# Presentation: 066123

## Coupled Nutrient-Plankton-Zooplankton-Fish Models

- Howard Townsend, NCBO
- Tom Wainwright, NWFSC
- Buck Stockhausen, AFSC
- Andrew Leising, SWFSC
- Hongguang Ma, NCBO

- August 29-31, 2007

## Major efforts within NOAA

- NEMURO (*N*orth Pacific *E*cosystem *M*odel for *U*nderstanding *R*egional *O*ceanography) – Modeling Suite
- NPZ model (NEMURO) dynamically linked to fish bioenergetics and population dynamics model
- NPZ-Cal (NPZ linked to Copepod IBM for the California Current)
- 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.
- 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
- CBWQM and FEM (Chesapeake Bay coupled Water Quality Model and Fisheries Ecosystem Model)
- 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.

- August 29-31, 2007

## More Information on Modeling Efforts:NEMURO

- Tom Wainwright, NWFSC
- Ecological Modelling 2007 special issue, v. 202 #1-2

- August 29-31, 2007

## More Information on Modeling Efforts:NPZ-Cal

- Prey Field

- More Information on Modeling Efforts:NPZ-Cal

- Andrew Leising, SWFSC-ERD

- Temperature

- Observations
-  or GCM model

- August 29-31, 2007

**Notes:**
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

- August 29-31, 2007

## 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

- August 29-31, 2007

## What is/has/will the model be used for? 

| NEMURO | Originally developed and extended for climate impacts and species-to-species interactions for small pelagics in the North Pacific basin.  |
| --- | --- |
| NPZ-Cal | Developed as separate projects (NPZ vs IBM), now used as testbed for merging these types of models, and development of zooplankton production indices for the California Current system vs climate variability. |
| DisMELS | Develop recruitment forecasts based on patterns of advective transport for early spring-spawning flat fish in the eastern Bering Sea. |
| CBWQM and FEM | Linkages developed to understand the impact of water quality management on fisheries productivity in the Chesapeake |

- August 29-31, 2007

## What are the data requirements? 

- HUGE for full validation:  physical circulation, temperature, plankton abundances, fish population biomass, fish individual weights, fish diet and foraging rates.
- If you’re lucky the physical modeling data and validation requirements have already been dealt with elsewhere.
- So you’re still left with the typical multi-species data needs plus info on phytoplankton and zooplankton

- August 29-31, 2007

## Are these data gaps informing monitoring efforts? 

| NEMURO | Rate parameters for plankton model, high frequency (space and time) plankton observations, juvenile fish abundance and weight time series.  |
| --- | --- |
| NPZ-Cal | Same problems as NEMURO for NPZ side. 
Lack of deep water (wintertime) copepod samples, and species-specific collections.  More (spatially and temporally) subsurface temperature data needed.  |
| DisMELS | Better early life history information for flatfish species. |
| CBWQM and FEM | Lack of fisheries stock assessments for key bay species.  Potentially untapped mines of historical data. |

- August 29-31, 2007

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

- TOO MANY TO LIST HERE – REFER TO EARLIER SLIEDES WITH REFERENCES FOR MORE INFORMATION

- August 29-31, 2007

## What are the strengths of this model? 

| NEMURO | Multi-size class representation of zooplankton, two-directional linkage between fish and plankton.  |
| --- | --- |
| NPZ-Cal | More realistic prey input to IBM, more realistic copepod behavior (DVM, Diapause etc.) -> more realistic copepod production estimates (hopefully), ability to address key climatic features (e.g. changes in timing of the spring transition/upwelling initiation). |
| DisMELS | Demonstrate that particle depth can substantially influence transport paths. Early life stage studies have shown that typical depth ranges for early stage flatfish change ontogenetically (e.g., as eggs change buoyancy with development), and for larvae diurnally.  |
| CBWQM and FEM | This effort has drawn attention to the fact that reduced nutrients may result in reduced system productivity- especially wrt pelagic vs benthic |

