# Presentation: 222521

## The Atlantis Ecosystem Modeling Framework

**Isaac Kaplan, Chris Harvey, Phil Levin, Jason Link, Howard Townsend**
**NOAA NMFS**
**Beth Fulton  CSIRO Australia**

**Notes:**
Al Hermann, PMEL

## 
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

- 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

## 3-dimensional structure of model

**3-dimensional structure of model**

**Daily oceanographic fluxes**
**(water, heat, salt)**
**into and out of each box are**
**controlled by a ROMS**
**oceanographic model**

**Biogeochemistry**

**Hydrographic**
**submodel**

**Climate and oceanography**

**Notes:**
Al Hermann, PMEL

## 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

**Beth**
**Tasmania**

**S.E. Australia**

**Santa Cruz**

**Long Island**

**N.E. **** U.S.**

**Cal.**** Current**

##   What are the key features/equations/functions/ assumptions of the model? 

## Primary producers

- Nutrients

- Space

- Disease, Lysis,
- Stress, Fouling

- Grazer A

- Detritus

- Light

- Grazer C

**Primary**
**producer**

## Invertebrate consumers

- Oxygen limitation

- Detritus

- Prey C

- Prey B

- Prey A

- Food availability

- Nutrients

- Predator B

- Predator A

- Predator C

**Invertebrate**

## Vertebrate consumers (age-structured)

- Reproduction

- Disease,
- Oxygen limitation

- Detritus

- Nutrients

**Vertebrate*****i***
- Reserve ║ Structure

- Prey C

- Prey B

- Prey A

- Gape limitation

- Predator B

- Predator A

- Predator C

## Vertebrate predation and reproduction

- Adults

- Prey abundance

- Prey Consumption per Predator

- Recruits

**Holling type II**

**Beverton Holt**

- OR
- Holling type I, Holling type III, Ecosim,  Size specific Holling type III, min-max

- OR
- Ricker, condition-dependent Beverton Holt, constant, lognormal, dependent on prim producers (Chla), dependent on all plankton, Bev-Holt with lognormal variation added, Bev-Holt with prescribed recovery, linearly dependent on maternal condition, pupping/calving a fixed number per adult spawning, or forced timeseries of recruitment

**Notes:**
Predation formulation switches. 0=Holling type II, 1=Holling type I, 2=Holling type III, 
# 3=ECOSIM (currently disabled), 4=min-max, 5=Size specific Holling type III
# 1=const, 2=dependent on prim producers (Chla), 3=Beverton-Holt, 4=lognormal, 5=dependent on all plankton
# groups not just Chla, 6=Bev-Holt with lognormal variation added, 7=Bev-Holt with "encourage recovery"   
# 8=Bev-Holt with perscribed "recovery", 9=Ricker, 10=Standard Bev-Holt (no explict use of spawn included)      
# 11=pupping/calving linearly dependent on maternal condition, 12=pupping/calving a fixed number per adult
# spawning, 13=forced timeseries of recruitment

## Spatially Explicit Output

- (Pleuronectids: Dover sole, rex sole, sanddab)
- (mg N/m3)

**Year 1**

**Year 40**

**Washington**

**Oregon**

**Cape Mendocino**

**Santa Cruz**

**Santa Barbara**

**Notes:**
Mar28b, 100-150m depth

## 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

**Notes:**
ADD MORE STUFF RE FISHERIES, CLIMATE, OCEANOGRAPHY

## 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

## Central California – Considering interactions between state and Sanctuary management

**S.E. Australia-Fleet Restructuring**
- Ecosystem-scale MSE
- 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)

**Central California – Considering interactions between state and Sanctuary management**

**Notes:**
For the southeast work - Atlantis used to ecosystem-scale EBFM MSE - highlighted pros and cons of 5 kinds of management strategies - results = none is a complete solution, but balanced use of levers is most effective vs objectives - facilitator of change - lead to further refinement of questions to ask (incentive systems, size of spatial management zones etc) For the indicators work - MSE tested hundreds proposed indicators (with fisheries dependent and independent "data") - Found: need a suite, cover range of species with different characteristics (fast turn-over, target, habitat, top predators), KISS, straw-man list shaped form of status indicator list - Into future hopefully shape reporting vs objectives and in decision rules (in tiered harvest strategies) 

