# Presentation: 763990

## Introduction to fisheries ecosystem modeling requirements

**Howard Townsend, Ph.D.**
**NOAA Chesapeake Bay Office (NMFS)**
**Cooperative Oxford Lab (NOS/NCCOS)**
**Jonathan Phinney, Ph.D.**
**Southwest Fisheries Science Center (NMFS))**
**December 9, 2008**

## Presentation Outline

- Introduction
- NMFS View of Modeling
- Models for Current Single Sector/Species Approach Fisheries Management
- Evolution of Models for Multi-Species/Multi-Sector/Ecosystem-based Approach to Fisheries Management
- Integrated Ecosystem Assessments
- UNDERLYING THEME: NEED MODELS THAT ARE USEFUL FOR FISHERIES MANAGERS
- Current and Potential uses of Environmental/Oceanographic models for  Single Sector/Species Approach Fisheries Management
- Environmental Parameters in Stock Assessment models
- Forecasting/projection models for fish movements (migration, spawning, larval transport)
- Current and Potential uses of Environmental/Oceanographic models for   Multi-Species/Multi-Sector/Ecosystem-based Fisheries Management
- Ecopath with Ecosim – Ecospace
- Atlantis models
- Other Modeling Efforts
- Other Ideas/suggestions
- Potential demonstration projects between NMFS and NWS NCEP
- Workshop with NMFS Ecosystem Modelers
- Use NCEP approach as a framework for making NMFS Ecosystem Models

**Notes:**
First, with out spending too much time looking under the hood, introduce the new direction of fisheries management and the Magnuson-Stevens mandate

Second, highlight potential and current applications where fisheries ecosystem modelers have or could use NCEP models and output

## NOAA Ecosystem Drivers

- NOAA Strategic Plan (2002)
- 		“Improve resource management by **advancing our understanding of ecosystems through better simulation and predictive models**.”
- NOAA Five-year Research Plan (2007)
- 		“NOAA forecasts will provide the needed decision-support tools for adaptive, ecosystem-based management of fisheries and marine resources, to predict human impacts on ecosystems, and to protect human health.”
- 		“Create biophysical coupled models of water mass movements and their effects on biological productivity including fisheries recruitment and population distribution.”

## Ecosystem Drivers (continued)

- Magnuson Stevens Fishery Conservation and Management Reauthorization Act (2006)
- 		“The Secretary shall undertake and complete a study on the state of the science for advancing the concepts and **integration of ecosystem considerations in regional fishery management**.”
- JSOST Ocean Research Priorities Plan (2007)
- 	“**New modeling and analysis procedures** will be developed to provide the foundation for comparative analyses and evaluation of ecosystems
- NMFS is moving towards ecosystem-based management – building the road as we go

## Brief Primer on NMFS Modeling

**Notes:**
NMFS View of Modeling 
Growing importance within NMFS in response to “Ecosystem Based Management” of fisheries (MSA reauthorization 2007)
Modelers are located at the 6 Regional Fisheries Science Centers
Ecosystem Modeling coordination through Fisheries HQ- Office of Science & Technology
 John Boreman (Director)
Ned Cyr (Head- Marine Ecosystem Division)

Some ad hoc efforts through Habitat Conservation (Chesapeake Bay Office)

## **Regional Ecosystem inland boundaries include the coastal watershed and the inland extent of the diadromous fish habitat see details at http://ecosystems.noaa.gov/workshops_&_meetings.htm

********Regional Ecosystem inland boundaries include the coastal watershed and the inland extent of the diadromous fish habitat** **see details at** http://ecosystems.noaa.gov/workshops_&_meetings.htm

- NOAA Regional Ecosystems in the US EEZ

**Notes:**
NMFS View of Modeling
In broad strokes, NMFS has purview over 8 large marine ecosystems in and around the US

## Example of NMFS Data for Transboundary fisheries in Atlantic and Pacific Ocean- Example Highly Migratory Species: sharks, tuna (albacore and big eye), billfish tagging and landings data

- Albacore

- Credit: Koehn SWFSC

**Notes:**
NMFS View of Modeling

Fisheries has concerns about fish species at a wide range of levels

From large cross -boundary ocean basins...

