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The Atlantis Ecosystem Modeling Framework - NOAA

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					The Atlantis Ecosystem
 Modeling Framework




  Isaac Kaplan, Chris Harvey, Phil Levin,
      Jason Link, Howard Townsend
               NOAA NMFS
       Beth Fulton CSIRO Australia
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
 Management
3-dimensional structure of model and policy decisions
                        Assessment
   submodel

                                                               a
  Fisheries
          g             f e d   c   ba                    c
                                                              b
 0m
 submodel
  50                                                     e
                                                          d
 100                                                   f
                                                   g
 150
 200


Community
 550
 submodel
                  Habitat
 1200
                                          Daily oceanographic fluxes
                                               (water, heat, salt)
 2400                                    into and out of each box are
                                            controlled by a ROMS
                                              Biogeochemistry
Hydrographic                                oceanographic model
 submodel
                            Climate and oceanography
                  Atlantis Models
Fully Developed
•       SE Australia
•       Port Phillip Bay, Aus.

Mostly Completed
       Westernport, Australia
•      Northeast US
•      California Current

Early Stages
•       Torres Strait
•       Coastal NSW
•       Clarence River NSW
•       SW Australia
•       Ningaloo Marine Park
•       SE Tasmania
•       Central California
 S.E. Australia

                       Cal.
  Beth                Current
Tasmania




N.E.
U.S.              Santa
                  Cruz


   Long Island
       What are the key
features/equations/functions/
 assumptions of the model?
Primary producers

                               Nutrients            Detritus
      Light


                     Primary                Disease, Lysis,
                    producer                Stress, Fouling


      Space
                       Grazer    Grazer    Grazer
                         A         B         C
dP
      P   light   nut   space   M grazing M linear
dt                                      grazers
Invertebrate consumers
                                           Nutrients        Detritus
 Food availability
                                                 Disease,
      Prey A                                  Oxygen limitation

      Prey B               Invertebrate
      Prey C
                            Predator     Predator      Predator
                               A            B             C

  dB
       B  Aprey   assim   oxygen   space   M pred M linear
  dt prey                                           preds
Vertebrate consumers (age-structured)
                                                      Nutrients         Detritus
      Prey availability
                                                                Disease,
      Gape limitation
                                                             Oxygen limitation

                                Vertebratei
                                                                      Predator A
       Prey A                  Reserve ║ Structure
                                                                      Predator B
       Prey B
                                                                     Predator C
       Prey C
                                             Reproduction
dB
         B  Aprey   assim   oxygen   space   M pred  M linear  M quad
 dt      prey                                        preds
  Vertebrate predation and reproduction
Prey Consumption per




                       Holling type II                                Beverton Holt
      Predator




                                                   Recruits
                       Prey abundance                                          Adults

                            OR                                                OR
                                                            Ricker, condition-dependent Beverton Holt,
                                                              constant, lognormal, dependent on prim
               Holling type I, Holling type III,         producers (Chla), dependent on all plankton, Bev-
             Ecosim, Size specific Holling type          Holt with lognormal variation added, Bev-Holt with
                                                            prescribed recovery, linearly dependent on
                         III, min-max                       maternal condition, pupping/calving a fixed
                                                          number per adult spawning, or forced timeseries
                                                                           of recruitment
          Spatially Explicit Output
                                     Washington


                                     Oregon

Small flatfish
(Pleuronectids:                  Cape
                                 Mendocino
Dover sole, rex
sole, sanddab)                               Santa Cruz

(mg N/m3)                  Santa Barbara




                  Year 1                                  Year 40
Spatially Aggregated Output
What are the data requirements?
      Atlantis biological parameters
For each species
• Abundance per area
• Individual growth rates, length-weight conversions
• Max age, and age-at-maturity
• General habitat preferences
• Dispersal and/or migratory characteristics, within
       and outside model
• Diets
• Recruitment parameters (e.g. Beverton Holt, Ricker)
For ecosystem map
• Habitat distribution (bottom type + biogenic habitat)
For calibration
• Historical catch and abundance data
What key data gaps have been identified?
Are these data gaps informing monitoring
                efforts?


