators and the refinement and validation of existing indicators. Such a research 

program should be broad, encompassing aquatic, terrestrial and atmospheric data, but should 

focus on providing information directly in support of EAM goals and regional species specific 

assessments. 
13

Habitat - Developing a quantitative understanding of the relationships between habitat and 

ecosystem function will be a critical component of an ecosystem approach to management. In 

particular, for many species, habitat quantity or quality are key factors limiting species 

abundance and productivity. For some protected species, habitat quality or quantity may be a 

direct factor limiting their recovery, while for others habitat impacts may be important through 

indirect effects on prey species. Human activities have both dramatic and subtle impacts on 

marine and coastal habitats, and predicting and managing the effects of such activities on species 

abundance, productivity, spatial structure and diversity will be essential to an ecosystem 

approach to management. Climatic variability is also likely to alter the structure of habitats 

reinforcing the need to include habitat information in any EAM approach. 

4. Based on the above, what changes in policy, governance or science administration are 

required to more effectively inform ecosystem approaches to protected species 

management? 

It is arguable that an ecosystem approach to manage PR is doable now. There are a plethora of 

legislative mandates that provide the basis for ecosystem considerations. For instance, the 

Endangered Species Act, Marine Mammal Protection Act, Magnuson-Stevens Fishery 

Conservation and Management Act, and the National Environmental Policy Act all have implicit 

ecosystem components. Additionally, NOAA’s Policy, Mission Statement, and Agency-wide 

goals have Ecosystem Approaches as a top element. 

Within the NOAA Ecosystem Approach to Management initiative, issues of internal and external 

governance are keystone concepts. Internal governance issues relate to how NOAA structures 

itself as an organization, how responsibilities are delegated, and how these actions are 

prioritized, planned and funded. Enhanced internal coordination (across NOAA line offices) is 

clearly needed. External governance covers issues of how NOAA relates to other federal, state, 

local, and international governments; particularly cooperative linkages, agreements, and 

NOAA’s role as a lead entity compared to one team member on any given issue. 

There is also a need to establish regional bodies, akin to those identified in the U.S. Oceans and 

Pew Commission reports. As envisioned in this working group, these bodies would receive and 

evaluate integrated assessments in a coordinated manner. These assessments would be for an 

entire ecosystem with explicit PR components. The point of such subregional bodies would be 

to provide a forum for addressing trade-offs in broader, LMR decision making. 

Finally, there is recognition that NOAA needs dedicated groups to perform integrated science 

within the context of national standards. Proceeding in an ad hoc, matrix-based manner has been 

tested at the operational, scientific level. The results clearly indicate major challenges and 

impediments for continued and escalating progress to actually implement an EAM for PR or 

other managed LMR. Within NOAA Fisheries, a dedicated group at each Science Center would 

greatly facilitate and rapidly increase our capability to implement EAM. 
14

B. Working Group 2: The Protected Species Vision - Protected Species Studies with an 

Ecosystem component 

In expanding protected species studies to include ecosystem components, the WG suggested that 

NMFS start with a few achievable elements, build up over time, and revisit and adapt 

periodically. Studies should strive to be interdisciplinary, integrating physical, biological, social, 

and economic components, as well as parasites (e.g., pathogens and other health issues). NMFS 

needs to focus attention on finding and using existing data, and build the flexibility to respond to 

unexpected events, such as post-hurricane monitoring. 

Building and formalizing partnerships is crucial within NOAA, as well as with other agencies, 

NGOs, academia, and international organizations. It may be necessary to re-think NMFS’ 

current organizational structures to facilitate collaboration, communication, and data-sharing. 

Partnerships may be useful in obtaining funding for new initiatives, and to ensure the necessary 

funding consistency to support long-term research projects. 

Finally, it is essential that NMFS efficiently communicate study results to researchers, 

management, and public in a way that addresses their concerns, demonstrates their connection to 

the resource, and is relevant and useful. 

1. What characteristics should a region-specific, national program have for this EAM 

theme? 

NOAA should create knowledge and procedures to make better informed decisions about 

protected species. These should take into account the species position in the ecosystem. For 

example, NOAA accounts for direct fishing impact on protected species through bycatch 

mitigation, but does not generally analyze the effect that fishing has on the prey of the protected 

species. Moving to this perspective will involve additional monitoring and process studies, and 

involve the development of new knowledge (models). It must encompass the public wherever 

possible and be presented in a way that encourages a “well informed public that acts as a steward 

of coastal and marine ecosystems.” It will necessitate coordination between groups within the 

science centers, within NOAA, with other Federal and state agencies, and with NGOs and 

stakeholders including the public. 

Development of these new procedures should begin with a baseline document describing the 

ecosystem, the protected species, and how these relate to each other. It should clearly identify 

what we do and do not know. It should clearly state the management goals, and be written in a 

non-technical way to engage a broad coalition of scientists, managers, and stakeholders. 

Facilitator: Salvini 

Science Chair: Swartz 

Participants: Balance, Coyle, Cunningham, DiGiovanni, Forst, Gulland, Hohn, McClure, 

Mesnick, Moy, Ogden, Pershing, Ruckelshaus, Schroeder, Schwacke, Thomas, 

Wabnitz, Ward, Wilkin 
15

Long-term monitoring programs are essential for any ecosystem approach to management. For a 

protected species, this has traditionally meant surveying for abundance, although recently, 

surveys have expanded to include distribution, stock structure, diet, and health. A truly 

ecosystem approach to management will require monitoring the quality of the protected species’ 

environment, including physical and chemical conditions and the abundance of predators and 

prey. Monitoring should also consider anthropogenic and other perturbations to protected 

populations including fishing, habitat destruction, disease, climate variability, pollutants, and 

noise. Long term monitoring requires stability, both in the sense of funding, and also 

methodology and data management. Detailed process studies are also needed and should be a 

regular part of protected species studies. These process studies provide depth of knowledge and 

should be responsive to management needs. They will also require development of new 

technology to improve our knowledge and ability to monitor protected species. 

Data from monitoring programs must eventually be used to guide decision making. Ecosystem 

based management models are needed that provide a formal representation of our knowledge of 

the species or ecosystem in question. Models provide a quantitative way to evaluate 

management options and can synthesize multiple data sources to provide better estimates of 

stock abundance. The modeling process should be transparent, with open access to code, 

documentation, and test cases. Because our knowledge is constantly changing as new data 

become available, it is essential that models be periodically revisited to assess their accuracy and 

ability to represent the system or process in question. Finally, models are never perfect, and it is 

vital that we quantify uncertainty and that this uncertainty is transmitted to decision makers. 

There are also issues of scale which need to be addressed: 

• NOAA has defined 8 Regional Marine Ecosystems (RMEs; Fig. 1). While the decision of 

demarcation was difficult, these RMEs are thought to adequately represent unique 

ecosystems, recognizing that each includes sub-units. The issue of what management area is 

too big to be managed or too small to be significant to the species in question is difficult. 

NOAA is now pursuing defining small regions within each RME to be more representative of 

“unique” areas within RMEs. 

• Many protected species migrate through multiple RMEs and rely on resources within each 

(e.g., feeding and breeding areas and migration routes). This is true for salmon, whales, 

turtles which are transboundary, and do not fit very well in the proposed NOAA ecosystem 

model 

The ecosystem approaches to management of protected species need to include all the 

components of ecosystems on which the protected species rely. Systems need to reach a state 

where they are not “out of balance” with respect to resource requirements for protected species. 

If a protected species recovers, the species and its habitats will need to be managed for 

sustainability. This presents potential problems with recovered populations that exceed the 

capacity of their ecosystems to support them. Culling is not popular, and historically has not 

been based on a complete understanding of the complex dynamics and relationships within the 

ecosystems in question. Management must apply to all aspects of ecosystem equally. 

Management should not focus on only some focal species at the expense of others in the 

community. While people care about marine mammals, sea turtles, and seabirds and these often 
16

are the focus of public concerns, other community species are equally at risk and are important 

within the ecosystem. 

When management action is taken, follow-up monitoring is necessary to quantify efficacy. 

Certain systems and actions may provide unique opportunities to design management actions as 

experiments. 

An ecosystem approach to management will require extensive collaboration and coordination. 

On the research and monitoring side, it is essential that NOAA scientists coordinate and 

collaborate with researchers in NOAA Line Offices, other federal and state agencies, NGOs, and 

academia. Coordination is also essential on the management side and will require 

communication within NOAA, with other Federal agencies, with fishery management councils, 

and with states and local governments. Finally, it is important to engage stakeholders, including 

the general public, in the process of monitoring, studying, and managing protected species. 

Opportunities for citizen science or cooperative research with fishermen should be encouraged. 

Results should be communicated to the public in an accessible format (e.g. regular “Ecosystem 

Considerations” reports as companion documents to fish or protected species stock assessment 

reports). 

2. Are there appropriate experiences worldwide that demonstrate how this theme can 

inform ecosystem-based protected species management? 

For NOAA’s Eastern Tropical Pacific Tuna/Dolphin Ecosystem Observation Program (ETP), the 

program driver is the Congressional mandate for information on the status on ETP dolphins. The 

core data collection effort supports an abundance estimate, which defines how the vessel surveys 

will be designed and the study area to be included. Additional ecosystem sampling then must 

conform to this survey design on a space available basis to maximize research opportunities. 

In the Northeast Region, protected species research has been conducted independently of 

fisheries studies (e.g., the semi-annual bottom trawl surveys). However, protected species 

abundance surveys in the Northeast collect a variety of data on the physical and biological 

oceanography along the track lines. Recent studies have also included dedicated seabird 

observers. Despite the expanded data collection effort, integration of these additional data into 

the assessments remains awkward. 

Pacific Northwest salmon population recovery actions & programs are good examples of 

approaches that obtain the necessary data on physical, biological, chemical, and socio-economic 

aspects for successful conservation. While many salmon stocks have yet to recover, the 

approach has been comprehensive and adequate to maintain most stocks even at low levels. 

As the preceding suggests, many of the NOAA Fisheries’ Science Centers (perhaps all) have 

made considerable progress in expanding the scope of the data collection effort to include 

ecosystem information. This has required better integration and coordination of survey designs 

between collaborators, development of tighter networks for data acquisition and exchange, and 

agreement upon spatial and temporal sampling scales. 
17

Similar problems will be encountered when incorporating terrestrial information into protected 

species ecosystem assessments. For most terrestrial ecosystems (e.g., coastal wetlands, etc) there 

is no one source for all the information needed. This is partly the result of overlapping 

jurisdictions. 

Examples of broad ecosystem approaches in a terrestrial context include the: 

• Nature Conservancy’s eco-regional planning program, 

• Pew strategy program, and their “Land Reserves” program 

• UK’s Royal Society for Protection of Birds which protects single species by managing their 

ecosystems and all their components based on the requirement of the birds 

• US National Audubon Society’s annual breeding bird survey which collects a nation-wide 

data set by volunteers. 

Examples in marine systems include: 

• Coral Reef diver’s organizations to collect data on reef communities and status. 

• Whale watching operators for information on whale location. 

• Citizen scientists (e.g., “environmental stewardship” programs) can potentially provide 

useful ecosystem data. Pelagic environments present other problems for volunteers and 

citizen observers because of the remote nature of these environments and difficult logistics 

(e.g., require large vessels). 

• Fishermen could also potentially collect environmental and ecosystem information (e.g., 

water samples for domoic acid testing) provided that specific collection instructions and 

sampling protocols are provided and complete information is obtained (e.g. location, day, 

time, depth, etc.). 

3. What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision making? 

Protected species studies having an ecosystem component will require a new approach to the 

species management paradigm, including an ecosystem approach to data collection and analysis. 

Both broad scale and fine studies will be required, for example, health assessment monitoring 

would need to include both scanning and targeted surveillance. Data needs will have to be 

identified at both a species and Regional Ecosystem level, and then prioritized. 

More attention will need to be placed on information systems and data management. 

Specifically, metadata standards need to be established, data sharing agreements and structure to 

facilitate data sharing need to be crafted, dedicated database managers need to be assigned, and 

databases need to be linked to GIS and models for further analysis. 

Further development is needed for EAM. In-house modeling capacity at the Centers needs to be 

strengthened. Risk-based models with probabilistic output should be developed to support 

management, and more attention should be paid to modeling experience from other disciplines 

and environments (terrestrial, economics, climates, disease, acoustic), including integration of 
18

existing complementary models (e.g., biochemical and trophic). Finally, criteria need to be 

established for validating models. 

4. Based on the above, what changes in policy, governance or science administration are 

required to more effectively inform ecosystem approaches to protected species 

management?

A first step will be for NOAA to deal with changes that are achievable within the next few years: 

• Construction of a “big-picture” document or knowledge inventory for each LME to include: 

identification of protected species occurring in the LME; general description of the physical 

and biological environments and other apex predators; identification of existing datasets and 

ongoing research activities, and research needs 

• Implementation of a NOAA Fisheries intranet site (integrated with and across Science 

Centers and Headquarters) to facilitate communication of opportunities and ongoing research 

• Establishment of a Seminar series highlighting multiple projects within a single ecosystem 

• Hosting of a NCEAS-style workshop to identify datasets, research needs, and ongoing 

projects with overlapping interests 

• Support of sabbaticals to allow scientists to interact with researchers involved in different 

disciplines and/or ecosystems 

• Increased opportunities for short-term rotational assignments 

• Increased use of existing opportunities to bring in visiting scholars (e.g. NRC Post-docs) 

• Formalization of partnerships across Centers of Excellence, both within the agency, and 

between other government agencies, academic institutions, and NGOs, so that individual 

scientists do not have to create those partnerships on their own. (Examples: Marine Mammal 

Health and Stranding Program with science centers and regions) 

NOAA should subsequently address permanent institutional changes which need to be made to 

incorporate EAM into daily business of the Agency. Because EAM is based on long-term 

monitoring of components of entire ecosystems, a long-term permanent source of funding is 

required. Clear prioritization of research needs (e.g. which components of the ecosystem will be 

monitored and what metrics for each will be used) is critical. 

The current PPBES structure funnels funding for EAM through three programs. The benefits of 

such an approach is that if one source is reduced, certain aspects of the research can continue. 

The costs are that piecemeal funding may lead to false assumptions that reducing the funding 

from any one program will not severely affect the research of other programs. To maintain 

current funding levels and then strategize on increasing funds, NOAA needs to combine efforts 

to improve visibility to Congressionals and constituents. 