**Example of Predictive Model for Salmon Pre-spawn Mortality in WA**

**Notes:**
NMFS View of Modeling

To small spawning habitat areas within counties

## National Ecosystem Modeling Workshop (NEMoW)

- A national workshop to standardize/unify methodologies and approaches when using ecosystem, bio-physical and multispecies models
- Responsive to a wide range of calls for EAM/EAF/IEA/etc.
- Analogous to NSAW and Nat’l Economists Meetings
- Report Published in February 2008 _[spo.nwr.noaa.gov/tm/tm87.pdf](http://spo.nwr.noaa.gov/tm/tm87.pdf)__[ ](http://spo.nwr.noaa.gov/tm/tm87.pdf)_
- NEMOW II planned for late FY09

**Notes:**
NMFS View of Modeling

Supported NEMoW as a way to begin unifying approaches

MSA- integration of ecosystem considerations in regional fishery management. 

## Changing View of Fisheries: Single Sector Management

- Changing View of Fisheries: **Single** Sector Management

**Notes:**
NMFS View of Modeling

A shift from management based on singles species concerns 

## Changing View of Fisheries: Ecosystem-based Management

- Changing View of Fisheries: Ecosystem-based Management

**Notes:**
NMFS View of Modeling

To multiple sector concerns is occurring.
NMFS needs to provide a framework for unifying methodologies and approaches when using ecosystem, bio-physical and multispecies models for resource managemnt and policymaking

## Simple Processes for Fish Management

**Notes:**
Models for Current Single Sector/Species Approach Fisheries Management

Historically, focus on simple fish population dynamics and harvest processes 

## "Simple" Fisheries Indicators

- Credit: Bonzek, VIMS

**Notes:**
Models for Current Single Sector/Species Approach Fisheries Management

 Models for fisheries stock assessments can be quite complex; however, implications for poilicy have to be boiled down into simpler terms for clear communications.

Similiarly, Adding environmental parameters and ecosystem factors will increase the complexity of fisheries management models Ultimately, the methods for translating from models to fisheries policy and regulation should be kept straightforward

## Gradient of Possibilities

- Stock/Single Species

- Ecosystem

- Multi-species

- Aggregate Biomass

- SS models, forget ecosystem issues

- Messy Picture Here

*Gadids*

*Flatfish*

*Pelagics*

**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 population dynamics

- Credit: Link, NEFSC

**Notes:**
Evolution of Models for Multi-Species/Multi-Sector/Ecosystem-based Approach to Fisheries Management

We are beginning to develop models that take more of the picture into account; however, management practices move slower than the pace of model development

## Infrastructure necessary for Integrated Ecosystem Assessments

**Notes:**
Integrated Ecosystem Assessments
-where NMFS, NOS etc goinig for Ecosystem-based manaagement

Will require integration of data and modeling...

So this type of meeting is a step in that direction

## Current and Potential uses of Environmental/Oceanographic models for Single Sector/Species Approach Fisheries Management

## Environmental Parameters in Stock Assessment models

- Integrating environmental time series into stock assessment models and to test the significance of correlations between population processes and the environmental time series
- Low-hanging fruit and is being done with products currently available
- STATUS; Simple correlations are being used, and has promise

**Notes:**
Environmental Parameters in Stock Assessment models

[Jonathan, if you have anything here to spice this up that would be great]

## Marine Mammal Density Field

**Marine Mammal Density Field**
** ****Forecasts**

**Marine Mammal Survey Data**

**Habitat Data**

**Mathematical Models of Marine Mammal Density**

**Marine Mammal Data 1986-2002:**
-  Ship and aerial surveys
*  **Southwest Fisheries   *
*  **Science Center*

**Habitat Data 1986-2002:**
-  In situ oceanographic
-   and prey data
*  **Southwest Fisheries *
*  **Science Center*
-  Remotely Sensed data