•Biomass estimates: nearshore and pelagic
     species, lower trophic levels (jellyfish,
     benthos, etc.)
•Diets
•Bycatch rates
•Fleet costs (US) and social factors
     governing fleet behavior
What is the model being used for?
  Is it used for management?
 Management Strategy Evaluation

             Observations       Monitoring and Indicators

 Ecology
   and
 Fishing          yr
                1 year
               1cycle               Assessments and
                                    Assessments and
                                       Parameter
                                       Parameter
Simulator       cycle
               cycle                   Estimation
                                       Estimation
(Atlantis)
               Implementation     Management policies:
                                          quotas,
                                   effort limits, MPAs
Central California – Considering   S.E. Australia-Fleet Restructuring
interactions between state and     •Ecosystem-scale MSE
    Sanctuary management
                                   •Pros and cons of 5 kinds of
                                   management strategies
                                   • Results = balanced use of levers
                                   is most effective
                                   •Led to refinement of questions
                                   (incentive systems, size of spatial
                                   management zones etc)
                                        S.E. Australia- Indicators
                                   •MSE tested hundreds proposed
                                   indicators (with fisheries dependent
                                   and independent "data")
                                   •Results=need a suite, cover range
                                   of species with different
                                   characteristics
                                   •Will shape reporting and decision
                                   rules (in tiered harvest strategies)
What are the strengths and
weaknesses of the model?
                         Atlantis
Pros                          Cons
• Flexible options for        •Build time (6 months)
predation, reproduction,
growth, gape limitation
                              •Run time (hours- days)
• MSE (monitoring,
assessments,                  •Lacks balancing routines
indicators, economics,
management)
                              •Cumbersome
• Nutrient handling, and      parameterization
interfaces with ROMS
oceanography output

•Migrations out of
region
       Model development and
           improvement
• Output graphics code for total




                                   Weight-at-age
  biomass time series, biomass
  per region, and weight-at-age

• Diet handling

• Improved user interface and
  parameter input
               Funding
• NOAA NMFS
• NOAA Fisheries and the Environment
  (FATE)
• NOAA NMFS Economics Program
• Moore Foundation
• Packard Foundation

               Contacts

Beth Fulton Beth.Fulton@csiro.au
Isaac Kaplan Isaac.Kaplan@noaa.gov
Jason Link Jason.Link@noaa.gov
                   Weight-at-age

  Weight-at-age                    Age class 1
   relative to
expectation from
 von Bertalanffy                   Age class 10
    Atlantis publications are peer reviewed
Journal Articles
• Fulton, E. A. 2004. Biogeochemical marine ecosystem models II: the effect of
   physiological detail on model performance. Ecological Modelling 173:371-406.
• Fulton, E. A., and A. D. M. Smith. 2004. Lessons learnt from a comparison of three
   ecosystem models for Port Phillip Bay, Australia. South African Journal of Marine
   Science 26:219-243.
• Fulton, E. A., A. D. M. Smith, and C. R. Johnson. 2003a. Effect of complexity on
   marine ecosystem models. Marine Ecology Progress Series 253:1-16.
• Fulton, E. A., A. D. M. Smith, and C. R. Johnson. 2003b. Mortality and predation in
   ecosystem models: is it important how these are expressed? Ecological Modelling
   169:157-178.
• Fulton, E. A., A. D. M. Smith, and C. R. Johnson. 2004. Effects of spatial resolution
   on the performance and interpretation of marine ecosystem models. Ecological
   Modelling 176:27-42.
• Fulton, E. A., Smith, A. D. M., and Punt, A. E. 2005. Which ecological indicators can
   robustly detect effects of fishing? ICES Journal of Marine Science, 62: 540-551.
Technical Documents
•    Brand, E. J., I. C. Kaplan, C. J. Harvey, E. A. Fulton, A. J. Hermann, J. C. Field and P.S. Levin. In press. A
     Spatially Explicit Ecosystem Model of the California Current’s Food Web and Oceanography. NOAA Tech Memo.
     NMFS-NWFSC.
•    Fulton, E.A., Fuller, M., Smith, A.D.M. and Punt, A., 2005. Ecological Indicators of the Ecosystem Effects of
     Fishing: Final Report. Australian Fisheries Management Authority Report, R99/1546.
•    Fulton, E.A., Slater J., Smith, A.D.M. and Webb, H., 2005. Ecological Indicators for the Impacts of Fishing on Non-
     Target Species, Communities and Ecosystems: Review of Potential Indicators. Australian Fisheries Management
     Authority Report, R99/1546-A.
•    Fulton, E. A., Smith, A. D. M., and Punt, A. E. 2003. Indicators of the Ecosystem Effects of Fishing: Case-Study 1
     – Temperate Bay Ecosystem. Milestone Project Report, CSIRO Marine Research, Hobart.