Better communications are needed within NOAA Fisheries, between NOAA Line Offices and 

other government agencies, and with academia and NGOs. Within the Science Centers, there are 

divisions that prevent EAM. For example, staff may be organized around taxonomic groups 

rather than around LMEs. Science Centers are often disconnected geographically and 

informationally from their respective Regional Offices. A similar lack of communication occurs 

between the Science Centers and Headquarters. 
19

 

Possible remedies include: 

• an internal grants program with preference for multidisciplinary participation 

• more integrated websites 

• new positions within the Science Centers with their primary functions being to filter 

information from various levels to the appropriate individuals (for example, a liaison position 

designed to identify and facilitate communication between persons involved in research in 

the same Regional Ecosystems, or to communicate research and funding needs between a 

particular Science Center and Headquarters) 

• Internal reorganization of Center science along Ecosystem lines 

NOAA also needs to formalize its partnerships. EAM by definition requires integration between 

scientists and researchers representing a vast range of disciplinary and taxonomic expertise. 

Rather than re-inventing the wheel at each Science Center, we suggest identification of “Centers 

of Excellence” for those disciplines and taxa that are essential for effective EAM in each 

Regional Ecosystem. Centers of Excellence can be located in other federal or state agencies, in 

NGOs, or in academia. For example, most Science Center are already allied with an adjacent 

university. Because EAM requires knowledge of the physical and biological oceanography in 

each Regional Ecosystem, NOAA scientists involved in EAM could partner with oceanographers 

in these universities to obtain the necessary data, rather than hiring their own cadre of 

oceanographers. 
20

C. Working Group 3: Ecosystem Based Stock Assessments For Protected Species 

Stock assessment refers to the synthesis of information to provide management advice. Often 

that synthesis involves quantitative models, but qualitative information is also relevant. 

Ecosystem-based stock assessment for protected resources therefore refers to those stock 

assessments that serve as the scientific basis for the management of protected species and include 

ecosystem considerations such as physical habitat, trophic and other biological interactions, 

pollutants, anthropogenic noise, disease, etc. 

Ecosystem-based stock assessments cover a wide range, both in terms of the degree to which 

ecosystem data are included (Appendix Table 2) and the degree to which quantitative models are 

used to provide a synthesis of available information. The first step in ecosystem-based 

assessments is the use of ecosystem information to augment or enrich the interpretation of a 

single-species stock assessment. At the other extreme are models of entire ecosystems that 

include trophic interactions of all major components of the ecosystem and geo-chemical factors 

that affect these components. We include this full range of assessments in our consideration of 

ecosystem-based stock assessment. 

Three guiding principles should be recognized in all assessments: 

• ecosystems include interactions among many components, and extracting any component 

from an ecosystem can be expected to affect the other components, 

• ecosystem interactions are complex, and there will always be considerable uncertainty in 

predicting indirect effects on other elements of the system, and 

• ecosystems may change abruptly from one domain or stable state to another; these changes 

may not be predictable and may not be reversible on a decadal time scale. 

Management advice from ecosystem assessments should emphasize these considerations. 

1. What characteristics should a region-specific, national program have for this EAM 

theme? 

To be most effective, a national program for incorporating ecosystem dimensions into protected 

resources assessments should have a region-specific focus. Moreover, it is likely that a variety 

of spatial scales will be appropriate when defining such regions. The eight Regional Ecosystems 

that NOAA has identified describe relevant regions at the broad scale. But within these Regional 

Ecosystems (two of which are considered LME “complexes” that encompass several diverse 

marine ecosystems), it would be desirable to define smaller areas defined by their ecological 

structure. Such “ecoregions” are likely to have a spatial extent of tens to hundreds of kilometers. 

Facilitator: Valette-Silver 

Science Chair: Palka, Ragen 

Participants: Abbott, Baker, Barlow, Bengtson, Chaloupka, Cornish, Eagle, Garrison, 

Lawson, Merrick, Rice, Rosel, Seminoff, Stenson 
21

They may be characterized by physical and biological features such as bathymetry, physical 

oceanography, biological productivity, and biodiversity. It is expected that defining ecological 

subregions within LMEs will facilitate ecosystem-based assessments by organizing both the 

implementation and coordination of research and monitoring programs around ecological 

criteria. 

A national program must have clear goals, be flexible, and be adaptive. The goals should be 

realistic under the time frames both for stock assessments and for ecosystem reviews. The 

national program should include: 

• A structure which breaks down barriers within Centers and between agencies, thereby 

facilitating coordinated, efficient ecosystem based stock assessments 

• Shared information systems 

• A communication process that ensures dissemination of data and ideas between different 

scientific disciplines, and between scientists, managers, decision makers, and the public 

• Staff that are knowledgeable of the EAM focus 

• A data collection program to gather new data on the various important components of the 

ecosystem at the frequency and scale necessary to adequately detect changes, when these occur. 

• Fora to discuss allocation among stakeholders (i.e., fishing industry, oil and gas, point source 

pollutant producers, etc.), and to review science and develop mitigation measures 

Ecosystem based assessments should be: 

• Multi-disciplinary and include appropriate biotic and abiotic factors, Allele and behavioral 

effects (if appropriate), anthropogenic interactions, and impacts that are acute (bycatch) and 

chronic (disease, pollutants). 

• Explicitly include the target species, if possible. 

• Simple, explainable, and effective. 

• Robust to data-poor areas and species. 

• Both quantitative and qualitative. 

• Based on standardized terms and approaches for different parts of ecosystem research. 

• Explicitly designed to deal with uncertainties, and include sensitivity analyses. 

• Designed to include studies of the impacts of single/multiple stressors on the species (or area) 

of interest; utilize both top-down components (e.g., region-specific ecosystem review) and 

bottom-up components (e.g., enriched single species stock assessment); and use the most 

appropriate model (within the single species to bio-geochemical ecosystem modeling continuum) 

for the species/area of interest. 

• Include a control law that builds upon the existing control laws and also explicitly 

incorporates ecosystem attributes. 

2. Are there appropriate experiences worldwide that demonstrate how this theme can 

inform ecosystem-based protected species management? 

There are a number of examples worldwide of incorporating ecosystem information into 

assessments and advice on management of marine populations. Many of the best cases are not of 

protected species but, as noted elsewhere, address ecosystem considerations which are generic to 
22

all aquatic species and populations, and not specifically to protected species. Hence, insights can 

be gained from successes with ecosystem assessments of many types of species. 

As described in the introduction, we define “assessments” as including more than just 

quantitative models of the dynamics of a population or aggregate of populations. There are both 

narrative and analytical components to an “assessment” and to the advice therein derived. 

Specific examples range from assessments that are largely narrative with very modest 

quantitative content to assessments which are heavily analytical and are associated with minimal 

text. With regard to successful examples of bringing ecosystem content into the analytical 

aspects of assessments, cases are presented here for several of the increasingly complex types of 

“analytical assessments.” 

“Enriched” Single-species Assessment Models 

These are stock assessment models designed to quantify the historic trajectory, current status and 

trend of species or stocks, and usually include short to medium term projections of a species’ or 

stock’s abundance. These models usually include as dynamic components (i.e. functional 

relationships are specified and parameterized) the effects of physical forces on population 

productivity (recruitment, growth or both) and first-order predator and prey linkages. The 

predator-prey linkages may be reflected in estimates of predation mortality, or in estimates of 

growth, maturity, fecundity or starvation due to the variability of prey species’ abundance. 

There are many examples of “enriched” single-species models, for example Barents Sea cod 

(both water temperature and prey availability captured dynamically), Baltic Sea cod (effects of 

salinity and dissolved oxygen levels on recruitment), sardine and anchovy stocks in Iberian 

waters (related to upwelling), and various capelin assessments (predation mortality). The 

Convention for the Conservation of Antarctic Marine Living Resources (CCAMLR) assessments 

of krill also includes predation mortality. The ETP tuna-dolphin model is another enriched 

single-species model, incorporating oceanographic forcing and other factors. In all of these 

cases the analytical model results may be directly incorporated into the scientific advice for 

management of the stocks, or used to provide insight into alternative options for management. 

Multi-species Assessment models 

These are assessments where a number of interacting predators and prey are linked dynamically, 

so increases in predators affect the mortality rate of their prey. In some cases, the effects are 

reciprocal, such that increases in prey affect growth and fecundity of predators; in other uses, it is 

assumed that prey included in the model obtain their energy from other prey not being explicitly 

modeled. 

The most widely used multispecies model has been the Multispecies-Virtual Population Analysis 

(MSVPA), used in the North Sea and Baltic Sea to estimate predation mortality. These estimates 

are then transferred as the natural mortality parameters of single species models of each of the 

species in the MSVPA. MSVPA has been used in the Barents Sea and Icelandic waters, and in 

both cases marine mammal predators are included explicitly. Custom-made multi-species 

models were also developed for the Benguela Current system; in this model, predation by marine 
23

mammals was a core dynamic relationship. As is commonly the case, this application of a multispecies model is used to inform management strategies rather than as a basis for annual harvest 

advice. Multispecies models, including MSVPA and other custom-made models were also 

effective in exploring relationships between Steller sea lions and Bering Sea walleye pollock, 

and informing management decisions about the walleye pollock fishery. 

Trophodynamic Models

Various trophodynamic models have been used to explore dynamic relationships among 

predators and prey, covering multiple trophic levels. Yields to harvesters and effects of physical 

forcing factors have often been included in these models. 

There are well over 150 applications of Ecopath to marine systems, and other mass-balance 

models have also been employed. These models have been are used primarily for scenario 

exploration and to gain qualitative insight into effects of different management strategies. There 

are very few cases where serve as a basis for quantitative harvest advice. References are 

available from the University of British Columbia Fisheries Centre (www.fisheries.ubc.ca) and 

The Sea Around Us (www.seaaroundus.org)websites. 

There have also been a number of size-based rather than species-based models of 

trophodynamics of interacting predators and prey. These models tend to include fewer trophic 

levels, and species – including protected species – are not represented explicitly, limiting the 

utility of these models as a source of advice for protected species. However, the models tend to 

be easily parameterized in systematic and rigorous ways, more readily constrained by available 

data, and can provide very useful results. They are in early stages of application as tools for 

evaluating management strategies in an ecosystem context, but are promising. 

 

Several efforts have been made to develop multiple, independent and structurally different 

ecosystem models for the same system for “ensemble forecasts”. These efforts are not intended 

to be actual assessments of the component species (or species groups), but rather identify system 

dynamics important to capture in much simpler assessment models, and to illustrate robustness 

of alternative management strategies to uncertainties about ecosystem structures and functions. 

The Atlantis model (Fulton et al. 2003) captures relationships among multiple trophic levels and 

effects of environmental forcing. Atlantis is not intended to be a basis for the annual (or regular) 

assessment process, but is used to evaluate the robustness of management strategies to 

uncertainties concerning relationships among ecosystem components and future states of nature. 

Using trophodynamic models, CCAMLR has explored many potential approaches for evaluating 

and testing robustness of management strategies. CCAMLR has several mechanisms for 

incorporating an “ecosystem approach” into fisheries management and conservation efforts in 

the Antarctic, although many involve data collection and harvest control rules rather than 

assessment models. The CCAMLR Ecosystem Monitoring Program (CEMP) monitors seabird 

and marine mammal status (e.g., abundance, reproductive success, vital rates, foraging ecology) 

to: 1) detect changes in key bird and mammal population parameters over time (i.e., to identify 

ecological changes within the marine ecosystem), and 2) differentiate between natural and 
24

anthropogenic (e.g., indirect effects of commercial fisheries) effects on the marine ecosystem 

(i.e., using protected resources as indicator species). 

The International Whaling Commission (IWC) also uses models with multi-species dynamics, 

and has several types of forcing functions. The IWC assessment models have a variety of levels 

of ecosystem content, reflecting variable levels of knowledge and information. The models are 

designed to test the robustness of harvest control rule and to provide a quantitative basis for 

advice on stock recovery potential (and possible trajectories), and harvests. 

Full bio-geo-chemical ecosystem models

The Everglades model (e.g., deAngelis and Cornutt 2002) builds all the way from basic primary 

productivity driven by nutrients and physical conditions to individually-based models (IBMs). It 

is a conspicuous success, but the costs (dollars and scientific expert time) for development and 

ongoing operations make it a challenging model to replicate. 

The Puget Sound Collective has model development as one aspect of its activities, and addresses 

problems similar in scope and complexity to those of the deAngelis Everglades team. The 

Collective’s approach is much “softer” and more qualitative, but still requires expertise from 

many sources (both formal science disciplines and types of experiential knowledge). Progress is 

faster, but the quantitative content of the results is not nearly as high. The resultant “models” are 

useful for interactive scenario exploration, but less so for formal testing of robustness of 

management strategies. 

Another activity in which ecosystems are considered is the evaluation process of ecocertification as developed by the Marine Stewardship Council (MSC; www.msc.org). The MSC 

process is a rigorous and systematic procedure for ensuring that the full range of ecosystem 

considerations are addressed in evaluating the status and the effectiveness of management 

actions. The MSC evaluation process addresses a large number of ecosystem factors, including 

environmental forcing, predator and prey relationships, and fishery effects on non-target species 

and habitats. Although the MSC’s evaluation of a fishery is not the same as evaluating the status 

of a protected species, the approach is comprehensive and operational, and there may be many 

useful lessons to be learned from the process. 

3. What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision making? 

Research and Data Requirements

 

Research and data collection to support ecosystem based stock assessments should relate to one 

of NOAA Fisheries’ three legislative mandates: Marine Mammal Protection Act, Endangered 

Species Act, or Magnusson-Stevens Fishery Conservation and Management Act. As such, the 

output of EAM needs to be augmented assessments. These assessments should include a broad 

range of biotic or abiotic factors into the assessment framework, and the outcomes need to be the 

delivery of scientific advice to the management decision processes. EAM assessments should 

include traditional single-species scientific advice, but also consider that 1) extracting resources 
25

from any systems affects other elements of the system, 2) these are complex systems and there 

will always be uncertainty in predictions about them, and 3) ecosystems changes may include 

abrupt state changes, that often do not reverse quickly. Research and data collection to support 

EAM should explicitly incorporate uncertainty and provide advice as to how uncertainty is 

treated in assessments and management advice. Finally, although these comments are directed 

toward Protected Resources, there is nothing unique in these suggestions. 