**Notes:**
Forecasting/projection models for fish movements (migration, spawning, larval transport)

This has been imporatant for southern california bight

Navy has been used for using sonar because it interferes with endangered species, so DOD has funded

## Forecast Coho salmon returns in the Columbia River

- 4.  Northern Copepods v Chinook

- Biological transition v. coho

- 3.  Northern Copepods v coho

- Hydrographic spring transition
- (upwelling event Pacific NW)

- (NWFSC- Bill Peterson -_[bill.peterson@noaa.gov](mailto:bill.peterson@noaa.gov)_ )

**Notes:**
Forecasting/projection models for fish movements (migration, spawning, larval transport)

Pacific States Fisheries Management Council – status of the California Current

Long-term record of hydrographic data correlates with important predators (copepods) and has relevance for fished species

2008 shutdown fishery, $170M in disaster relief

## Other Pilots

- Madden Julian Oscillation wind fields and timing and duration of upwelling in Pacific NW for salmon (NCEP and NMFS NW/SWFSC)
- • SST and Sardine Habitat and Productivity (SIO and NMFS SWFSC)
- SST and Loggerhead Turtle distribution for HI Longline fishery.
- GFDL MOM downscaling for CA Current salmon fishery. (OAR-NMFS Joint Post-doc)

## Forecast Marine Mammal Distribution in Southeast Atlantic

- Run existing HYCOM variables (120 d, surface currents, T0, Salinity, thermocline depth and intensity, fronts):
- Right whale calving on Southeast Atlantic Shelf (Cape Hatteras to FL Bay)
- (NCEP– Hendrik Tolman, Carlos Lorzano and SEFSC Lance Garrison -Lance.Garrison@noaa.gov)

**Notes:**
[Jonathan, we have 5 demo projects under forecasting, is there just  1 or two that have progressed and we could highlight?]
[Jonathan – any other info?]

Work is being done at the hobby level

## Ongoing: Nowcasting Sea nettles in the Chesapeake Bay

- Credit; Brown, NESDIS

**Notes:**
Forecasting/projection models for fish movements (migration, spawning, larval transport)

Basic Approach could be applied to many fish populations in Chesapeake Bay and in other estuarine and coastal systems-

Would be good to be able to forecast SST, salinity, etc

Use basic environmental parameters (SST, salinity, etc) and couple with statistical models based on species life histories

We have some success working with partners to demonstrate physico-chemical and biological connections in a way that is useful for the public-

The next step is to overlay model estimates of where organisms ought to be –with actual data on where they are, then we can perhaps move towards predicting where and
How much there will be in a population

## Environmental/Oceanographic models for Multi-Species/Multi-Sector/Ecosystem-based Fisheries Management

- STATUS: Maturing – with environmental parameters included in the ecosystem models

**Notes:**
Discuss briefly the current leading approaches /software (EwE and Atlantis0

Discuss briefly some other efforts around the NOAA regions

## Ecopath with Ecosim:Biomass dynamics equations

- For Biomass of group i,
- dBi /dt = 	GEi ∑prey Q(BiBprey) consumption gain
- 			- FiBi  		   fishing loss
- 			- M0iBi  		   other mortality loss
- 			- ∑pred Q(BpredBi) 	   predation loss
- 			+I			   immigration rate

**Notes:**
Ecopath with Ecosim – Ecospace

Ecopath created 25 years ago  by Jeff Polovina (NMFS, PIFSC)
Most commonly used software and still beiung developed, refined and supported
Strength in simplicity

## Ecopath with Ecosim - Ecospace

**Notes:**
Ecopath with Ecosim – Ecospace

Currently, runs using preprogrammed migration route on monthly time step – 
 New modularized EwE6 could allow applications
Recently  have  added spatial field handling for Ecospace (any number of fields, e.g., salinity, oC, O2, pH)