The code base is not (but is the product of 10+ years of
              work by many at CSIRO)
Fisheries: age-specific catch

                                                                            Carrion
                    Effort                                  Catch
Fleet A
                Availability
Fleet B
                                                   Fish, age i
Fleet C        Catchability

                 Selectivity


          Fi  Bi  effort i  icatchability  i avail  i selectivity
• Key elements for each presentation:    What is/has/will the model
  be used for?
   What are the data requirements?
   What key data gaps have been identified?
   Are these data gaps informing monitoring efforts?
   What are the key features/equations/functions/assumptions of the
  model?
   What are the strengths of this model?
   What are the weaknesses of this model?
   Has the model been published in the peer reviewed literature?
   Has the model & software been through a formal peer review?
   Have the model outputs been through a formal peer review?
   How portable is the model software package?
   What remains for model
  development/improvement/enhancement?
   Has/is/will the model outputs be used in LMR management?
 Improved Diet Handling
(Jason Link and Robert Gamble)
Atlantis Model
of the
California
Current
Model food web has 56 functional groups, including:
• 3 primary producer groups
• 2 bacteria groups
• 3 infaunal invertebrate groups
• 9 epifaunal invertebrate groups
• 5 pelagic invertebrate groups
• 21 fish groups
• 3 seabird groups
• 6 marine mammal groups
• 2 detritus pools
California Current Ecosim model
      Field (2004, 2006)
  Fisheries

To date:
PacFIN catch per region,
1981-2004

Future work:
Fleet dynamics calibrated
to historical catches, and
limited by spatial or
seasonal closures, quotas
or effort limits
                             Groundfish trawling effort off
                             central Oregon Coast, 2003
Model Dynamics
       Outputs with No Fishing
                                   Cape Flattery


                                        Columbia River

 Chloro-
 phyll a                      Cape Blanco



(mg N/m3)                    Cape Mendocino



                                                   Monterey
                                                   Bay


                     Point Conception




            Year 1                                            Year 40
        Outputs with No Fishing


Deep corals
   and
anemones
(mg N/m3)




              Year 1              Year 40
          Outputs with No Fishing


Small flatfish
(Pleuronectids:
Dover sole, rex
sole, sanddab)

(mg N/m3)




                  Year 1            Year 40
                                    Scoping
                          Identify goals of EBM and
                          threats to achieving goals




                        Develop ecosystem indicators
                                and targets




                        Risk Analysis
                       Characterization of   Characterization of
                        susceptibility to      resiliency to
                          perturbation          perturbation
  Data Acquisition

   Monitoring of
Ecosystem Indicators

                       Assessment of ecosystem status
                            relative to EBM goals




                              Management Actions
                          Testing Ecosystem Indicators
                                    – Changes in ecosystem pressure (e.g., temperature) or
                                      ecosystem attribute of interest (trophic structure)


                                                                                                                                          2
                                                                                                                                         1.




                                                                                                                                          1




                                                                                                                                     Indicator
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                          1.2                                          Indicator                                                         0.
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Attribute and Indicator




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                           0
                                    Attribute
                                1   3   5   7   9   11   13 15   17   19 21 23 25 27 29   31 33 35 37 39   41 43 45 47 49   51 53
                                                                               Time
  Project 1: Indicators of Fishing
              Impacts
• A first cut…
  – For fished species, remove a fixed
    amount of biomass annually from
    standing stock
    • We show removals as a % of baseline
      biomass
  – After 25 years, examine changes in
    ecosystem structure
  – What indicators reveal this change?
             Piscivore : Planktivore
0.6
0.5
0.4
0.3
0.2
0.1
 0
      0




                                       0.1


                                                    0.2
                                                          0.3
                                                                0.5
                                                                      0.7
          0.01
                 0.03
                         0.05
                                0.08


                                             0.15
                        Removal scenario
                     4                                all
                                                      target species
Mean trophic level



                     3



                     2



                     1
                         0   0.03 0.08 0.15     0.3
                             Removal scenario
Project 2: English Sole and Canary Rockfish
             Current Management

             Observations of Stock

                                     Stock Synthesis II

Real World                           Assessments and
                                        Parameter
                                        Estimation
 Ecology
                    2 yr
                   cycle


                  Implementation      Decision Rule
                      + error
    Management Strategy Evaluation
 Climate Indicators in Assessments and
 Management Decisions (w/ Ian Stewart, NWFSC)
              Observations of Stock

                                         Stock Synthesis II
                 Ecological Indicators
  Atlantis                               Assessments and
                                            Parameter
  Ecology                                   Estimation
and Fishing          2 yr
 Simulator
                    cycle


                   Implementation         Decision Rule
                       + error
             Atlantis
• Management Strategy Evaluation
    Test monitoring, indicators,
    assessments and regulations

• Integrating ecosystem information
• Strategic planning for fisheries
  management
               Contacts:
• Phil Levin phil.levin@noaa.gov
  (206)860-3473

• Isaac Kaplan isaac.kaplan@noaa.gov
  (206)302-2446

				
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