A number of initial steps can be made prior to the initiation of an EAM program using 

information now available. The first group of activities can be accomplished with research and 

data programs that presently exist within Protected Resources: 

• There needs to be an initial review of existing information. 

• This would lead to data inventories of accessible data and metadata. 

• Equally important we need to identify what we don’t know. It is imperative to get basic 

fundamental information on poorly characterized stocks. Stock structure, abundance, 

distribution, and trends need to be elevated to Tier II levels. 

• There needs to be a synthesis of current research efforts. We need synthesis papers 1) that 

examine why certain stocks have failed to recover while others have, as well as 2) process 

case studies of indirect ecosystem impacts, and 3) case studies of ecosystem state changes. 

• EAM research and data collection programs need to develop research program review 

structures, and must include periodic outside reviews. 

• A system should be developed to codify best practices about how to transfer knowledge from 

one area to another. Again, a need exists to inventory data and metadata. 

• We should review data on the distribution in space and magnitude of diverse human activities 

on the seas, on coastal boundaries, and terrestrial systems. 

• There needs to be a review of data on human demography, distribution, and resource needs. 

• Abiotic data needs to be collected for thermal components of marine and terrestrial systems. 

Appendix V includes a list of research topics identified by the working group. 

Models

Incorporating ecosystem considerations into assessment models primarily involves increasing the 

complexity of models (i.e., adding parameters), thereby increasing the uncertainty in both model 

outcomes and data demands. Ecosystem approaches to fisheries assessment have proceeded 

along a gradient of increasing complexity from the single species approaches (where all 

processes except for fisheries removals are implicit in a small number of parameters) to 

trophodynamic and biogeochemical models (which attempt to model energetic flows and 

environmental forcing among multiple ecosystem components and across trophic levels and 

scales). Generally, the increased complexity of these models requires greater aggregation of 

nodes and processes such that the specificity of management advice declines. Therefore, for 

assessing the dynamics and status of specific species and/or stocks, models best categorized as 

“augmented” single species approaches are likely to be the most tractable. Ideally, this 

augmented model structure will be standardized across species (and perhaps species groups) so 

as to create, at least conceptually, consistency in the methods used to assess and manage 

protected species within an ecosystem context. 
26

The majority of fisheries based augmented and multispecies assessment tools have focused on 

understanding trophic dynamics so as to improve estimates of predation mortality and identify 

potential linkages between commercially exploited and non-target species. However, for many 

protected species, trophic dynamics will not be the primary factor limiting population dynamics 

and recovery. Likewise, many protected species do not play a significant energetic role in their 

ecosystems. A suite of processes including disease, exposure to persistent organic pollutants, 

toxicity due to algal blooms, exposure to noise, and other factors are important acute and chronic 

stressors. Significant research and model development efforts will be required to incorporate 

these environmental effects into assessments. As well, there will be increased data demands to 

understand population-level effects of chronic and acute exposure to environmental stressors. 

Spatially explicit and habitat based models will also be important for assessing risks and 

environmental impacts on protected species stocks. To some extent, this need for improved 

understanding of fine-scale spatial patterning is incorporated in existing standards for Tier II 

assessments. However, it will also be important to relate population movements to exposure to 

various stressors. For example, large scale migratory movements of calving right whales may 

increase their exposure to vessel strikes. Seasonal residence of bottlenose dolphins inside of 

estuaries may increase exposure to pollutants and toxins arising from terrestrial sources. Thus, 

linking movements and habitat use to exposure to risks will be an important added component of 

assessment models. 

No single model framework will be sufficient to incorporate all extant data and serve as the best 

mechanism to represent all important processes. Therefore, an ensemble approach to assessment 

using multiple model types may be a more appropriate framework. This is consistent with many 

of the larger ecosystem approaches where multiple, independent models have been developed 

and applied to the same system. Evaluating the performance and uncertainty associated with 

different models may improve the understanding of the system, identify major processes, and 

highlight critical data gaps. 

Ultimately, assessment models enhanced by ecosystem considerations should result in clearly 

defined control rules to inform management decisions. Several basic principles should guide the 

development of this framework. First, models and the control rules they support should have an 

explicit approach for dealing with uncertainty in model structure, data limitations, and process 

variability. Second, formal procedures should be developed to verify model/control rule 

performance including simulation studies and sensitivity analyses. Third, recognizing that some 

processes can only be dealt with through qualitative assessment and advice, there should be a 

specific decision support framework for incorporating information into assessments, control 

rules, and management decisions. The assessment framework should explicitly identify the 

qualitative components of the management advice and how they should be incorporated into 

decision rules. A Bayesian risk assessment framework will be likely be a fruitful approach for 

augmented assessment tools; however, there are a variety of decision support approaches that are 

available across multiple disciplines. 
27

Information systems

Expanding the scope of assessment models necessitates the use and integration of additional 

data. The majority of these data cannot be collected within the framework of a “protected 

species” focused program. This is particularly the case with data derived from remote sensing, 

data on pollution sources, land use information, etc. However, these data collection programs do 

exist within other line offices of NOAA, in other federal and state agencies, and in academic 

institutions. Thus, a core goal of a developing an ecosystem assessment program should be the 

development of information systems which will facilitate warehousing, exchange, and access to a 

broad suite of environmental data. Further, collaborations across institutional boundaries must 

be developed to allow a more diverse suite of expertise to be actively involved in the assessment 

process. 

As the scope of users will expand under EAM, it is essential that information systems contain 

appropriate and standardized metadata to allow the effective search, download, and use by a 

range of users. Likewise, for each data type or monitoring program, a codified set of best 

practices should be developed so that data quality is well understood. 

The primary goal of the information management system is to facilitate access and sharing of 

collected data across line offices and institutions. Some attention must be focused on the 

effective translation of information to managers and on access to information to support risk 

assessments or decision rules. A unified information management system would therefore 

include not only data inputs for assessment models, but would also facilitate access to and 

exploration of outputs. 

4. What changes in policy, governance or science administration are required to more 

effectively inform ecosystem approaches to protected species management? 

The current mandates of the MMPA and ESA, with respect to ecosystem-based management, 

compel us to move forward using existing knowledge. Rather than wait for an ecosystem-driven 

policy and governance structure, we have the components and drivers to implement EAM right 

now. 

The unique characteristics of an ecosystem-based protected species management program should 

be emphasized within any EAM document. However, such a document should also recognize 

the commonalities between research geared towards fisheries and protected species, and 

capitalize on these developing integrated ecosystem-based research programs. 

Public education should be considered when planning ecosystem-based research and 

management program, to elicit awareness and support for such programs. 

Policy

Policy level commitment to EAM is wide-spread and strong. The missing elements are clear 

structures and practices to implement policies. Some of these require, or would be facilitated by 
28

changes to legislation. Others require regulatory modifications, different emphases or 

modification of agency-level practices. 

Legislation: Identify and link language supporting EAM into existing statutes. For example, 

PBR could be expanded to include direct or indirect sublethal (chronic) effects. However, direct 

mortality is simple to assess compared to non-lethal stressors; thus, the two types of factors 

should not be easily mixed. 

Another approach would be to create a mixed body of stakeholders, scientists and managers (like 

a TRT) to account for all activities that affect protected species and design an overall approach to 

limit take or habitat modification that would allow protected species to remain functioning 

elements of their ecosystems. 

Regulations: Consolidate fishery management and protected species regulations to clarify the 

full range of requirements. 

In both regulations and explicit policy statements, specific guidance is needed for management 

practices. This guidance could be developed using simple, transparent support rules for 

ecosystem considerations that explicitly consider uncertainty. If feasible, such rules should be 

incorporated directly into statutes. The issue of rights versus privileges is important in granting 

access to resources or governance of resources. 

Agency-level changes in practice include greater use of qualitative information in decision 

making using more risk averse strategies (accept a lower standard of evidence for supporting 

protective measures), and thinking in terms of aggregate rather than cumulative impacts. The 

latter would remove the constraint that the last resource user in the ecosystem has to use existing 

levels of take or modification as a baseline. Rather, an ecosystem advisory body would consider 

the aggregate effects of all potential users in the affected areas. 

Policies and practices need to address human elements in the ecosystem. Humans clearly affect 

other components of ecosystems and are, in turn, affected by other components. Human 

behavior and cultural factors also need to be incorporated in the EAM. 

Governance 

The concept of a Marine Ecosystem Council was proposed as the ideal governance instrument by 

which all of the current species-based governance structures (e.g., Fishery Management Councils 

[FMC], Take Reduction Teams [TRT]) would be overseen (and perhaps even subsumed). This 

would allow for better integration and incorporation of ecosystem-based principles in actual 

practice. 

Recognizing that there may be considerable resistance to a new governance structure, a more 

pragmatic recommendation was for the current species-based structures to have broader 

representation from all ecosystem components. For example, protected species and habitat 

representatives would serve as active members of Fishery Management Councils. 
29

The group also strongly encouraged expanding the authority of current protected species-based 

governance structures (such as TRTs) so that they have a broader stewardship mandate and a 

broader group of stakeholders. This was in recognition that “objectives-based management” is 

now widely accepted, but in practice there are few fora for reconciling objectives across multiple 

interest groups and industries/communities. In the case of Alaska, there are currently no TRTs 

from which to build this type of structure, therefore, an alternate forum would need to be 

implemented there. 

There needs to be a clarification between central and regional roles in existing governance 

structures, and a mechanism should be developed for funding critical governance structures and 

operations, such as observer programs and enforcement. 

Science Administration - Structure and Execution

Implementing EAM will mean that institutional inertia in NOAA Fisheries must be overcome. 

To do so, a clear mandate and directive is required from HQ to the Science Center Directors 

regarding the need to conduct ecosystem/integrative research. In turn, Center Directors must 

structure their Centers’ scientific enterprise to facilitate ecosystem studies. This will involve 

budgets, personnel, ship time, and external partnerships. There should also be a coordinated 

information system support across Center organizational units. 

The above process will necessarily involve eliminating barriers between PR, Fisheries, habitat, 

and oceanographic researchers and then bringing them together to conduct Ecosystem 

Assessments (will also likely include State, FWS and others). This could involve multidisciplinary task forces/working groups to address areas rather than species groups. 

Success stories exist in fully integrated priority and objective setting, knowledge integration, 

planning and management (i.e. Puget Sound salmon example). Recognizing that the science and 

communication overhead to make these efforts work is huge, and cannot be replicated for all 

species and areas, there is a need to develop ways to transfer lessons learned without duplicating 

efforts each time. Along the same lines, NOAA should look to other agencies that have 

attempted to implement EAM, and learn about their experiences. 

Review/Evaluation 

The group recognized that evaluation of ecosystem assessments is an important element. One 

aspect of this is an honest and transparent accounting of the costs for conducting such 

assessments. While these may be high, it was noted that integrated research would likely involve 

cost efficiencies compared to independent studies. 

Two suggestions were offered for reviewing ecosystem science. The first was to create a forum 

for reviewing ecosystem assessments akin to the MMPA’s Scientific Review Groups. Another 

suggestion was to hold multi-disciplinary workshops/conferences into people working on various 

aspects in the same or similar ecosystems to facilitate exchange of data, develop partnerships 

and provide peer review. 
30

Other Issues

It was agreed that a great need exists to ensure that science for supporting management 

(including ecosystem science) is independent (not biased toward pre-determined outcomes). 

Finally, there was a suggestion based on the Canadian experience that there should be just “one 

window” for science advice for all NOAA clients (fisheries, protected resources, sanctuaries, 

etc.) to ensure a consistent message. 
31

D. Working Group 4: Governance-Incorporating EAM for Protected Species 

1. What characteristics should a region-specific, national program have for this EAM 

theme have? 

Vision

A governance system that sustains and nurtures healthy and productive ecosystems by managing 

the impact of human activities on ecosystems while taking into account natural variation and 

change in the systems. 

Goal 

Create a governance framework supporting the vision [allowing for input and integration of 

information to make decisions] with the following characteristics: 

• Retain the authority of existing legal mandates (including, but not limited to ESA, MSA, 

MMPA, NMSA); 

• Emphasize a precautionary approach to management in response to uncertainty at various 

levels; 

• Maintain a healthy and productive ecosystem while allowing sustainable use; 

• Manage in a “placed-based” fashion, focusing on issues/threats to the ecosystem, rather than 

species-specific management; 

• Identify the scale of management units taking into consideration nested and transboundary 

ecosystem components; 

• Manage human activities to identify and separate conflicting uses and account for variability 

and patchiness within ecosystems (e.g., zoning); 

• Make proactive decisions using a NEPA-like process (i.e., examine broad social, economic, 

biological, and cumulative impacts prior to making management decisions); 

• Facilitate transparent communication of knowledge, experience, and the decision-making 

process; 

• Support collaboration between stakeholders/constituents and state, federal, and international 

agencies/governments; 

• Create synergy among groups resulting in improved cost effectiveness; 

• Support partnerships for joint management and research initiatives on national and 

international scales; 

• Recognize adaptive and incremental processes and be flexible enough to allow changes 

suggested by information acquired through process and outcome reviews; 

• Dedicate appropriate levels of funding for adequate durations, providing long-term and stable 

fiscal support required for cost-effective science and management; 

Facilitator: Kelty 

Science Chair: Gouveia, Payne 

Participants: Barnes, Bernhardt, English, Fahy, Hill, Jacobs-Spaulding, Kinan, Mengerink, 

Rusin, Scida, Simpkins, Thom, Trumble, Wakeford, Williams, Wilson, Yuen 
32

• Make science-based decisions using multidisciplinary information from social science, 

ecology, biology, oceanography, and climatology; 

• Address data needs through identification of data gaps, prioritization of data needs, data 

collection to address research questions and management needs, establishment of targets or 

thresholds, including precautionary targets for data poor components of an ecosystem; and 

monitoring and evaluation of EAM processes and outcomes. 

2. Are there appropriate experiences worldwide that demonstrate how this theme can 

inform ecosystem-based protected species management? 