## What are the strengths and weaknesses of the model?

## Atlantis

**Pros**
** ****Flexible options for predation, reproduction, growth, gape limitation**
** ****MSE (monitoring,  assessments, indicators, economics, management)**
** ****Nutrient handling, and interfaces with ROMS oceanography output**
**Migrations out of region**

**Cons**
**Build time (6 months)**
**Run time (hours-****	****days)**
**Lacks balancing routines**
**Cumbersome parameterization**

**Notes:**
Adaptive environmental assessment (AEA) tradition for ecospace
Sensitivity runs difficult

## Model development and improvement

- Output graphics code for total biomass time series, biomass per region, and weight-at-age
- Diet handling
- Improved user interface and parameter input

**Weight-at-age**

## Funding

- NOAA NMFS
- NOAA Fisheries and the Environment (FATE)
- NOAA NMFS Economics Program
- Moore Foundation
- Packard Foundation
- Contacts
- Beth Fulton  _[Beth.Fulton@csiro.au](mailto:Beth.Fulton@csiro.au)_
- Isaac Kaplan _[Isaac.Kaplan@noaa.gov](mailto:Isaac.Kaplan@noaa.gov)_
- Jason Link   _[Jason.Link@noaa.gov](mailto:Jason.Link@noaa.gov)_

## Weight-at-age

**Weight-at-age relative to expectation from von Bertalanffy**

**Age class 1**

**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

- Catch

- Carrion

- Catchability

- Availability

- Selectivity

- Fish, age *i*

- Effort

- Fleet B

- Fleet A

- Fleet C

## 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

- 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

**Chloro- phyll a**
**(mg N/m****3****)**

**Year 1**

**Year 40**

**Notes:**
March28b

## Outputs with No Fishing

- (mg N/m3)

**Year 1**

**Year 40**

**Notes:**
Mar28b, 100-150m depth

## Outputs with No Fishing

- (Pleuronectids: Dover sole, rex sole, sanddab)
- (mg N/m3)

**Year 1**

**Year 40**

**Notes:**
Mar28b, 100-150m depth

## Scoping

- Identify goals of EBM and

- threats to achieving goals

- Develop ecosystem indicators

- and targets

- Risk Analysis

- Characterization of

- susceptibility to

- perturbation

- Characterization of

- resiliency to

- perturbation

- Assessment of ecosystem status

- relative to EBM goals

- Management Actions

- Data Acquisition

- Monitoring of

- Ecosystem Indicators

## Testing Ecosystem Indicators

- Changes in ecosystem pressure (e.g., temperature) or ecosystem attribute of interest (trophic structure)

**Indicator**

**Attribute**

**Attribute**

**Indicator**

## 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?

## Slide 40

## Slide 41

## Project 2: English Sole and Canary Rockfish

**Real World**
**Ecology**

**Decision Rule**

**Stock Synthesis II**
**Assessments and Parameter Estimation**

**Implementation**
**+ error**

**2 yr **
**cycle**

**Observations of Stock**

- Current Management

## Management Strategy Evaluation

**Atlantis Ecology and Fishing Simulator**

**Decision Rule**

**Stock Synthesis II**
**Assessments and Parameter Estimation**

**Implementation**
**+ error**

**Ecological Indicators**

**2 yr **
**cycle**

**Observations of Stock**

**Climate Indicators in Assessments and Management Decisions   ****(w/ Ian Stewart, NWFSC)**

## Atlantis	

**Management Strategy Evaluation**** ****	****Test **_**monitoring**_**, **_**indicators**_**, ****	**_**assessments and regulations**_
**Integrating**** ecosystem information**
**Strategic planning**** for fisheries management**

**Notes:**
MENTION ITQ PLANNING. 

## Contacts:

- Phil Levin _[phil.levin@noaa.gov](mailto:phil.levin@noaa.gov)_
- 	(206)860-3473
- Isaac Kaplan _[isaac.kaplan@noaa.gov](mailto:isaac.kaplan@noaa.gov)_
- 	(206)302-2446