fisheries ecosystem models: technical details and prospects for partnerships howard townsend, ph.d....

Fisheries Ecosystem

Models: Technical

Details and Prospects for Partnerships

Howard Townsend, Ph.D.

NOAA Chesapeake Bay Office (NMFS)

- Cooperative Oxford Lab

(NOS/NCCOS)January 15, 2008

Science, Service, & Stewardship

NOAA Chesapeake Bay Office

"It was the Law of the Sea, they said. Civilization ends at the waterline. Beyond that, we all enter the food chain, and not always right at the top."

-Dr. Hunter S. Thompson



Presentation Outline

• Introduction– Chesapeake Bay Fisheries Ecosystem Model– NOAA/NMFS Ecosystem Modeling and International

Efforts: • NEMoW• UN Reports

• Technical Details (Major Models/Model Types/Software)– Ecopath with Ecosim (EwE)– Atlantis– Gadget

• Opportunities for Partnerships– NEMoW Members– Plans for future NEMoW



CB Fisheries Ecosystem Model

• Developed in cooperation between NOAA CBO/Oxford, CRC, UBC with support from many bay researchers using Ecopath with Ecosim software (code base)

• A companion to the CB Fisheries Ecosystem Plan• Technical report (230 p) completed/in review • Chesapeake Bay tidal waters• 45 functional groups • Replicates ecosystem history 1950 – present



Inputs and Links to EwE

Input

Monitoring

Stock assessment

Literature

CBREEM

Mediation

Forcing

Habitat and water quality (e.g., SAV, DO)

Management

scenarios

Ecopath

Ecosim



Chesapeake Bay Regional Estuarine Ecology Model (CBREEM)

• Purpose– Generate historical patterns in primary productivity for

EwE

• Introduction & Methods – Two layer, simple hydrographic model (monthly time steps

for 50+ years)– Use wind, rainfall, gage inflow, and relative loading

as inputs– Solve for equilibrium velocity fields on Richardson grids

and make chemical mass-balanced calculations (Wright et al. 1986, Hunter and Hearn 1991)

• Results– Chla (used as nutrient loading forcing function for

EwE)



Forcing Data (Input) for CBREEM

• Wind– Thomas Point, Maryland (TPLM2, 1985-2002, NOAA

National Buoy Data Center) and trigonometric functions (1950-1985)

• Rainfall – Monthly average from ten stations (1950-1997, NOAA

National Climate Data Center) and a reference index in Washington D.C. (1998-2002)

• Gage inflow– Nine gauged rivers (USGS)

• Relative loading (Nitrogen)– 1984 to 2003 from monitoring (average: 0.9126 mg/l)– Susquehanna river (1945-1984) from Dr. Hagy– Other eight rivers (1945-1984) – monthly average from

1984 to 2003



Model Interface

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

1950 1960 1970 1980 1990 2000

Nu

trie

nt

loa

din

g (

re

lati

ve

)

Chla



Summary

1.5

2

2.5

3

3.5

1 13 25 37 49 61 73 85 97 109

Months (1985-1994)

Bio

ma

ss

(to

n/k

m^

2)

Input

Monitoring

Stock assessment

Literature

CBREEMMediation

Forcing

Habitat and water quality (e.g., SAV, DO) Managemen

t

scenarios

Ecopath

Ecosim

Habitat mediation for blue crab YOY via SAV Physical forcing through DO for striped bass

Menhaden B changes under different SB Fs

DO data (1985-2006)

Long-term forcing function Sij4

6

8

10

1 13 25 37 49 61 73 85 97 109

Months (1985-1994)

Bio

ma

ss

(to

n/k

m^

2)

0

0.3

0.6

0.9

1.2

0 2 4 6 8

DO

fc (

DO

)



CBFEM Plans

Applications• Support development of ecosystem-based fisheries management plan• Tool for exploring ecosystem impacts of fisheries management

decisions in developing EBFM• Provide guidance in identifying research, monitoring and assessment

needs

Development• Review of current model data (basic input, drivers, and validation)

guided by EMTAP under the purview of FSC• Improve data and ensure we have adequately mined data (Maddy)• Link FEM with Water Quality and other physico-chemical models

(Hongguang)• Explore other ecological, climatological, etc. impacts on the

Chesapeake fisheries ecosystem

The ultimate goal is to use CBFEM (and other ecosystem management models) in a process similar to single species stock assessment models. The CBFEM will be developed, reviewed, applied and updated on a regular cycle with oversight from a technical committee.



NOAA/NMFS and International Ecosystem Modeling Efforts

Fisheries Ecosystem Modeling is new and needs regulatory/management foundations



NOAA Ecosystem Modeling Team

Funding NEMoW– National Ecosystem Modeling

Workshop– Approved and Sponsored by

NMFS Science Advisory Board Meeting

– 1st meeting August 2007 to exchange ideas on approaches and develop best practices for fisheries ecosystem/multi-species models

– A national workshop to standardize methodologies and approaches when using ecosystem, bio-physical and multispecies models

– Responsive to a wide range of calls for EAM/EAF/IEA/etc.