The WG suggested that there were a number of good examples of EAM: 

Aleutian Islands Fishery Ecosystem Plan 

The North Pacific Fishery Management Council is considering preparing a Fishery Ecosystem 

Plan (FEP) for the Aleutian Islands region. This FEP would be a pilot initiative to begin the 

Council’s development of a process for ecosystem-based fishery management in the North 

Pacific. The FEP would describe the environmental processes of the Aleutian Islands ecosystem 

and how fisheries and fishery management interact with these processes. Initially, at least, the 

FEP would have no regulatory authority. Rather, the FEP would help the Council explicitly 

focus and consider ecosystem components when considering fishery management actions. 

 

Puget Sound Restoration Plan 

The Puget Sound region of Washington State has used a collaborative, multi-agency and public 

process to develop and implement a regional anadromous salmon recovery plan. The 

collaborative process created a non-profit group—the Shared Strategy—that coordinates and 

works with federal, tribal, state and local governments, and with interests from business, 

agriculture, forestry, fishing, conservation and the general public. Fourteen watershed groups 

plus a nearshore-marine group identified the actions to recover salmon and commitments needed 

to achieve them. They also worked with state and tribal co-managers to incorporate hatchery and 

harvest actions to ensure these are consistent with salmon recovery. The Puget Sound Technical 

Recovery Team (TRT) is an independent group of scientists that provided ESA delisting criteria 

and technical guidance for evaluating alternative sets of watershed- and regional-scale actions for 

the recovery plan. The Shared Strategy builds on assessments, processes, programs, and 

regulations already underway and knits them together into a comprehensive strategy to recover 

salmon at a regional scale. The regional consensus process ensured that the recovery plan 

ultimately reflected local needs and priorities while meeting ESA requirements. The plan was 

published in the Federal Register in January, 2006, and has broad support and a robust financing 

strategy. The Shared Strategy continues as a body to coordinate early funding priorities and 

implementation of the hatchery, harvest, and habitat actions outlined in the plan. 

The Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR)

CCAMLR was established in 1982 as part of the Antarctic Treaty System. Central to the 

Convention is Article II, which providers the three guiding principles of conservation for the 
33

conservation of Antarctic marine living resources: (a) prevention of declines in any harvested 

population to levels below those which ensure stable recruitment; (b) maintenance of ecological 

relationships between harvested, dependent and related populations, and (c) prevention of 

changes or minimization of the risk of changes in the marine ecosystem which are not potentially 

reversible over two or three decades. 

CCAMLR approached the first and last parts of Article II by applying standard fisheries 

management techniques to Antarctic problems. A working group on Fish Stock Assessment was 

created in 1984 and one on Krill in 1986. The second part of Article II, the ‘ecosystems 

approach’ required the development in 1985 of an Ecosystem Monitoring Program for the 

Antarctic marine environment which involves monitoring selected predator, prey and 

environmental indicators of ecosystem performance. The aim of the program is to detect changes 

in these indicators and evaluate whether these changes are due to natural events or harvesting 

activities. 

3. What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision making? 

There is a major need for a better Decision Support System (including relevant models). 

Such a System should: (a) provide a framework for incorporating science into decision-making; 

(b) facilitate the evaluation of alternative sets of ecosystem management strategies using 

conceptual and quantitative ecological and socioeconomic models; and (c) provide a set of 

scientific tools that help policy makers identify and minimize potential conflicts (Mangel 2000). 

The complexity of managing an ecosystem requires a decision-support system that relates the 

ecological and socioeconomic consequences of potential specific management actions to broader 

policy goals. Sainsbury et al. (2000) coined the phrase Management Strategy Evaluation (Fig. 2) 

to describe a decision-support system that uses the following elements: 

• Evaluate the status of the system being managed as a whole (not just isolated parts); 

• Specify policy objectives and performance measures that are connected to those objectives; 

• Relate alternative management strategies to predicted changes in the performance measures; 

• Monitor the system; and 

• Provide for iterative decision making that is based on data from the monitoring program. 

This formal adaptive-management approach can be used to investigate the consequences of a 

variety of scenarios derived from a range of models. The approach is designed to enable 

decisions in data poor environments, and can be transparent and collaborative if resource 

managers and stakeholders have input into selecting candidate models and management 

scenarios. The approach encourages all participants to be explicit about their goals, and helps 

make the decision-making process more transparent to the public. 

Building a decision-support system requires both scientific and policy inputs, with the two 

spheres interacting as the framework is developed and implemented. A formal decision-support 

system contributes to the transparency of making management decisions and encourages a 

collaborative process which strengthens the system. Formal modeling (conceptual and 
34

quantitative) of both the ecological and socioeconomic components of the ecosystem is an 

important element of a decision-support system. 

Figure 2. General framework for management strategy evaluation (Sainsbury et al. 2000) 

Such a system will require an inventory of partners, collaborators, stakeholders, and constituents 

within an ecosystem, including: 

• Who will participate? 

• Who will coordinate data collection and sharing? 

• What are the jurisdictions and authorities? 

• Who can take action? 

It will also require an information management system feeding the decision support system with 

data inputs, data and model output, and an identification and prioritization of data gaps. 

4. What changes in policy, governance or science administration are required to more 

effectively inform ecosystem approaches to protected species management? 

A functional governance structure for EAM must be developed. A variety of governance 

structures could provide adequate support for EAM (Appendix Table 3) but, in all cases, several 

crucial governance roles must be assigned to specific entities: 

• Setting a national vision and goal(s) for EAM 

• Setting national EAM policy (e.g., approved EAM measures, decision rules, required 

responses to “ecosystem problems,” and regional management and decision-making 

structures) 

• Collection and integration of scientific data necessary for EAM (e.g., conducting ecosystem 

studies, evaluating ecosystem health via decision rules) 
35

• Making EAM decisions regarding the need for action to address ecosystem problems and 

identifying agencies that must respond to problems 

• Implementation of EAM decisions 

• Monitoring and evaluation of the effectiveness of EAM implementation, including the 

decision-making process and the outcomes of management actions. 

As mentioned above, a decision support system will be necessary to support an EAM governance 

structure, and the support structure should be seamlessly integrated into the governance structure. 

Similarly, scientific advice and stakeholder input must be integrated seamlessly into the 

governance structure. This may involve the creation of science and stakeholder advisory boards 

or integrated ecosystem advisory boards. 

As governance roles are distributed among existing or new entities, several important issues 

should be considered. At each level, one must decide what source(s) of information will be used 

to fulfill the assigned roles. For example, at the highest level, will a national vision and goals be 

set based solely on scientific information, and will they include input from diverse government 

agencies, stakeholders, and/or the public. Such decisions become especially important when 

determining the source(s) of information making and implementing EAM decisions. The level 

of stakeholder input, in particular, must be determined as this can range from simply informing 

decisions to participating in developing consensus decisions. The trade-offs between developing 

support for EAM decisions among stakeholders (thereby promoting compliance with EAM 

guidelines or regulations) vs. the potential for stakeholders to promote less precautionary EAM 

actions (which are less detrimental to stakeholders’ vested interests in the ecosystem) must be 

considered carefully. 
36

IV. Summary and Conclusions 

A. What characteristics should a region-specific, national program have for EAM? 

Each of the four WG provided a different perspective in answering this question; however, all 

the groups generally agreed on the same general characteristics. NOAA’s vision of EAM 

explicitly calls for an interdisciplinary, cross-sector approach for managing coastal and oceanic 

resources (EGT, etc.). Thus, in the context of protected species, it will be necessary to consider a 

broader range of factors than under current single species protected resource management 

strategies. A national program to support EAM with explicit protected species components 

should be based on: 

• A clearly stated national mission or vision, which is flexible enough to reflect regional needs 

• Goals, objectives and performance measures which are responsive to broader ecosystem 

information. 

• A response to legislative ecosystem mandates. 

• Coordination and collaboration across line offices and other programs 

• An ability to address major issues by providing germane information required by other 

NOAA partners and stakeholders as well as EGT or PR. 

• Collaboration with (and inclusion of) stakeholders, partners, and end-users. 

• Transparent communication of knowledge, experience, and decision-making. 

• Precautionary, proactive approaches to management. 

• Management in a place-based fashion, focusing on issues/threats to ecosystem, rather than 

species-specific management 

 

The scientific program should: 

• Focus on the eight regional ecosystems, while recognizing the nested and cross-boundary 

nature of many protected species. 

• Establish a standardized process to evaluate the most prominent ecosystem factors in each 

regional ecosystem. 

• Be as exhaustive and inclusive as feasible of all ecosystem components. 

• Provide for and support an ecosystem based management model. 

• Provide a reference document describing each ecosystem. 

• Recognize adaptive and incremental processes and be flexible enough to allow changes 

suggested by information learned through process and outcome reviews. 

• Provide for long term monitoring of the components of the eight regional ecosystems 

• Support partnerships for joint management and research initiatives on national and 

international scales. 

• Coordinate funding, research, and research platforms. 

• Foster science-based decisions using multidisciplinary information. 

B. Are there appropriate experiences worldwide that demonstrate how this theme can 

inform ecosystem-based protected species management? 
37

All of the Working Groups were able to provide examples of existing approaches to ecosystembased protected species management, and consistently listed the following examples: 

• NOAA Fisheries’ Alaska work conducted by the NPFMC, Alaska Fisheries Science Center, 

and Alaska Regional Office on Steller sea lion and groundfish interactions, including the 

developing Aleutian Islands Fishery Ecosystem Plan 

• Convention for the Conservation of Antarctic Marine Living Resources (CCAMLR) 

• The International Whaling Commission (IWC) 

• Northwest salmon recovery efforts, including the Puget Sound Restoration Plan and the 

Puget Sound Collective Process 

• Various Northern European efforts, including BORMICON, MULTISPEC, Barents, North, 

and Baltic Sea multispecies models 

A number of other examples are provided in Appendix Table 4. Through not accomplished at 

the Workshop, a review document summarizing these efforts would provide useful guidance to 

further advance NOAA’s Ecosystem Approaches to Protected Species Management. 

C. What new research, data, models, or information management systems are required to 

advance the discipline and provide the basis for ecosystem-based decision making? 

Guidance varied among the WG based on their group theme. The Governance WG identified the 

need for a better Decision Support system (including relevant models). Such a system would 

provide a framework for incorporating ecosystem science into decision-making, and provide a 

set of scientific tools that help policy makers identify and minimize potential conflicts and 

impacts. WG1 identified six broad themes for which tools are needed: trophodynamics, 

acoustics, health, climate, habitat, and social science. 

With respect to EAM protected species assessments, WG3 suggested that these assessments 

should include traditional single-species scientific advice, but also include ecosystem 

considerations. An “ensemble approach” to assessment using multiple model types may be an 

appropriate framework. Assessment models enhanced by ecosystem considerations need to 

result in clearly defined control rules to inform management decisions. 

A core goal in developing an ecosystem assessment program should be the establishment of 

information systems that will facilitate warehousing, exchange, and access to a broad suite of 

environmental data. 

Further, it is essential that collaborations across institutional boundaries be developed to 

facilitate a more diverse suite of expertise to be actively involved in the assessment process. 

D. What changes in policy, governance, or science administration are required to more 

effectively inform ecosystem approaches to protected species management? 

The WGs generally agreed that existing NOAA mandates under the MSFCMA, ESA, MMPA, 

NEPA, and other legislative drivers provided ample statutory authority for the NMFS to proceed 

with implementation of EAM. 
38

Actual governance remains a thorny issue, however. This was a central issue in the U.S. Oceans 

and Pew Commission reports. The WGs suggested that perhaps the establishment of a new 

regional governance body (e.g., a Marine Ecosystem Council) would fill this role. The Puget 

Sound Collective may provide a model for such a body. In the short term, the authority of 

existing governance structures (e.g., Fishery Management Councils, Take Reduction Teams) 

should be expanded to cover ecosystem aspects so that they have a broader stewardship 

responsibilities and a broader spectrum of stakeholders. 

Science needs to be better integrated across taxa and discipline, and this may require the 

establishment of integrated national and regional marine science groups. This will further 

require a clear mandate from NMFS HQ to the field that the Centers and Regions conduct 

ecosystem/integrative research and management. 

Other charges that were identified by the WGs included: 

• Need to have a clear definition of what kind of Assessments are most relevant for ecosystem 

purposes. There is a continuum from single species assessment to ecosystem assessments 

• Work on all the above should proceed at the same time 

• Examples exist worldwide that demonstrate how assessments can be accomplished in an 

ecosystem framework (Everglades, ICES, etc) 

• We need to learn from the successes and failures of other projects 

• To accomplish our ecosystem goals, investments must be made in: 

o Multidisciplinary basic and applied research to understand processes including 

economic and social sciences 

o Data acquisition and reanalysis of data to ensure all sets are compatible and available 

o New and more integrated models that allow for forecasting of management decision 

impact and results 

o Improved communications using information systems that allow for seamless 

management of data, sharing of information, and best practices. 

• Changes in policy, governance and science administration: 

o Changes in policy include: consolidation of legislation using a common language, and 

more emphasis on the human element 

o Changes in governance: creation of ecosystem councils as an umbrella under which 

government structures might function. 

o Changes in science administration: eliminate institutional barriers in units within the 

NMFS Science Centers and Regional Offices, other NOAA Lines Offices, and other 

Agencies of the Federal government 

All of these activities or changes will be challenging to implement, because they require changes 

in structure, reallocation of budgets, support of stakeholders, partners, etc. Consequently, 

incremental implementation must be pursued. 

None the less, progress towards ecosystem-based assessments of protected species can be made 

immediately by fostering better communications and by including a section on ecosystem 

consideration in all MMPA Stock Assessment reports and ESA status reviews. 
39

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42

Acknowledgments 

We, the Convenors, gratefully acknowledge the many individuals that helped to make this 

workshop possible. First of all, our thanks to NOAA staff who provided tremendous background 

logistical support including Angela Collins-Payne, Michelle Ordono, and Karen Salvini. 

Secondly, the speakers all provided impressive presentations and deserve our great thanks for 

coming, in many cases, thousands of miles to present a brief talk and then hang-on to contribute 

invaluably to the WG discussions. Thus, we thank Elliott Norse (our keynote speaker), Lisa 

Ballance, Andrew Cunningham, Andy Dobson, Jason Link, Michelle McClure, John Ogden, 

Andrew Pershing, Christian Reiss, Jake Rice, Teri Rowles, Mary Ruckelshaus, Garry Stenson, 

Steve Swartz, and Colette Wabnitz. A special thanks for Steve Murawski for breaking from his 

busy schedule to present and prove that NOAA is indeed intent on implementing an Ecosystem 

Approach to Management for all species within the NOAA trust. 