## Ecospace Applications –linkages and coupling to hydro/ocean models 

- ROMS, hydrodynamic, and climate models
- NOAA Geophysical Fluid Dynamics Lab/Princeton
- Florida Bay Ecosystem Model (FLEM)
- /Chesapeake Bay Regional Estuarine Ecology Model (CBREEM)
- European Regional Seas Ecosystem Modeling (ERSEM)
- EwE-Marine Protected Area optimization & MARXAN bridge
- Potential to add HYCOM connection
- Villy Christensen, University of British Columbia Fisheries Centre (v.christensen@fisheries.ubc.ca)

**Notes:**
Ecopath with Ecosim – Ecospace

Currently, runs using preprogrammed migration route on monthly time step – 
 New modularized EwE6 could allow applications
Updated to a modern Integrated Development Environment (.NET) to ensure compatibility and extensibility with modern and future techniques
Fully OOP-implementation
Allow components of EwE to connect to other programming environments
Localization
The European Regional Seas Ecosystem Model (ERSEM) is a set of biogeochemical modules describing the cycling of carbon, the macro-nutrients N, P and Si and oxygen (O) through the lower trophic levels in temperate shelf seas. 

## Atlantis: Management Strategy Evaluation

- Simulate management cycle to explore policy effectiveness and impacts -  to explore multiple policy alternatives

- Credit: B. Fulton, CSIRO

**Notes:**
Atlantis models

Strategic tool in that it is designed to be used for management strategy evaluation (MSE).  So links with 

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)

## N.E.  U.S.

**Santa Cruz**

**Long Island**

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

**Cal.**** Current**

**Chesapeake Bay**

- Atlantis being used by NMFS in these areas

**Notes:**
Atlantis models

Are beginning to pop up around the US

## More Information on Modeling Efforts:Chesapeake Bay coupled Water Quality Model and Fisheries Ecosystem Model

- Hongguang Ma, NCBO
- http://www.chesapeakebay.net/pubs/subcommittee/mdsc/doc-2002_Eutrophication_Model.pdf
- http://noaa.chesapeakebay.net/EcosystemModel.aspx

**Notes:**
Other Modeling Efforts

The Chesapeake Bay Water Quality modeling suite includes the linked Airshed Model, Watershed Model, Estuarine Hydrodynamic Model, Estuarine Water Quality Model, and Living Resources Model developed by the Chesapeake Bay Program (led by EPA).  Chesapeake Bay Fisheries Ecosystem Model (using EwE) was developed by NOAA Chesapeake Bay Office.  The modeling suites are linked using physical forcing functions.

## The way forward – linking NCEP and NMFS efforts

- Workshop with NMFS Ecosystem Modelers from regional science centers and NCEP
- Continued development of pilot projects around the country
- Use NCEP operational approach as a framework for developing NMFS Ecosystem Models and Modeling Approaches

**Notes:**
Discsussion

## Additional Pilot Demonstration:  Larval fish and shrimp connectivity in the Gulf of Mexico

- Develop Ekman Transport index to test whether larvae are transported into coastal estuaries.
- “Intelligent” particle tracking model.
- Existing work at the Stennis Space Center uses NRL NGOMNFS.
- (SEFSC- Woody Nero Woody.Nero@noaa.gov)

**Notes:**
[Jonathan, we have 5 demo projects under forecasting, is there just  1 or two that have progressed and we could highlight?]

## Additional Demonstration Project: Forecasting coastal and ocean salinity in the Chesapeake

- Many Bay species (e.g., blue crab, striped, bass, menhaden) are dependent on ocean currents and bay SST and salinity for successful migration and recruitment
- Create forecast system based on ocean currents and bay environmental forecast to predict recruitment success

## For more info and discussion about NMFS environmental and ecosystem modeling

- Contact
- Howard Townsend (_[Howard.Townsend@noaa.gov](mailto:Howard.Townsend@noaa.gov)_)
- Jonathan Phinney (_[Jonathan.Phinney@noaa.gov](mailto:Jonathan.Phinney@noaa.gov)_)