Why NEMOW?

• There have been only limited and ad hoc efforts to provide a standardized approach for Eco/MS models:– software packages– recommendations for use– parameterization protocols– validation protocols– data requirements



Stock/Single Species

EcosystemMulti-species Aggregate Biomass

SS models, forget ecosystem issues

Messy Picture Here

Gadids

FlatfishPelagics

Gradient of Possibilities

Multiple SS assessments in

“harmony”

SS assessments with explicit M2 or habitat or climate

considerations

Multi-species assessments

Aggregate Biomass Models

Whole System Models, forget

pop dy



What – NEMoW Products

• Workshop Report – Howard Townsend, Jason Link, Kenric Osgood, Todd

Gedamke, George Watters, Jeff Polovina, Phil Levin, Ned Cyr, and Kerim Aydin. 2008 (Submitted). Report on NOAA National Ecosystem Modeling Workshop. NOAA/NMFS Technical Memorandum)

• Evaluation of Models• Recommendations for National EM

Standards/Guidelines of use & review• Recommendations for Standardized

Approaches



International Efforts

• United Nations Food and Agriculture Organization– Report on Classes/Categories and

uses of Ecosystem Models for Fisheries (out Aug 2007) Reference: Plagányi 2007. Models for an Ecosystem Approach to Fisheries. FAO Fisheries Technical paper 477 →

– Report of Modelling Ecosystem Interactions for Informing an Ecosystem Approach to Fisheries: Best Practices in Ecosystem Modeling, Tivoli, July 3-6, 2007 (out soon)



Conclusions from External Efforts

• Ecosystem Models and Management Advice– Conceptual/understanding: of the structure, functioning and

interactions of the ecosystem, or sub-system, under consideration. May not be used explicitly in decision-making or scientific advice but forms the underlying context for any detailed management planning and decision-making

– Strategic decisions: linked to policy goals and are generally long-range, broadly-based and inherently adaptable

– Tactical decisions: aimed at the short-term (e.g. next 3-5 years), linked to an operational objective and in the form of a rigid set of instructions e.g. tactical decision to change quota

• Model typesI. Whole ecosystem models: models that attempt to take into

account all trophic levels in the ecosystemII. Minimum Realistic Models (MRM): limited number of species

most likely to have important interactions with a target species of interest

III. Dynamic System Models (Biophysical): represent both bottom-up (physical) and top-down (biological) forces interacting in an ecosystem

IV. Extensions of single-species assessment models (ESAM): expand on current single-species assessment models taking only a few additional inter-specific interactions into account



Conclusions from NMFS & International Efforts

Belie f in m od e l

Insi

gh

ts g

ain

ed

“Pure skeptic” “Believer”

“Realist”

Pyrrho 360-270 BCE



Technical Details (Major Models/Model Types/Software)

EwE, Atlantis, and Gadget



EwE: An Overview

Data Model Research Application

Biol.: B, P/B, Q/B, diet.

Fleet catches

Manual

Ecoranger

Automatic

Pedigree

M.Carlo

Vulnerability, mediation, …

Mass-balance (Ecopath)

Time-dynamic(Ecosim)

Spatial-dynamic(Ecospace)

Nutrient-O2

seagrass, …

Habitat preference,

dispersal, migration etc.

Spatial cost of fishing

Prim.prod.(SeaWIFS)

Runoff, nutri-ents, depth, …

Persistent pollutants

Tracer-dynamic

(Ecotrace)

Who eats whom?Network analysis

Biol. & fishing time series

Fisheries vs.environment

Protectedarea dynamics. Spatial effort

allocation

Environmental time series

Policy exploration

Economics,social info.

Fisheriesmanagement

Functionalresponse, etc.

Ocean zoning

Academic (ecol. theory)

MPA size(Ecoseed)

Legend:

Facultative input

Optional input

Seaso-nality

Sensitivityanalysis



EwE - Simpler Overview

• ECOPATH– Began with Polovina 1984, updated by Christensen and Pauly

(early 1990s) - statistics added until current (year 2000) version. But basic equations are unchanged (and well-examined) for over 10 years.

• ECOSIM (and ECOSPACE) – Recent work to make a food web dynamic, theory and practice

new (some is un-reviewed with ad-hoc corrections).– Designed for quick running and exploring policy scenarios

• Strengths– Unified format is strength– Recent re-programming (Visual Basic 6→ .NET) October 2007

• Allows easier access to code and • Facilitates 2-way model coupling (interoperability)• Enhanced visualization

– Developers are creating basic database-driven models of all LMEs



Practical Application of EwE: Ecosystem Trophic Modeling

• Ecopath is used to organize data (esp. historical) on trophic interactions and population sizes. Has routines for entry of key data on the biology and exploitation of ecosystem groups, and for creating a mass-balance “snapshot” of an ecosystem.