The individuals who acted as facilitators and rapporteurs made the working group sessions 

possible. This included Kelsey Abbott, Ney Cyr, Sarah Howlett, Mary Jacobs-Spaulding, Ruth 

Kelty, Patricia Lawson, Kate McFadden, Karen Salvini, Nathalie Valette-Silver, and Sarah 

Wilkin. The chairs of our working groups, David Gouveia, Jason Link, Debra Palka, Michael 

Payne, Tim Ragen, Teri Rowles, and Steve Swartz, kept the WGs focused and on track. 

A special thanks to the few individuals who took the time to wade through early drafts of this 

manuscript and provided extremely helpful comments—Jason Link, Nathalie Valette-Silver, and 

Fred Serchuk. 

Finally, our thanks to NMFS, NOS and the Marine Mammal Commission for providing financial 

support for the Workshop! 
43

Appendix I 

Agenda 

Day 1 

9-10:15 Welcome, Intent/Scope of the Workshop – Jim Lecky, F/PR 

 SAIP Background -- Richard Merrick, NEFSC 

 PPBES and Ecosystems GT -- Steve Swartz, F/S&T 

 How this meeting will progress – Richard Merrick, NEFSC 

10:15-10:30 Break 

10:30-12:00 Big picture talk on Ecosystems Approach to Management – Elliot Norse 

 The Global EAM Perspective & NOAA’s Approach to EAM – Steve Murawski 

12:00-1:00 Lunch 

1:00-5:00 Ecosystem Studies with A Protected Species Component (30 min case studies)

Disease and Ecosystems – Andy Dobson 

ICES Ecosystem Assessment WG – Jake Rice, DFO

CCAMLR/SCAR – Christian Reiss, SWFSC

2:30-2:45 Break 

EMAX – Jason Link, NEFSC

Ocean and Human Health Initiative – Teri Rowles, NMFS/NOS

Panel Discussion -- The afternoon’s presenters summarize what they conceive off as the lessons 

that can be learned from their experience with EAM. 

5:00 Break for Day 
44

Day 2 

8:30-1:00 Protected Species Studies with an Ecosystem Component (30 min case studies)

Frogs – Andrew Cunningham

Ecopath/Ecosim model for green turtles in the Caribbean, Colette Wabnitz, Univ of British 

Columbia

Canadian Research on Cod-Seal Interactions – Garry Stenson, DFO

10:00-10:15 - Break 

Ecosystem-scale analyses in support of management in Puget Sound - Mary Ruckelshaus and 

Michelle McClure, NWFSC

 

ETP Dolphin Studies – Lisa Ballance, SWFSC

Linkages Between North Atlantic Right Whales and their Habitat – Andrew Pershing, Cornell

Ecosystem-Based Approaches to the Management of Coral Reefs – John Ogden, Univ Florida

Panel Discussion -- The morning’s presenters summarize what they conceive off as the lessons 

that can be learned from their experience with EAM. 

1:00-2:00 Lunch 

2:00-2:15 Charge for Working Group (Merrick) 

2:15-5:00 Working Group (WG) sessions begin 

5:00-5:30 Working Group Rapporteur and Chairs meet to discuss progress 

5:30 Break for day 

DAY 3 

8:30-9:00 Convene in Plenary: Working Groups give Brief Status Reports 

9:00-12:00 Continue WG discussions 

12:00-1:00 Lunch 

1:00-5:00 Continue WG discussions 
45

5:00-5:30 Working Group Rapporteur and Chairs meet to discuss results and presentation 

5:30 Break for Day 

DAY 4 

8:30-10:00 Convene in Plenary: Working Groups present findings 

10:00-10:15 Break 

10:15-1:00 Synthesis discussion of WG results 

 Discuss next steps 

1:00 Adjourn Workshop 
46

Appendix II 

List of Participants 

Last Name First Name Organization State Zip Code Phone Fax Abbott Kelsey 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2289 ke

Adams Peter NOAA Fisheries/SWFSC CA 831-420-3922 peBaker Jason NOAA Fisheries/PIFSC HI 96822 808-983-5711 808-983-2902 jaBallance Lisa NOAA Fisheries/SWFSC CA 92037 858-546-7173 858-546-7003 LisCassandra Barnes NOAA OAR DC cassBengtson John NOAA Fisheries/AFSC WA 98115 206-526-4016 206-526-6615 johBigford Tom 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-4300 301-713-4305 tho

Chaloupka Milani 

Western Pacific Regional Fishery Management Council HI 

96816 m.

Clapham Phillip NOAA Fisheries/AFSC WA 98115 206-526-4037 206-526-6615 philCollins M. Anthony NOAA/NOS/CCEHBR SC 29412 843-762-8597 AnthConant Therese 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2322 301-427-2522 the

Cornish Vicki NOAA Fisheries/SERO FL 33701 727-551-5771 727-824-5309 vicCoyle Carol 

National Center for Cool and Cold Water Aquaculture MD 21701 301-698-2425 ccoy

Cunningham Andrew 

Institute of Zoology, Zoological Society of London UK 

0 207-449-6674 a.c

DiGiovanni Robert 

The Riverhead Foundation for Marine Research and Preservation NY 

11901 631-369-9840 631-369-9826 rdigo

Dortch Quay 

NOAA/NOS/NCCOS/CSCOR Qu

Eagle Tom 

NOAA Fisheries, Office of Protected Resources MD 20852 301-713-2322 301-427-2522 T

English Elizabethann NOAA Fisheries MD 20910 301-713-2276 L
47

Last Name First Name Organization State Zip Code Phone Fax Fahy Christina 

National Marine Fisheries Service/SWRO CA 90802 562-980-4023 562-980-4027 Chr

Fair Pat NOAA/NOS/CCEHBR SC 29412 843-762-8597 Ford Michael NOAA Fisheries/NWFSC WA 98112 206-860-5612 mForst Mark Shippensburg University PA 18972 presGarrison Lance NOAA Fisheries/SEFSC FL 33027 305-361-4488 LanGerke Brandee NOAA Fisheries/PIRO HI 96814 808-944-2239 braGill Tracy NCCOS MD 20910 301-713-4384 tGittings Steve 

NOAA - National Marine Sanctuary Program MD 20910 301-713-7274 301-713-0404 ste

Gouveia David NOAA Fisheries/NERO MA 01930 978-281-9280 978-281-9394 davGulland Frances The Marine Mammal Center CA 94965 415-289-7344 415-289-7333 Hall Ailsa Sea Mammal Research Unit UK ajHill Scott NOAA Fisheries/SWRO CA 90740 562-980-4029 562-980-4027 Hoffman Philip 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2319 301-427-2524 phi

Hohn Aleta NOAA Fisheries/SEFSC NC 28516 252-728-8797 252-728-8784 aJacobsSpaulding Mary NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2332 301-427-2520 

s

Kelty Ruth NCCOS NY 12518 845-534-4836 rKinan Irene 

Western Pacific Regional Fishery Management Cncl. HI 96816 808-522-8220 808-522-8226 Ir

Lang William National Science Foundation VA 22230 703-292-7857 703-292-9085 Larsen Kirsten 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2322 301-427-2522 kir

Lawson Patricia 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2322 301-427-2522 patr

Lecky Jim 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2332 301-713-0376 j

Lent Rebecca NOAA Fisheries MD 20910 301-713-2276 reLewandowski Jill 

Department of Interior/Minerals Management Service VA 

20170 703-787-1703 703-787-1026 Jill.L

Link Jason NOAA Fisheries MA 02543 508-495-2340 508-495-2258 JLoSchiavo Andrew NOAA Fisheries MD 20910 301-713-4300 301-713-4305 and
48

Last Name First Name Organization State Zip Code Phone Fax McClure Michelle NOAA Fisheries/NWFSC WA 98112 206-860-3402 206-860-3400 michMcFadden Kate NOAA Fisheries MD 20910 301-713-1401 kathMenashes Emily NOAA Fisheries MD 20910 301-713-9075 EmiMengerink Kathryn Environmental Law Institute DC 20036 202-939-3825 202-939-3868 Merrick Richard NOAA Fisheries/NEFSC MA 02543 508-495-2291 508-495-2066 richMesnick Sarah NOAA Fisheries/SWFSC CA 92037 858-546-7148 858-546-7003 sarMoy Connie 

NOAA/NOS/NCCOS/CCMA/Biogeography Team MD 20910 301-713-3028 co

Nojek Larissa NOAA Fisheries MD 20910 301-713-2251 larNorse Elliot 

Marine Conservation Biology Institute WA 98004 425 968 0449 425 274 1183 

Ogden John 

Florida Institute of Oceanography FL 33701 727-553-1100 727-553-1109 jo

Palka Debra 

NOAA/Northeast Fisheries Science Center MA 

02543 508-495- 23878 508-495-2066 de

Pershing Andrew Cornell University NY 14853 607 255-5552 607 255-2106 Pittman Simon NOAA NOS/Biogeography MD 20910 301-713-3028 simRagen Tim 

Marine Mammal Commission MD 20814 301-504-0087 301-504-0099 

Reilly Steve NOAA Fisheries/SWFSC CA 92037 858-546-7173 858-546-7003 stReiss Christian NOAA Fisheries/SWFSC CA 92037 858-546-7173 858-546-7003 chrRice Jake 

Department of Fisheries and Oceans - Canada Can 613-990-0288 613-954-0807 r

Roden Carol 

Department of Interior/Minerals Management Service LA 

70123 504-736-2877 504-736-2901 Ca

Rosel Patricia NOAA Fisheries/SEFSC LA 70506 337-291-2123 paRowles Teri 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2322 301-427-2522 te

Ruckelshaus Mary NOAA Fisheries/NWFSC WA 98112 206-860-3266 206-860-3335 maryRusin Jeremy NOAA Fisheries/SWFSC CA 92037 858-546-7101 858-546-7003 JerSalvini Karen 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2319 301-427-2514 Ka

Sandifer Paul 

NOAA NOS/Hollings Marine Laboratory SC 29412 843-762-8814 843-762-8737 pa
49

Last Name First Name Organization State Zip Code Phone Fax Schroeder Barbara 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2322 301-427-2522 barb

Schwacke Lori NOAA NOS SC 29412 843-762-8541 843-762-8700 LorScida Pasquale 

NOAA Fisheries/Northeast Regional Office MA 1930 978-281-9208 978-281-9394 pas

Seminoff Jeffrey 

NOAA - National Marine Fisheries Service CA 92117 858-546-7152 858-546-7003 jeffr

Shenot Jeff 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-0174 je

Simpkins Michael 

Marine Mammal Commission MD 20814 301-504-0087 301-504-0099 m

Southall Brandon 

NOAA Fisheries, Office of Science & Technology MD 20910 301-713-2363 Bran

Stenson Garry 

Dept. of Fisheries and Oceans, Canada Can 709-772-5598 709-772-4105 ste

Swartz Steven 

NOAA Fisheries, Office of Science & Technology MD 20910 301-713-2363 301-713-1875 ste

Thom Barry 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2319 301-427-2524 b

Thomas James 

NOAA Fisheries, Office Habitat Conservation MD 20910 301-713-0299 301-713-1043 Jam

Trumble Robert MRAG Americas FL 33609 813-639-9519 bob.tValette-Silver Nathalie NOAA/NOS MD 20910 301-713-3020 301-713-4353 Wabnitz Colette 

Fisheries Centre (University of British Columbia) BC 

 604-822-1636 604-822-8934 c.w

Wakeford Robert MRAG Americas FL 33609 913-639-9519 robeWard John NOAA Fisheries MD 20910 301-713-9507 301-713-2384 JohWedell Vicki 

NOAA NOS/National Marine Sanctuary Program MD 20910 301-713-3125 vi

Whaley Janet 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2322 301-427-2525 Jan

Wilkin Sarah 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2322 301-427-2522 sa
50

Last Name First Name Organization State Zip Code Phone Fax Williams Mike 

NOAA Fisheries/Alaska Regional Office AK 99508 907-271-5117 907-271-3030 mich

Williams Phil 

NOAA Fisheries, Office of Protected Resources MD 20910 301-713-2332 301-713-0376 ph

Wilson Bill 

North Pacific Fishery Management Council AK 99501 907-271-2809 907-271-2817 b

Yuen Michelle 

NOAA Fisheries/Pacific Islands Regional Office HI 96814 808-944-2243 808-944-2124 mi
51

Appendix III 

Suggested Readings in Ecosystem Approaches To Management 

for Workshop Participants 

Background Readings 

Babcock, E. A. and E. K. Pikitch. 2004. Can We Reach Agreement On A Standardized 

Approach To Ecosystem-Based Fishery Management? Bull. Mar. Sci., 74(3): 685–692. 

Boesch, D.F. 2006. Scientific requirements for ecosystem-based management in the 

restoration of Chesapeake Bay and Coastal Louisiana. Ecol. Eng. 26: 6–26. 

Brodziak, J. K. T., P. M. Mace, W. J. Overholtz, and P. Rago. 2004. Ecosystem Trade-Offs In 

Managing New England Fisheries. Bull. Mar. Sci. 74(3): 529–548. 

Dunnigan, J.H. 2006. NOAA's Ecosystem Approach To Management. Presentation. NOS 

Science Seminar. February 7, 2006. 

Greene, C. H. and A. J. Pershing. 2004. Climate and the conservation biology of North 

Atlantic right whales: the right whale at the wrong time? Front Ecol Environ 2004; 

2(1): 29–34. (Protected Species in EAM working group) 

ICES. 2005. Report of the Study Group on Multispecies Assessment in the North Sea 

(SGMSNS), 5–8 April 2005, ICES Headquarters. ICES CM 2005/D:06. 163 pp. 

(Protected Species in EAM working group) 

Link, J.S. 2002. Ecological considerations in Fisheries Management-When does it matter? 

Fish. 27: 10-17. 

Link, J.S. 2002. What does ecosystem-based fisheries management mean? Fish. 27: 18-21. 

Mangel, M., et al. 1996. Principles for the conservation of wild living resources. Ecol. App. 

6(2): 338–372. 

Meyerson, L. A., J. Baron, J. M. Melillo, R. J. Naiman, R. I. O'Malley, G. Orians, M. A. 

Palmer, A. S. P. Pfaff , S. W. Running, and O. E. Sala. 2005. Aggregate measures of 

ecosystem services: can we take the pulse of nature? Front. Ecol. Environ. 3(1): 56–59. 