## Extra slides

- Run through if time available

## Potential Demonstration project #1: Run existing HYCOM variables (120 d, surface T0, salinity, thermocline depth and intensity, fronts) for: Larval fish connectivity in Western Pacific

- 1000E 800W longitude; 300S 600N Latitude
- 1650W 1500W long.; 150N 250N lat.
- 1600E 1400W long.; 00 450N lat. (HI)
- HMS, Turtles, sea birds distribution in North Pacific (PISFC)
- 1000E 800W longitude; 00 600N
- (PIFSC-Donald Kobayashi -Donald.Kobayashi@noaa.gov)

**Notes:**
[Jonathan, we have 5 demo projects under forecasting, is there just  1 or two that have progressed and we could highlight?]

## Potential Demonstration Project #3: Marine Mammal Distribution in Eastern Tropical Pacific

- Run existing HYCOM variables (120 d, surface T0, Salinity, thermocline depth and intensity, fronts):
- Existing cetacean-habitat model predictions(colored dots) of offshore spotted dolphin population density compared to sighting locations (black triangles).
- SWFSC- Megan Ferguson (Megan.Ferguson@noaa.gov)

**Notes:**
[Jonathan, we have 5 demo projects under forecasting, is there just  1 or two that have progressed and we could highlight?]

Maybe highlight this one?

## Potential Demonstration Project # 4: Sea Ice distribution and fishing pressure in Antarctica

- 120 d, surface currents, T0, Salinity, thermocline depth and intensity, fronts)
- Determine overwintering of distribution of seals and penguins and fishing patterns with sea ice.
- SWFSC- Christian Reiss christian.reiss@noaa.gov

**Notes:**
[Jonathan, we have 5 demo projects under forecasting, is there just  1 or two that have progressed and we could highlight?]

Maybe highlight this one?

## More Information on Modeling Efforts:NPZ-Cal

- Prey Field

- Andrew Leising, SWFSC-ERD

- Temperature

- Observations
-  or GCM model

**Notes:**
Other Modeling Efforts

NPZ model driven by assimilated or observed physical data or environmental indices (e.g. upwelling index), which then serves as prey fields for more complex Calanus spp. individual-based model.  Run in 1D (vertical )boxes covering various west coast locations. No fish yet.

Either physical observations (in this case, I show an interpolated temperature field from MBARI’s M2 mooring on the edge of Monterey Bay) or output from a physical model is used as the physical input, primarily temperature and mixing dynamics, for both an NPZ and the IBM.
The NPZ then provides detailed prey field which can be fed to the IBM (e.g. different life stages consume different “boxes” or prey types).
The copepod IBM (to date, we’ve done simulations for Calanus pacificus, Calanus marshallae, and some runs on the Atlantic congener, Calanus finmarchicus) uses the NPZ output, and the temperature field from observation or physical model data.
Output from the IBM then includes multiple indices, such as egg production, and adult biomss, which could then be used as inputs into higher trophic level models. 

## More Information on Modeling Efforts: DisMELS

- Buck Stockhausen, AFSC
- http://www.afsc.noaa.gov/quarterly/jas2006/divrptsREFM6.htm

**Notes:**
Other Modeling Efforts

DisMELS (Dispersal Model for Early Life Stages)
A coupled biophysical individual-based model that incorporates ontogenetic changes in early life stage parameters and simulates egg and larval dispersal under 3-dimensional (3D) oceanographic currents

## PICES NEMURO Model Suite

- NEMURO
- 11-box plankton model, tracking N and Si
- Variants: e-NEMURO, fe-NEMURO, ROMS-NEMURO, NEMURO-ESMF
- NEMURO.FISH
- Saury/herring bioenergetics model linked to NEMURO
- NEMURO.SAN (under development)
- 3-species (sardine & anchovy + predator) 2-D IBM linked to NEMURO
- Ecological Modelling special issue, v. 202 #1-2

**Notes:**
Other Modeling Efforts

The NEMURO (North pacific Ecosystem Model for Understanding Regional Oceanography) suite of models has been developed by the North Pacific Marine Science Organization (PICES) MODEL Task Team for examining the influence of ocean variation on plankton and fish production around the North Pacific.  It consists of a base nutrient-plankton model (NEMURO) with a number of variants, with linked fish bioenergetic models:  NEMURO.FISH (single-pool mass-balance Wisconsin-type bioenergetics model) and NEMURO.SAN (two-species IBM migration and bioenergetics model).
The models are documented in a recent special issue of Ecological Modelling.