- August 29-31, 2007

## What are the weaknesses of this model? 

| NEMURO | Difficult to validate and/or verify.  Limited options for functional grazing response. |
| --- | --- |
| NPZ-Cal | Difficult to parameterize IBM.  Lacking adequate copepod abundance data for most regions for verification. (NPZ problems- same as NEMURO)  |
| DisMELS | Tides are not currently included in the physical model, whereas tidal currents are substantially larger than mean currents on the EBS shelf, thus model may substantially underestimate dispersion rates. |
| CBWQM and FEM | Because the linkage is unidirectional and effects of hypoxia have not been well-quantified, the detrimental effects of eutrophication have not been completely incorporated. |

- August 29-31, 2007

## Model 1)in peer-review literature, 2)formally peer-reviewed, 3)outputs formally reviewed? 

| NEMURO | Yes
Yes
Yes |
| --- | --- |
| NPZ-Cal | No (2 x ms in prep, 1 submitted; on IBM)
No
No |
| DisMELS | No?
No?
No? |
| CBWQM and FEM | Software-Yes; coupling of models-No
Software-Yes; coupling of models-No
No |

- August 29-31, 2007

## How portable is the model software package? 

| NEMURO | Runs on anything with a Fortran-90/95 compiler.  |
| --- | --- |
| NPZ-Cal | Matlab.  90% GUI driven. Physical input files and model forcing can be many 100’s of MB’s, though.  |
| DisMELS | IBM is written in Java—should run anywhere (RAM will limit number of individ.s simulated). Requires ROMS model output. |
| CBWQM and FEM | Not Very.  FEM component is highly portable as it uses EwE package.   |

- August 29-31, 2007

## What remains for model development/ improvement/enhancement? 

| NEMURO | Currently re-implementing the model in a modular format within the Earth Systems Modeling Framework which will allow direct linkages with a variety of 3-D ocean circulation models and most U.S. climate prediction models.  NEMURO.SAN (under development) will enable work with two fish species (sardine and anchovy) interacting in space and time.  |
| --- | --- |
| NPZ-Cal | Validation and peer review of the separate model components (The IBM and the NPZ), then peer review of the linked product.  Methodology of the linked product is still under development; IBM and NPZ components mostly done. |
| DisMELS | Develop bioenergetics-based growth models, incorporate NPZ fields from lower trophic level model.
Revise GUI interface and improve computational performance.  Validation and peer review. |
| CBWQM and FEM | Peer review. Creating dynamic linkages between the models or between FEM and other physical models. |

- August 29-31, 2007

## Has/is/will the model outputs be used in LMR management? 

| NEMURO | Not yet, but planned.  |
| --- | --- |
| NPZ-Cal | Plan that results primarily conveyed through peer-reviewed literature.  Copepod production indices will be available via LAS web server. (So no formal use)  |
| DisMELS | Results will be incorporated into stock assessment advice provided to NPFMC |
| CBWQM and FEM | Model and outputs have been demonstrated to local resource managers. No formal governance structure in place to use ecosystem models for management yet. “Give a man a watch and he knows what time it is.  Give a man 2 watches and he has no idea what time it is.” |

- August 29-31, 2007

## Partners external to NMFS required to accomplish model coupling development, etc? 

| NEMURO | Originally, developed as a PICES project |
| --- | --- |
| NPZ-Cal | IBM project is joint GLOBEC work with University of Maine and DFO personnel.  Physical inputs from major observing programs.  If used, physical model input from ROMS or other modeling efforts.   |
| DisMELS | Pacific Marine Environmental Laboratory provides ROMS model output. |
| CBWQM and FEM | Yes.  Major- Environmental Protection Agency, biologists from regional/state resource management agencies, regional academics. |

- August 29-31, 2007

## Take Home Point

- Different NPZ-Fish modeling approaches have arisen across NMFS, and these approaches have been published and have had some value in providing management advice.
- Development of an NPS-Fish model for a NMFS Ecosystem Modeling Toolbox may be useful

- August 29-31, 2007