(EAM with Protected Species working group) 

NMFS. 2001. Marine Fisheries Stock Assessment Improvement Plan. Report of the National 

Marine Fisheries Service National Task Force for Improving Fish Stock Assessments. 

U.S. Dep. Commer. NOAA Tech. Memo. NMFS-F/SPO-56. 69 pp. 
52

Pew Oceans Commission on Ocean Policy. 2005. America's Living Oceans, Charting a Course 

for Change. Washington, DC. 166 pp. 

Pikitch, E. K., C. Santora, E. A. Babcock, A. Bakun, R. Bonfil, D. O. Conover, P. Dayton, P. 

Doukakis, D. Fluharty, B. Heneman, E. D. Houde, J. Link, P. A. Livingston, M. 

Mangel, M. K. McAllister, J. Pope, K. J. Sainsbury. 2004. Ecosystem-Based Fishery 

Management. Science 305:346-347. 

Sherman, K., P. Celone, and S. Adams. 2005. NOAA Fisheries Service's Large Marine 

Ecosystems Program: Status Report. U.S. Dep. Commer. NOAA Tech. Memo. NMFSNE-183, 21 pp. 

U.S. Commission on Ocean Policy. 2004. An Ocean Blueprint for the 21st Century. Final 

Report. Washington, DC. 676 pp. 

Recommended Readings 

Barnes, C., L. Bozzi, and K. McFadden. 2005. Exploring An Ecosystem Approach To 

Management: A Review Of The Pertinent Literature. Unpubl. rpt. Ecosystem Goal 

Team, NOAA. 19 pp. 

Browman, H. I., And K. I. Stergiou. 2005. Theme Section: Politics and Socio-Economics of 

Ecosystem-Based Management Of Marine Resources . Marine Ecology Progress 

Series. 300: 241–296. (Governance working group) 

Evans, D. and B. Wilson. 2005. Role of the North Pacific Fishery Management Council in the 

development of an Ecosystem Approach to Management for the Alaska large marine 

ecosystems. Unpubl rpt. 23 p. Available North Pacific Fisheries Management Council, 

Anchorage, AK. (Governance working group) 

Ferguson, M.C., J. Barlow, P. Fiedler, S.B. Reilly, and T. Gerrodette. 2006. Spatial models of 

delphinid (family Delphinidae) encounter rate and group size in the eastern tropical 

Pacific Ocean. Ecological Modelling 193: 645-662. 

Guerry, A. D. 2005. Icarus and Daedalus: conceptual and tactical lessons for marine 

ecosystem-based management. Front. Ecol. Environ. 3(4): 202–211. 

NMFS. 2004. A Requirements Plan for Improving the Understanding of the Status of U.S. 

Protected Marine Species. Report of the NOAA Fisheries National Task Force for 

Improving Marine Mammal and Turtle Stock Assessments. U.S. Dep. Commerce, 

NOAA Tech. Memo. NMFS-F/SPO-63. 112 p. 

NMFS. 2005. Workshop on Ecosystem-Based Decision Support Tools for Fisheries 

Management. February 14–18, 2005, Key Largo, FL. 
53

NOAA Regional Ecosystem Delineation Workgroup. 2004. Report on the Delineation of 

Regional Ecosystems. Regional Ecosystem Delineation Workshop. August 31–

September 1, 2004. Charleston, S.C. 54 pp. 

Reilly, S. B., M. A. Donahue, T. Gerrodette, K. Forney, P. Wade, L. Ballance, J. Forcada, P. 

Fiedler, A. Dizon, W. Perryman, F. A. Archer, and E. F. Edwards. 2005. Report of the 

scientific research program under the International Dolphin Conservation Act. U.S. 

Dep. Commer. NOAA Tech. Memo. NMFS-SWFSC-372. 100 pp. 
54

Appendix IV 

Expanded WG1 Answer to Question 3 – New Research, Data 

Collection, Models and Data Management Required To Support 

And EAM.

Trophodynamics 

Population size and structure of prey and competitor species: While some prey/competitor 

species populations can be addressed through fishery assessment methods, other methods of 

population assessment are needed for many species which are either not fished commercially, or 

which are only fished incidentally to more commercially valuable species. Surveys are therefore 

required to provide at least indices of abundance. Not all relevant species will be adequately 

sampled by a single survey method, and it is therefore likely that several survey methods might 

be required to estimate the abundance of all the relevant prey or competitor species. It is clear 

that for any surveys some definition or assessment of selectivity is required, as the assumption 

that all species and size classes are equally catchable under any one survey method will lead to 

biased assessments. 

Consumption rates by protected species: There are a number of studies that have used estimates 

of daily rates of prey consumption by protected species in ecosystem models. Many of these the 

studies scaled prey consumption rates to body mass of the predator using the general relationship 

R = A MB

, where R is the consumption rate, M is body mass, with A and B estimated from a 

number of different data sources. These data sources all relied on consideration of allometric 

relationships between energy requirements and body size rather than direct measurements of 

food consumed. For large whales, the value of B is the most influential but this is invariably 

derived from a regression with few data points for larger species. The studies considered fell 

into three categories, low values of B around 0.5-0.6, medium values of around 0.75-0.8, and the 

high value of 1 when consumption is just a straight percentage of body mass. This range of 

values creates considerable uncertainty about the energy requirements of large whales. This 

uncertainty increases with body mass because of the non-linear relationship between body mass 

and consumption and the difficulties of studying metabolic rates in larger animals. For a forty 

tonne whale the estimates of daily food requirements considered differed by a factor of ten. 

Some alternative approaches to estimating consumption rates in large whales were also 

considered including direct measurement of intake from behavioural studies, estimates of intake 

based on analysis of stomach contents, and estimates of energy requirements based on utilisation 

of blubber stores. Estimates of maximum daily consumption based on feeding rates were 

considered for filter feeding whales based on measurements of plankton concentrations and 

estimates of the volume of water filtered. North Atlantic right whales were chosen as a case 

study and it appeared very unlikely that they could physically achieve the consumption estimates 

generated using the above equation with medium to high values of B. In addition, filter feeding 

whales suggest a theoretical basis for values of B of less than 0.67 otherwise larger whales would 

need to spend longer feeding, or swim faster. Estimates of energy requirements in fin whales 

based on measurements from whaling data of the amount of blubber stored on feeding grounds in 
55

the Southern Ocean and North Pacific fell below all the allometric predictions. Direct estimates 

from stomach contents for fin and sei whales were also lower than the allometric predictions, 

except for the lowest value of B of 0.52. 

The studies reviewed indicated that neither theoretical considerations or data support high values 

of B close to 1 and there is evidence for values of 0.67 or less. Although from a modelling 

perspective consumption rates may not be the greatest source of uncertainty, it is nevertheless 

important to understand the sensitivity of any model predictions to uncertainty in consumption 

rates. Hence, estimates of consumption based on low values of B should also be included within 

the range of input values for large whales. 

By extension, many of these approaches are germane to odontocetes and pinnipeds. However, 

other protected species such as corals or chelonians have had much less work executed on 

estimates of their consumption. 

These estimates coupled with estimates of prey population allow one to evaluate the relative 

impacts of protected resources on prey populations, the potential production limitations of prey 

populations on protected resources, and for predators the relative effects of removals on 

protected resources. 

Diet composition: Several reviews have noted various approaches to assess diet composition, 

with comments on their potential and limitations. Five approaches were presented. Only one of 

these, analyses of contents from stomachs, intestines and scats, had been developed specifically 

to address questions relating to predator diets. Four other approaches, fatty acid signatures, stable 

isotopes, genetics, and remote monitoring were originally developed for other purposes, but have 

in recent years been adapted for use in marine mammal diet studies. Application of these new 

methods in cetacean diet studies has been particularly motivated by the need to develop nonlethal methodologies. 

Studies of the diets of protected species based on analyses of either stomach, intestinal or scat 

(faeces) contents is based on the assumption that the relative frequencies of recovered undigested 

specimens, including otoliths, beaks, exoskeletons and other hard parts, reflect the frequencies of 

fish, cephalopods, crustaceans and other invertebrates in the diet in some known manner. The 

methodological problem with erosion of otoliths, which has been well studied in the context of 

seal diets, is less conspicuous in studies of whale diets. Most cetaceans have a multi-chambered 

stomach system, starting with the non-glandular forestomach where otoliths and various other 

calcareous remains usually stay undigested. Certainly, differential passage and degradation rates 

of different fish and cephalopod types, and also the possible accumulation of some hard parts, 

represent methodological problems that have yet to be accounted for adequately in cetacean diet 

analyses. 

The fatty acid composition of a prey is species specific and, as these compounds are assimilated 

through the diet and accumulated in the fatty tissues of predators (e.g. in blubber), they can be 

used as tracers of diet. To assess the diet of the predator, fatty acid signatures from its blubber 

are compared with fatty acid signatures from a variety of potential prey species using 

classification and regression tree analysis. The principle of the stable isotope method is that 

ratios of heavier vs lighter isotopes of particular elements (carbon, nitrogen, oxygen sulphur) in 

tissues of predators can be traced to those of their prey as they are assimilated in the diet. Both 

the fatty acid method and the stable isotope method require a prey library. Assuming that food 

web fatty acid and isotopic signatures are reflected in the tissues of organisms and that such 
56

signatures can vary spatially based on a variety of biogeochemical processes, both methods can 

be used to trace nutritional origin and migration in animals. 

Genetic analyses of remains from scats or contents in the gastrointestinal tract may be used to 

identify prey species consumed. Originally the method was applied in combination with more 

traditional scat analyses, primarily to identify the individual predator or species for individual 

scats, assuming that epithelial cells from the colon wall, sloughed off and deposited in scats, are 

a reliable source of DNA to determine species of origin. A reference database for the genetic 

signature of actual prey species is needed. 

Remote monitoring of protected species, using either data loggers or satellite-linked time-depth 

recorders, has been used to indicate potential prey or feeding areas. The approach is based on 

comparing data on temporal and spatial distribution of the predator, including the vertical 

movements (dive depths), with related data for potential prey species, to identify matches that 

may indicate the likely prey species of the predator. For co-occurrence of predators and prey in 

time and space to be indicative of predation, confirmatory observations by other means are 

always required. 

Although identifying and measuring items in vomit, scats, and gastrointestinal contents has 

several disadvantages and sources of errors, it still provides more information at considerably 

less cost than other new methods (such as fatty acid signatures, stable isotopes and genetics), and 

has not been replaced effectively by any other method at present. Advantages of the traditional 

methods over the new ones include that they: 

• provide information on meal size and relative composition of prey for each predator 

• provide knowledge of size classes of prey 

• allow for understanding of small scale spatial and temporal distribution of diets 

• allow for small scale studies of predator-prey dynamics 

• are subject to easily obtainable samples from hunts, bycatch, culling or strandings 

• are subject to laboratory treatment of samples that are simple. 

The main problem with several of the new methods is the very coarse spatial and temporal 

resolution that prevents quantitative descriptions of relative diet composition. However, new 

methods based on fatty acid signatures and stable isotopes have some advantages over the 

traditional methods in that they: 

• integrate data over a longer period 

• may detect shifts in diet 

• may yield knowledge of distribution, migration and stock structure. 

These methods also allow for the understanding of habitat utilisation and trophic relationships of 

the predators. All of the new methods will certainly be useful in studies of depleted, threatened 

and endangered species. 
57

Linkages – inter/intra species predation: A discussion on predator-prey linkages and trophic 

complexity relative to model structure and characterization is key for any ecosystem approach to 

management. Determining what predator-prey linkages should be included in a model depends 

on the types of questions being raised, the modelling approach and data availability. One key 

issue in modelling is whether there is an optimal level of realism, and hence complexity, in 

relation to model performance. Reducing complexity can be achieved by removing linkages or 

by aggregating linkages, both approaches resulting in a reduced number of weak links being 

represented in the model. Previous work on weak links has shown that they may have an 

important influence on model stability. The effects of model complexity, removal and 

aggregation of linkages, is an area of research that warrants further study. Other key issues 

include: 

• The effects of model ‘biases’ (marine mammal centric versus fish centric versus benthos 

centric model ‘designs’), 

• The inclusion of size/age structure (what level of complexity is necessary to consider 

ontogenetic changes in diets?), 

• Spatial and temporal heterogeneity in linkages: the way that available prey are defined 

(different approaches in models - vulnerability, suitability, spatial overlap) 

• Multispecies functional responses. 

It was agreed that systematic and thorough investigations of trophic complexity in models 

relevant to whale-fishery interactions are needed to address the necessary levels of complexity 

needed in models posing questions about cetaceans and fishery competition. 

Interactions between Protected Resources and Fisheries: The interaction between fisheries and 

protected resources is an important trophodynamic consideration. To evaluate these potential 

interactions, knowledge of fishery spatial/temporal distribution integrated with protected species 

spatial/temporal distribution is needed. More specifically:

• Stage specific information on prey items and overlap with fishery (ontogenetic diet 

composition, life stage targeted by fishery, etc.) 

• Foraging behaviour integrated with depth overlap with fishery 

• Indirect effects of fishery removals on protected species prey availability or foraging ability 

(stage-composition shifts and consequences to spawner recruitment, trophic cascading resulting 

from fishery removals, localized depletion, etc.) 

• Direct mortality of protected species – not linked to obvious energetic changes in the system 

• Economic analyses of alternate fishery management regimes to protect species 

The key point is to evaluate the relative source of mortality caused by protected species and 

fisheries on a targeted stock. In some cases, the potential for competition between protected 

resources and fisheries can be quite high. 

Interactions between Protected Resources and other Competitors: The question of whether, 

how, and under what circumstances certain species or conspecifics out compete others for 

available resources has long been debated in ecology. Connell (1983) reviewed experimental 

field studies of competition (both intra- and inter-specific) and found that competition among 

conspecifics was as strong or stronger than that between species in three-quarters of the studies 

in which the two types could be separated. He also noted that there was a greater incidence of 
58

competition among marine organisms than in terrestrial or freshwater species, and that largesized organisms were more prone than smaller ones to competitive interactions. Schoener (1983) 

conducted a similar review, and also found a greater tendency toward competition among large 

(compared to small) heterotrophs. In addition, he concluded that greater ecological overlap 

between species resulted in a greater likelihood of competition, and noted that larger species 

were significantly more likely to out compete smaller ones. Neither review dealt with cetaceans, 

but both emphasized the complexity of interactions involved and the difficulty of elucidating 

genuine competitive effects in a non-experimental situation. In addition, Schoener noted the lack 

of any obvious patterns in competition within and between marine species. A further level of 

difficulty exists when one attempts to use short-term data to predict future effects; Yodzis (1988) 

concluded that short-term observations of systems subject to perturbations are not useful for 

estimating long-term impacts. 