## NEMURO.FISH

- Megrey et al. 2006 Ecol. Model.

**Notes:**
Other Modeling Efforts

This shows the structure of the NEMURO plankton model linked with a fish compartment in NEMURO.FISH.

## Slide 42

**Notes:**
Other Modeling Efforts

We are currently re-implementing NEMURO and NEMURO.FISH within the Earth Systems Modeling Framework, which is a modular software framework for developing gridded component models for global climate change simulation projects.  This effort will provide a modular interface for the biological models, allowing them to be “effortlessly” linked with a variety of ocean physics and climate models.  This allows each component model to be maintained and modified independently of the other model components in an analytic system.

## “Tuna Forage” 1

- 3 groups in multiple layers

- 6 groups in 3 layers

- SEAPODYM

- APECOSM

- horizontal movement via advection (currents)
- and diffusion (randomness)

**Notes:**
Other Modeling Efforts

A Spatial Ecosystem and Populations Dynamics Model 
SEAPODYM is a numerical model initially developed for investigating physical-biological interaction between tuna populations and the pelagic ecosystem of the Pacific Ocean. Using predicted environment from ocean-biogeochemical models, SEAPODYM integrates spatio-temporal and multi-population dynamics and considers interactions among populations of different species and between populations and their physical and biological environment (including intermediate trophic levels). The model also includes a description of multiple fisheries and then predicts spatio-temporal distribution of catch catch rates, and length-frequencies of catch based either on observed or simulated fishing effort, allowing respectively to evaluate the model or to test management options (e.g., changing the fishing effort, implementing marine reserves, etc...). 

APECOSM - Apex Predators ECOSystem Model 
aims to represent the spatialized dynamics of open ocean pelagic ecosystems in the global ocean. Physical forcings (winds, temperature and currents from the OPA circulation model), biogeochemical forcings (primary production and oxygen from the PISCES biogeochemical model) as well as the effects of fishing are explicitely taken into account in the model. The model represents the energy flow through the Open Ocean Pelagic Ecosystem (OOPE) with a size-structured energy flux equation in 4 explicit dimensions (space /x /, / y/, time /t/ and organisms weight /w/). The epipelagic community is distinguished from the mesopelagic migratory community. The energy input at the basis of the OOPE comes from the PISCES biogeochemical model. The tuna species under interest (yellowfin, skipjack, bigeye, albacore) belongs to the OOPE (/i.e./: interact trophically with it) but have a finer structure. Tuna population dynamics are indeed represented with a DEB-based (Dynamic Energy Budget) physiologicaly structured advection-diffusion flux equation which transports individuals through a 6 dimensional space (space /x /, / y/, time /t/, reserves /E/, structure /V/, gonades /G/). Behaviour of fish is related to their physiological status. A sub-model enables to take into account the small-scale vertical movements of tunas into the larger scale ecosystem dynamics model and drives the interactions between tunas and OOPE. 

## “Tuna Forage” 2

- SEAPODYM

- APECOSM

- size-spectrum dynamics with a bioenergetics basis

- delay-differential dynamics with a phenomenological basis

**Notes:**
Other Modeling Efforts

## Tuna Dynamics 1

- size-specific advection and diffusion
- advection based on an IBM
- decisions to maximize egg production when energy content below some threshold
- decisions to maximize larval survival otherwise
- vertical behavior described from archival-tag data

- SEAPODYM

- APECOSM

- size-specific advection (towards good “adult habitat” but modified by currents) and diffusion (decreases in good habitat)

- depth frequency

**Notes:**
Other Modeling Efforts