Ecosystem Modeling and Forecasting

Research focused upon improved forecasting of the structure and function of marine ecosystems including the provision of ecosystem services, particularly in the Southeast U.S. coastal ocean, the Caribbean Sea, and Gulf of Mexico Large Marine Ecosystems. These regions are the primary geographic focus of this and the following two research theme areas. Modeling and forecasting topics include: human health (e.g., beach closings, fish contaminants, and harmful algal blooms), fish recruitment and productivity, and protected species sustainability and recovery, all of which are deemed relevant to NOAA’s responsibilities with respect to the assessment and management of living marine resources and their habitats.

Two representative projects under this themes are:

Representative Projects

Development of Biological and Physical Indices for Stock Evaluation in the Dry Tortugas Pink Shrimp Fishery. FATE Project

M.M. Criales, C.B. Paris and L. Cherubin (UM/RSMAS); J.A. Browder (NOAA/SEFSC)

Long Term Research Objectives and Strategy to Achieve Theme:

Objectives: To refine stock assessments of the pink shrimp stock in south Florida in relation to environmental and climatic variation to better inform fishery managers about the factors contributing to stock changes.

Strategy: to develop physical and biological indices for of recruitment from existing data and a biophysical Lagrangian model for the species.


A coupled biophysical Individual-Based Model (IBM) has been developed to simulate the life history and migratory movements of pink shrimp (Farfantepenaeus duorarum) in south Florida. Pink shrimp migrate from spawning grounds on the southwest Florida shelf off the Dry Tortugas and nursery grounds in Florida Bay. The model will help determine the main environmental factors that affect their journey and successful recruitment to the bay.

The Regional Ocean Modeling System (ROMS), a coastal hydrodynamic model with tidal flux, is the physical hydrodynamic component of the biophysical model. This model has been adapted and tested for the region. A 2-grid-level model was developed for the Florida Keys region. First, a parent circulation simulation grid at 2.8 km horizontal resolution grid was set up and then a 0.7 km horizontal resolution grid was nested within the parent model (Fig. 1). the circulation model is forced at the surface by the NCEP North American Regional Reanalysis (NARR) which provides a very accurate wind speed and direction in the coastal waters of South Florida. The model’s lateral boundaries are provided by the HYCOM TOPAZ Atlantic Ocean 1989-to present reanalysis. Freshwater input is a critical component of the regional dynamics and affects the circulation in Florida Bay and the inner SW Florida Shelf. Therefore, the current simulation now includes the southern Florida watersheds up to the Peace and Myakka Rivers, the Big Cypress and Shark Slough drainages, and water flow to Florida Bay from Everglades National Park. Model results are showing a highly dynamic circulation on the SW Florida shelf with spin off eddies traveling along the edge of the Florida Current (Fig 2). The model is also showing that circulation at the middle shelf bifurcates upon
approaching the Florida Keys with a portion of the flow turning to Florida Bay and another porting turning further offshore.

Figure 1. ROMS model output depicting sea surface salinity SST (February 2, 1994), bathymetry and parent and nested models.

Figure 2. ROMS modeling results (January 29 and February 15, 1994) for sea surface temperature and surface current velocity including tides. Model outputs clearly indicate spin off eddies traveling along the edge of the Florida Current and onshore currents with a strong northward flow on the inner SW Florida shelf.

The biophysical model simulates the selective tidal stream transport (STST) of pink shrimp larvae on the SW Florida shelf. In STST transport, pink shrimp postlarvae move up in the water column during the flood tide to progress inshore and sink to the bottom of the water column during ebb tide to avoid being carried offshore. Our previous research suggested that STST was important to pink shrimp migration across the SW Florida Shelf. The pink shrimp model is tide driven and based on the phase of the tide and larval developmental stage at each individual particle (shrimp larvae) location. Test-runs of the IBM were conducted with 7 days of hourly outputs of the ocean circulation model. Simulations of particles with a STST behavior showed that larval transport patterns varied substantially in direction and distance, even when starting from nearby locations, compared to passive particles. Longer time scale simulations are ongoing since the literature suggests it takes about 30 days for young pink shrimp to reach the bay. Decadal ROMS simulations coupled with the pink shrimp IBM will be used to assess the effect of environmental factors on pink shrimp stock variability over the 1995-2005 period.


Predicting the Effects of Climate Change on Bluefin Tuna(Thunnus thynnus) Spawning in the Gulf of Mexico Using Downscaled Climate Models

B. Muhling and S.-K. Lee (UM/CIMAS); J. Lamkin, W. Ingram and M. Schirripa (NOAA/SEFSC)

Long Term Research Objectives and Strategy to Achieve Them:

Objectives: To quantify potential impacts of climate change on bluefin tuna spawning habitat in the Gulf of Mexico.

Strategy: To downscale global climate models to the scale of the Gulf of Mexico, and predict changes in spawning habitat using habitat preference models


We will be projecting the impact of climate change on environmental indicators in the northern Gulf of Mexico (GOM). Initially, this project will apply statistically downscaled climate predictions to bluefin tuna habitat models in the GOM. This will allow predictive forecasts to be integrated into
stock assessment models under various climate change scenarios, and quantitative forecasts of favorable bluefin tuna spawning habitat.
Our research objectives are to:

  1. Downscale IPCC climate models to a regional scale, focusing on the GOM.
  2. Formulate seasonal and decadal predictions of sea surface temperature and salinity across the GOM under a range of scenarios, derived from the downscaled model.
  3. Use an existing larval habitat model to calculate the increase, or decrease, in the spatial and temporal extent of suitable larval habitat, under conditions predicted by the downscaled model. This will allow us to estimate potential effects of climate change on spawning activity of adult bluefin tuna in the GOM, by use of a simple index (size of suitable habitat across the spawning season).

Figure 1. Predicted bluefin tuna spawning habitat extent in April, May and June for the late 20th century (top), 2045-2055 (middle), and 2085 – 2095 (bottom). Habitat suitability is measured by probability of larval occurrence (/1), and is using interpolated temperature data from an ensemble of 19 climate models.