For competition between species to be demonstrated, reliable data on several variables must be 

obtained. First, the species in question must be shown to be resource-limited (Milne, 1961); that 

is, the availability of food cannot be effectively unbounded, either absolutely or in such areas as 

individuals are limited (by time, energetics, experience or other factors) to searching. Second, 

there must be substantial overlap in spatio-temporal distribution of the two species. Third, both 

species must occupy essentially ecological similar niches. Note that it is not necessarily 

sufficient to demonstrate that both feed on the same prey; they must also exploit similar types 

(e.g. age class) of that prey, and forage at a similar level (e.g. depth, patch size, et cetera). 

Finally, opposite population trajectories are also a needed requirement indicative of competition. 

Overall- Key variables for trophodynamic considerations:

• Abundance and rate of increase 

• Vital rates (survival/mortality, maturity, reproduction) 

• Bioenergetic rates: metabolism, consumption, respiration 

• Diet composition 

• Foraging behaviour 

• Interspecific relationships (niche separation, competition, spatial/temporal overlap, dietary 

overlap among species) 

Acoustics 

Owing to the physical properties of water, sound is the principal means by which information is 

transferred over any appreciable distance. Sounds associated with marine biota, physical forces, 

and human activities can provide detailed information with which both people and animals can 

sense the marine environment. Further, sound may be used actively as an investigative tool for 

locating objects. Because of the wide range of biotic and abiotic information that may be 

obtained, an ecosystem approach to marine research and management should rely strongly on 

acoustic sensing. Specifically, passive acoustic sensors should be integrated into ocean 

observing systems to: 1) detect seasonal presence, activity, and (in some instances) abundance 

of species within ecosystems; 2) provide remote measurements of climatological and geological 

processes (e.g., rain and earthquakes); and 3) assess ecosystem-specific, spatial and temporal 

trends in ambient noise ‘budgets’ from the range of source contributions. Active acoustic 
59

sensing should be applied and advanced, where appropriate, as a means of identifying specific 

features of marine ecosystems (e.g., temperature, prey abundance, or the presence of specific 

species). 

A systematic approach to assessing marine ecosystem elements using passive acoustics is 

required. Specific questions regarding biotic and abiotic contributions to marine ambient noise 

should be identified and relevant sampling regimes (e.g., bandwidth, duty cycle, directionality) 

specified. Passive acoustic deployments to date have identified seasonal presence of specified 

marine species, demonstrated human sound source contributions to marine ambient noise, and 

contributed to meteorological measurements. Further deployments and sampling regimes should 

be selected that maximize the ability to assess spatial and temporal trends for a range of 

ecosystem features. Comparative ambient noise measurements should be made across various 

marine ecosystems with variable anthropogenic influence. Acoustic data should be integrated 

with information on habitat and ecological factors to derive predictive ambient noise models. 

These will be distinct from the fairly well-derived sound propagation models for predicting 

received levels from a specified sound source. Ambient noise models would prove useful in 

gauging not only estimated baseline conditions against which to assess anthropogenic input, but 

also environmental features relevant for active acoustic deployments. Data management should 

ensure maximal retention of raw data but be amenable to auto-recognition and other analyses. 

Ocean and Health 

Research:

• What is the fate and transport of contaminants/ pathogens/ nutrients/ toxins through the 

ecosystem? 

• What is the basic ecology and pathogenesis of emerging and resurging infectious agents? 

• What are the biological effects (dose response, identification of sensitivity to vital rates 

• How can protected species be used as indicators and sentinels and models 

• How can tools to detect exposure and effects of multiple stressors in a cost effective manner 

be developed? 

• Can protected resources be used as effective platforms for ocean observations for these 

compounds? 

• What are the links between terrestrial and marine ecosystems? 

• What are the links between man’s exploitation of marine resources (e.g. aquaculture) and the 

risk of pathogen transmission and ocean health risk? 

• What are the linkages between the stressors (directly or indirectly via host-pathogen 

interactions), not just effects independently in organisms? 

• Are protected resources vectors of pathogens and how do they move between ecosystems? 

• Could diseases be transported into novel ecosystems, both marine and terrestrial in this way? 

Data (monitoring and observations):

• Inter-disciplinary collaborations 

• Long term monitoring of all identified stressors 

• Standardization of tools and techniques and validation thereof 

• Expand use of protected resource sentinels and other early warning indicators to detect 

anomalies, perturbations and trends 
60

• Sample archiving for future retrospective analysis 

• Quality assurance systems 

• Identify surrogates for monitoring (use of in vitro approaches) 

Models:

• Develop models to understand linkages/impacts of ocean health on protected resources 

• Identify existing models to use (inventory of models) 

• Ensure existing ecosystem models are sufficiently flexible so that ocean health data can be 

incorporated. 

• Expand use of risk assessment models 

• Frameworks for model testing and validation 

Data Management:

• Must include system for easy retrieval and interpretation for managers and public 

Climate 

Annual or less frequent fishery and protected resource assessments have found correlations 

between environmental or climatic variability and abundance and distribution of species at two 

principal time scales: The quasi-decadal variability (ACW, NAO and PDO) and the more 

variable ENSO type (4 to 6 yr) variability. Little information exists to link changes in weather 

(<12 months periodicity) and the productivity of ecosystems and the corresponding direct or 

indirect impacts on PR. Such research is critical in ascertaining the long-term effects of single 

large events (Hurricane Katrina) vs. longer term changes in weather (more violent or frequent 

storm events). 

Tele-connections (ocean-atmosphere connections) that are associated with climate variability are 

not well understood at a number of ecosystem levels. Yet, regime shifts in the Southern Ocean 

(1989-1990) have occurred at the same time as in other high latitude systems (Bering Sea; 1989-

1990). For large, highly migratory PR, whose ecosystem extends many degrees of latitude there 

is little understanding of the role of these global scale climatic teleconnections on their life 

history or productivity. 

Regional data and indicators, while important, are less so for a national strategy, as effort to 

develop such indices cannot be scaled up to describe the general state of the ecosystem. In 

contrast, large, LME scale, or broader indicators have a greater justification precisely because 

they inform about the ecosystem at the scale of the species, or population range. Smaller scale 

indices may be important (river quality indices) but are probably not where the national program 

should focus. An example is the 500 mb pressure field used to understand national weather. 

Daily maps provide information for local weather to be predicted. Local weather maps provide 

no information about the national weather picture. But, over the long-term, local weather data 

will be able to track low frequency, broad scale climate patterns, much like individual SST data 

track the low frequency climate shifts in the north pacific. 

Data (monitoring and observations): Current data acquisition programs include shipborne, 

moored, and satellite data. Any EAM with a protected species component will require 
61

continuous (annual, semi-annual, monthly (region and ecosystem specific)) data collection 

programs. Fortunately, much of this abiotic data is currently collected as part of resource 

surveys. However, where high frequency (mostly very local in space or time) data may be 

necessary emerging technology (environmental monitoring by animals or autonomous vehicles) 

may provide important abiotic and biotic data at regional scales. Augmenting data collection on 

current ecosystem surveys using towed, or expendable instrumentation will provide future 

interpretations with up-to-date climate data, as such data sets become part of the long-term datastream. 

Models: Climatic models, both statistical and numerical, are advancing at a very rapid rate. An 

EAM with protected resources component should actively encourage and support the use and 

development of climate modeling. NOAA has expertise in several areas of climate modeling, and 

NMFS has particular expertise in serving these data. Such models or output will provide the 

canvas of background information to build interpretations about the ocean and coastal 

environment. Models or model output will need to be validated as part of the longer term 

monitoring program. 

Data management: Under current auspices of NOAA, and under the IOOS banner, climatic data 

derived from surveys, or from models will be required to be available in a timely manner, and to 

be served to users. Under an EAM with a protected species component, climatic, and 

environmental data will be integrated and served in both raw form (available to individual 

researchers) and in product form (time and space series). 

Habitat 

Research: The primary habitat-related research need is to develop a good understanding of the 

relationship between measurable habitat attributes and species abundance and productivity. This 

is necessary to predict how changes in habitat attributes will affect the viability (abundance, 

productivity, and diversity) of species of interest, including protected species and other species 

upon which they many depend. Specific examples include (among many others): effects of 

alternative watershed management or restoration strategies on anadromous fish production, 

effects of trawling on species composition and abundance, effects of noise on marine mammal 

and fish behavior and productivity, effects of coastal development (including alternative 

mitigation strategies) on fish, marine mammal, or turtle abundance. Much of this research will 

be of necessity long-term and will need to be conducted on a spatial scale much larger than has 

been typical for most ecological experiments. For example, many populations of marine species 

have vast ranges (thousands to millions of square kilometers), and measuring a population 

response to habitat perturbations may therefore require experiments or monitoring on a similar 

scale. 

Monitoring: For many protected species there is a need for basic information on where the 

species live and what habitat they utilize throughout their life-cycle. For example, some 

protected species (including fish, turtle and marine mammal species) are observed only during a 

portion of their life-cycle. An effective ecosystem approach to management will require at least 

a basic understanding of what habitat a protected species is utilizing over its entire life-cycle. In 

addition, there is a need for standardized and statistically valid habitat monitoring across multiple 
62

scales and jurisdictions. Long-term monitoring data are essential for detecting trends and for 

developing hypotheses for functional relationships between habitat attributes and ecosystem 

function. To be most effective, however, such monitoring needs to occur in a systematic, 

unbiased manner, and data collected by multiple agencies and institutions needs to be 

standardized. 

Models: A number of useful models already exist for relating habitat attributes to 

species/population abundance [citations]. Parameterizing and validating these models is 

probably more important than developing new models. 

Data management: Standard needs (accessible, integrated across sources, etc). Habitat data 

needs to be collected on same scale as the population/species of interest. 
63

Appendix V 

WG3’s List of Research Priorities for Incorporating Ecosystem 

Considerations into Protected Resource’s Assessments.

The list of issues raised by participants in a round robin discussion of “research and data needs” 

for ecosystem based stock assessments for protected species included: 

Very important 

• better long-term spatially resolved monitoring data to better understand environmental 

variability 

• better long-term spatially resolved data on human marine/maritime activities for risk 

assessment 

• better time series data to help calibrate and validate numerical models 

• better trend, biomass and abundance estimates 

• better estimation of trophic transfer rates 

• better historical data series (reconstructed?) 

• better information on habitat use and dispersal to estimate exposure to various anthropogenic 

hazards 

• better understanding of the acute and chronic effects of various stressors on morbidity not 

just mortality 

• better understanding of marine species behaviour to better evaluate effects of external 

stressors 

• better information on disease/parasite effects 

• better information on stock structure (age-sex, spatial) 

Important 

• ask more insightful ecological questions 

• consider boundary issues such as land-sea interface 

• better methods for data assimilation in ecological models 

• better evaluation of the efficacy of management actions to reduce mortality 

• better information on foraging ecology 

• better indices to support objective decision making 

• better sub-sea surface oceanographic data (temperature, currents etc) 

• better understanding of environmental forcing 

• better understanding of food habitat requirements (use bycatch) 

• better understanding of life history traits 

• better understanding of the effects of anthropogenic sound 

• better understanding of the effects of catastrophic events on species viability and survival 

(especially at low population levels) 

• contemporaneous sampling of environmental factors 

• develop indicators to help monitor health of protected species 

• development of informative case studies of ecosystem change 
64

• diagnosis of reasons for why some stocks fail to recover while others do recover 

• external review of research projects 

• readily accessible data inventories and meta-data 

• socio-economic research (human demands for resources) 

• undertake comparative life history studies 
65

Appendix VI 

Glossary of Terms 

ACFM – ICES Advisory Committee on Fishery Management 

AKFSC – NMFS’ Alaska Fisheries Science Center 

BORMICON – Boreal Migration and Consumption model 

CCAMLR – Convention for the Conservation of Antarctic Marine Living Resources 

CEMP – CCAMLR Ecosystem Monitoring Program 

DFO – Canadian Department of Fisheries and Oceans 

DOC – U.S. Department of Commerce 

DOI – U.S. Department of Interior 

EAM – Ecosystem Approaches to Management 

ECOPATH – Ecosystem mass balance simulation model 

ECOSIM – Ecosystem Simulation model (usually used with ECOPATH as a time dynamic 

 simulation module for policy exploration) 

EGT – NOAA’s Ecosystem Goal Team 

EMAX – Energy Modeling and Analysis Exercise 

EPA – U.S. Environmental Protection Agency 

ESA – U.S. Endangered Species Act 

ESU - Evolutionary Significant Unit 

ETP – Eastern Tropical Pacific tuna/dolphin research program 

F/PR – NMFS Headquarters Office of Protected Resources 

F/SF – NMFS Headquarters Office of Sustainable Fisheries 

F/ST - NMFS Headquarters Office of Science and Technology 

FEP – Fishery Ecosystem Plan 

FMC – Fisheries Management Council 

GIS – Geographic Information System 

GLOBEC - Global Ocean Ecosystem Dynamics program 

ICES – International Council for Exploration of the Sea 

IWC – International Whaling Commission 

LME – Large Marine Ecosystem 

LMR – Living Marine Resources 

MMC – U.S. Marine Mammal Commission 

MMPA – Marine Mammal Protection Act 

MSC – Marine Stewardship Council 

MSA – Magnusson Stevens (Fishery Conservation) Act 

MSVPA – Multispecies Virtual Population Analysis model 

MULTISPEC – Multispecies Assessment fishery model 

NAMMCO – North Atlantic Marine Mammal Commission 

NCCOS – National Centers for Coastal and Ocean Science 

NEFMC – New England Fisheries Management Commission 

NEPA – National Environmental Policy Act 

NERR – National Estuarine Research Reserve 

NGO – Non Governmental Organization 
66

NMFS – National Marine Fisheries Service 

NOAA – National Oceanic and Atmospheric Administration 

NOS – NOAA’s Ocean Service 

NEFSC – NMFS’ Northeast Fisheries Science Center 

NMSA – U.S. National Marine Sanctuaries Act 

NPFMC – North Pacific Fisheries Management Commission 

NWFSC – NMFS’ Northwest Fisheries Science Center 

OHHI – Ocean and Human Health Initiative 

PBR – Potential Biological Removal (under the MMPA) 

REA – Regional Ecosystem Area 

SAIP – Stock Assessment Improvement Plan 

SARA – Canadian Species At Risk Act 

SCAR – Scientific Committee on Antarctic Research 

SWFSC – NMFS’ Southwest Fisheries Science Center 

TNC – The Nature Conservancy 

TRT – Take Reduction Team 

USFWS – U.S. Fish and Wildlife Service 

VPA – Virtual Population Analysis model 

WG – Working Group 
67

Appendix Table 1. Major themes to consider for ecosystem-based decision making relative to EAM for Protecte

Theme Tropho-dynamics Acoustics Ocean and Human Health Climate 

Research 

(Process 

studies) 

1) What are the relative removals of/by protected resources? 2) What is role of prey to production of protected resources? 3) What are indirect effects of changes to prey on protected resources and their competitors? 