• Ecosim builds dynamic predictions by combining the data with foraging arena theory. Provides dynamic simulation of effect changes in fishing or environmental regimes may have on fisheries catches (volume and value) and the abundance of various groups in the ecosystem.

• Ecospace for addressing spatial policy questions, esp. marine protected areas.

• Ecotrace for exploring ecosystem effects of persistent pollutants



What are the strengths of EwE model approach?• Ecosim is freely available, large user community• Improved understanding of data systems (multiple

agency, multiple scale data assimilation)• Functional response parameterization is very

flexible, much more advanced than many published forms

• Simulates a wide variety of fishing scenarios, including spatial management in Ecospace

• Simulates changes in production regimes• Ability to represent age structure for many groups• Biomass dynamics of whole ecosystem considered,

see both direct effects and side effects of scenarios• Broad user-group



Ecosystem models can improve our understanding of interactions between species, climate, fishing, and habitat.

The Atlantis ecosystem model (Fulton et al. 2004) is a strategic tool used to:

1. synthesize this information; 2. simulate possible ecosystem responses;3. identify key processes that govern ecosystem condition

Atlantis is programmed in C++ and is freely available (and become increasingly well-documented)

Atlantis (code base)



ab

cd

efg

3-dimensional structure of model

abcdefg0 m50

100150

550

1200

2400

200

Daily oceanographic fluxes(water, heat, salt)

into and out of each box arecontrolled by a ROMSoceanographic modelBiogeochemistry

Hydrographicsubmodel

Communitysubmodel

Habitat

Fisheriessubmodel

Climate and oceanography

Managementsubmodel

Assessment and policy decisions



Uses for Atlantis: Management Strategy Evaluation

Ecology and

Fishing Simulator(Atlantis)

Monitoring and Indicators

Assessments and Parameter Estimation

Implementation

Observations

1 year cycle

Observations

1 year cycle1 yr

cycle

Assessments and Parameter Estimation

Management policies: quotas,

effort limits, MPAs



Pros• Flexible options for predation, reproduction, growth, gape limitation

• MSE (monitoring, assessments, indicators, economics, management)

• Nutrient handling, and interfaces with ROMS oceanography output (and other hydrodynamics model output)

•Migrations out of region

Cons•Build time (6-12 months)

•Run time (hours- days)

•Lacks balancing routines

•Cumbersome parameterization

Atlantis – Pros & Cons



GADGET

• Forward simulation model• Create a virtual population within the model• Follow the fish through their lives

– Fishing, mortality, growth, maturation, etc.

• Process driven– E.g. percentage becoming mature, not percentage mature

at age



GADGET - Software

• Written in C++• Can be run under UNIX/Linux and PC (using cygwin)• Source code has to be downloaded, and then compiled on

local computer• Code has been used for many years – well tested• Documentation and examples available on-line• Graphics not included in package – only numerical output• Further development of code not decided at the moment –

main programmers have got new jobs



Gadget - Strengths

• Flexible tool• May integrate a wide variety of information on different

resolution (biological/spatial/temporal)• Model and data independent• Well documented• Suitable for modelling systems with a few main

species/interactions (e.g. boreal ecosystems)• Age data not needed• Gaps in data/knowledge may be identified – no hidden

assumptions



Opportunities for Parterships

NEMoW Steering Committee,Current Software Developers



Potential Partners in NEMoW (NMFS)

• NEMoW Steering Committee (NMFS)– Jason Link Northeast FSC– Howard Townsend NOAA Chesapeake Bay Office– Kerim Aydin Alaska FSC– Ned Cyr Office of Science &

Technology– Kenric Osgood Office of Science &

Technology– Todd Gedamke Southeast FSC– Jeff Polovina Pacific Islands FSC– Phil Levin Northwest FSC– George Watters Southwest FSC

• NEMoW Web Site– http://www.st.nmfs.noaa.gov/st7/nemow.htm



Potential Partners for Software Development

• Ecopath with Ecosim (EwE) – Villy Christensen, University of British Columbia Fisheries

Centre, Vancouver, British Columbia

• Atlantis– Beth Fulton, Commonwealth Scientific and Industrial

Research Organisation, Hobart, Tasmania

• GADGET - Globally applicable Area Disaggregated General Ecosystem Toolbox, www.hafro.is/gadget– Bjarte Bogstad, Institute of Marine Research, Bergen,

Norway

fisheries ecosystem models: technical details and prospects for partnerships howard townsend, ph.d....

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