1) Passive acoustic sensing of animals, natural processes, human input 2) Ability to char. spatial/temporal trends in ambient noise 3) Ability to identify discreet acoustic events 4) Biological sensing (including protected resources) 

1) Fate/transport of high priority contaminants & toxins; 2) Biological effects 3) Use of Protected Species as indicators 4) Development of tools to detect multiple pathogens at once 5) Where contaminants end up and their effects 6) Links between terrestrial and marine ecosystems 7) Standardizing tools/techniques 8) Tests of appropriate models 

1) Data not at same long-term scale (climate effects at regional scales, decadal scale variability, severe weather events) 2) How does climate effect distribution and abundance of protected species 3) Under various climate scenarios, do we expect recovery plans to meet their goals? 

1sth2bp3to 4te56mh

Data 

(Monitoring 

and 

Observation) 

1) Population vital rates 2) Diet composition 3) Abundance of predators, prey, and competitors, 4) Interactions with fisheries 

1) Info contained in passive sensing of anthropogenic sources, protected species, natural processes, using animals as sensors 

1) Collaboration; need to collect pathogen data 2) Start standardized tools/techniques 3) Expand use of protected species sentinels to use for early warning 

1) Physical oceanography and climatology measurements 2) Measures of abundance, vital rates 

1spm2
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Theme Tropho-dynamics Acoustics Ocean and Human Health Climate 

Models 1) Need to 

parameterize models that already exist 2) Information about ecosystem models that are out there; 3) Set up review process for models (run data on different models, etc) 

1) Propagation models (limitations in shallow water/complex areas) 2) Predictive models of ambient noise based on biological, physical, anthropogenic sources 3) Observation system must be comparative. 

1) Develop models to understand linkages/impacts of ocean health on protected resources; 2) Identifying existing models to use (inventory of models) 

1) Question specific models need to be developed 

1md

Data Mgmt 1) Integration of 

different data sources 2) Data online and available 

1) Value in having as much raw data as possible 2) Provide more bandwidth 

1) All needs improved 

1) Data integration 1
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Appendix Table 2. Types and attributes of stock assessments for protected species. 

Stressors Activiti

Type of 

Assessment 

“Target” 

species of 

mgmt 

Physical 

Oceanographic 

Forcers 

Predators& 

Prey 

Lower trophic 

level Processes Direct 

Mortality Ch

“Classic” Single Species Assessment 

Explicit; Dynamic 

Static; Observed series or average recruitment and growth 

Static; Fixed external Parameters 

Absent Usually 

Fisheries  (Single type of mortality) 

Rare 

“Augmented” or “Enriched” Single Species Assessment 

Explicit; Dynamic 

Dynamic (or static) External inputs 

Dynamic & unidirectional (or Static); External inputs 

Absent Usually 

Fisheries  (Single type of mortality) 

Rare 

Multi-species Assessment 

Explicit; Dynamic 

Static (usually) recruitment, dynamic or static growth 

Dynamic & reciprocal; Explicit 

Absent Multiple 

Fisheries (single type of mortality 

Rare 

Trophodynamic Ecosystem Models 

Explicit or Implicit 

Usually static Dynamic & 

reciprocal; Explicit 

Dynamic & reciprocal; Explicit 

Single or Multiple 

Rare 

Bio-geochemical Ecosystem Models 

Rarely Explicit 

Dynamic; Explicit 

Dynamic and reciprocal; Explicit 

Dynamic & reciprocal; Explicit 

Single or multiple 

Pollutieutropothers 

Assessments For Protected Resources 

Usually explicit 

Often explicit & dynamic, external, esp if associated with a risk. 

Explicit, dynamic, reciprocal 

Dynamic only when threat is lower trophic level issues 

Usually multiple explicit 

Usuallmultipexplici
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Appendix Table 3. Matrix of governance options. 

Governance levels/roles Options 

Sets national vision and goals for EAM Legislation Interagency 

Committee (IAC)* 

IAC with stakeholder input (SI)** 

Sets national EAM policy Legislation IAC IAC with SI NOA

EcosGoal (EGT

Collects/integrates scientific data necessary for EAM Regional 

interagency science boards 

NOAA Fisheries Science Centers 

Makes EAM decisions Regional 

interagency ecosystem teams (RET) 

RET with SI NMFS’ 

regional offices (with partner agencies via NEPA) 

Implements EAM decisions Relevant 

agencies 

Relevant agencies with SI 

Monitors effectiveness of EAM implementation (process and outcomes of management actions) 

RET NOAA 

Fisheries Science Centers 

*For all Committees, Boards, and Teams, must decide whether membership is mandated/required or voluntary. **For stakeholder input, must decide (for each instance) the level of input, ranging from simply informing decisi

decisions to developing consensus decisions. 
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Appendix Table 4. Summary of Working Group responses to the four questions. 

Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

What characteristics should a regionspecific, national program for this EAM theme have? 

1. Set national standards but be adaptable to regional needs 2. Be responsive of legislative mandates 3. Have a clearly stated national mission. 4. They would need to be operable at the regional level 5. Coordinate and collaborate across line offices and other programs 6. Be as exhaustive and inclusive as feasible of all germane ecosystem factors. 

1. NOAA should create knowledge and procedures to make better informed decisions about protected species. 2. Development of these new procedures should begin with a reference document describing the ecosystem 3. Long-term monitoring programs are essential for any ecosystem approach to management. 4. Data from monitoring programs must eventually be used to guide decision making. 5. There are issues of scale which need to be dealt with. 6. Ecosystem 

1. To be most effective, a national program for incorporating ecosystem dimensions into protected resources assessments should have a region-specific focus. 2. A variety of spatial scales will be appropriate when defining such regions. 3. A national program must have clear goals, be flexible, and adaptive. 4. Ecosystem assessments should be a national priority. 5. They should break down stove pipes within Centers and between agencies to allow coordinated, efficient ecosystem based stock assessments. 6. EAM should provide 

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72

Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

approaches to management for Protected Species needs to include all the components of ecosystem on which the Protected Species rely. 7. An ecosystem approach to management will require extensive collaboration and coordination. 

forums to discuss allocation among stakeholders, review science, and Develop mitigation measures from any stakeholder 7. EAM should be based on realistic goals 8. Ecosystem based assessments should be multi-disciplinary and include appropriate biotic and abiotic factors 9. The Assessment methodology should be robust to data-poor areas and species 10. Assessments can be both quantitative and qualitative. 11. Assessment should use standardize terms and approaches for different parts of ecosystem research. 12. Assessments should explicitly deal with uncertainties, and should 

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73

Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

include sensitivity analyses 13. They should include studies of the impacts of single/multiple stressors on the species (or area) of interest; 14. They should utilize both top-down components and bottomup components 15. Should be the most appropriate type (within the single species to biogeochemical ecosystem model continuum) for the species/area of interest. 16. Assessment should include a control law that builds upon the existing control laws and also explicitly incorporates ecosystem attributes. 

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Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

Are there appropriate experiences worldwide that demonstrate how this theme can inform ecosystem-based protected species management (include appropriate references)? 

1. Convention for the Conservation of Antarctic Marine Living Resources (CCAMLR) Southern ocean GLOBEC 2. NAMMCO 3. Norway/IcelandBORMICON/MULTSPEC4. International Whaling Commission working groups 5. Yodzis et al. model from Argentina and Yodzis et al. model from South Africa 6. Review by Trites re: Ecopath w/Ecosim and marine mammals 7. Australian Dugong management 8. NMFS AKFSC- Steller Sea Lions and groundfish 9. NMFS NEFSCEMAX 10. Sea otter, kelp interactions and trophic cascades 11. NOAA’s Ocean and 

1. ETP tuna-dolphin research 2. NEFSC cetacean surveys 3. Pacific NW salmon 4. Nature Conservancy ecoregional planning 5. PEW strategy program 6. U.K. Royal Society for Protection of Birds 7. U.S. Audubon Christmas bird counts 8. Citizen activism efforts 

1. “Enriched” singlespecies models: a. Barents’s Sea cod b. Baltic Sea cod c. Sardine and anchovy stocks in Iberian waters d. Most capelin assessments e. CCAMLR assessments of krill f. South-central Pacific tuna-dolphin model 2. Multi-species Assessment models - a. The most widely used multispecies model is the multispecies –VPA (e.g., North Sea and Baltic Sea marine fish assessments) 3. Trophodynamic models – a. there are well over 150 applications of Ecopath to marine systems, and other mass1. 

Re2. 3. Fis- 
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Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

Human Health initiative 12. Discovery of toxoplasmosis in sea otters leading to evaluation of run-off from feral and domestic cats which may have human health implications 13. Cold-water coral management in the North Atlantic (ICES, NMFS) 14. Australia’s Great Barrier Reef initiative 15. NW salmon 

balance models have also been tried. b. CCAMLR International Whaling Commission 4. Full bio-geochemical ecosystem models – a. The Everglades model developed by deAngelis et al. b. The Puget Sound Collective process 

What new research, data, models, or information management system is required to advance the discipline so that its products form the basis for ecosystem-based decision making? 

The Working Group divided its charge into five broad themes: trophodynamics, acoustics, ocean health, climate, and habitat (see Appendix Table 1) 

1. Information Systems & Data Management: a. Establish metadata standards b. Establish data sharing agreements and structure to facilitate data sharing c. Dedicated database managers d. Databases linked to GIS and models for further analysis (multi1. Research and data collection to support ecosystem based stock assessment will have to relate back to one of NOAA Fisheries’ three legislative mandates. 2. The output of EAM needs to be augmented assessments. 3. These EAM assessments would need to include traditional single-species scientific Th

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76

Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

criteria evaluation) 2. Data Needs -There should be an iterative approach to management, data collection and analysis 3. Modeling – a. Expand and strengthen in-house modeling capacity b. Develop risk-based models with probabilistic output to support management c. Draw from modeling experience from other disciplines and environments (terrestrial, economics, climates, disease, acoustic), including integration of existing complementary models (e.g., biochemical and trophic) d. Develop “metadata” for models to ensure reproducibility (e.g., 

advice, but also include wider considerations. 4. Incorporate ecosystem considerations into assessment models 5. An ensemble approach to assessment using multiple model types may be an appropriate framework. 6. Assessment models enhanced by ecosystem considerations need to result in clearly defined control rules to inform management decisions. support approaches that are used across multiple disciplines. 7. Expanding the scope of assessment models necessitates the use and integration of additional data. 8. A core goal of a developing ecosystem assessment program 

cothe
77

Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

assumptions and initial conditions) e. Develop a set of criteria for validating models 

should be the development of information systems that will facilitate warehousing, exchange, and access a broad suite of environmental data. 9. Further, it is essential that collaborations across institutional boundaries be developed to allow a more diverse suite of expertise to be actively involved in the assessment process. 

Based on the above, what changes in policy, governance, or science administration are required to more effectively inform ecosystem approaches to protected species management? 

1. There are a plethora of legislative mandates that provide the basis for these ecosystem considerations (Endangered Species Act, Marine Mammal Protection Act, MagnusonStevens Fishery Conservation and Management Act, and the National Environmental 

1. First a. Construction of a “big-picture” document or knowledge inventory for each LME b. More effective NOAA Fisheries website c. Seminar series d. NCEAS-style workshop 

1. Overarching - The current mandates of the MMPA and ESA, with respect to ecosystembased management, compel us to move forward with the state of knowledge that exists today. 2. Policy - Policy level commitment to EAM is 

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78

Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

Policy Act, among the 46 other legislative drivers for NOAA) 2. Issues of internal and external governance are keystone concepts need to establish regional bodies, akin to those calls from the U.S. Oceans and Pew Commission reports 3. Need dedicated groups to perform integrated science within the context of national standards. . 

e. Paid sabbaticals f. Formalize partnerships across Centers of Excellence 2. Then a. Provide a long-term commitment to a permanent source of funding. b. Clear prioritization of research needs c. NOAA should also provide for better communication, within NOAA Fisheries, between government agencies, with academia and NGOs. Formalize partnerships by identification of “Centers of Excellence” for those disciplines and taxa that are essential for effective EAM in each LME. 

abundant and strong. 3. Legislation: Identify and link language supporting EAM into existing statutes. 4. Regulations: Consolidate fishery management and protected species regulations to clarify that governing bodies need to consider the full range of requirements. 5. Governance - The concept of a Marine Ecosystem Council was strongly recommended as the ideal governance system by which all of the current speciesbased governance structures 6. The group also strongly encouraged expanding the authority of current species-based governance structures (such as TRTs) so that 

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Questions 

WG 1 – Supporting the 

NOAA vision of EAM - 

Ecosystem Studies with A 

Protected Species 

Component 

WG 2 – The Protected 

Resources Vision - 

Protected Species 

Studies with An 

Ecosystem Component 

WG 3 – Assessments –

Ecosystem Based Stock 

Assessments for 

Protected Species 

W

In

they have a broader stewardship mandate and a broader group of stakeholders. 7. Science Administration, Structure and ExecutionA clear mandate and directive is required from HQ to the Science Center Directors that they must conduct ecosystem/integrative research. 8. Review/Evaluation - create a forum for reviewing ecosystem assessments akin to the Scientific Review Groups (SRGs), and hold multi-disciplinary workshops/conferences