School of sardines swimming

Research Projects

Atlantis and Integrated Ecosystem Assessments

Schematic diagram of Atlantis, showing linked boxes that represent oceanographic submodel, ecology submodel, and fisheries/managment submodel A radar plot (resembling a spider web) with 6 axes, representing the following performance goals for management: habitat, avoiding rockfish bycatch, landed value, mammal and bird biomass, prop rockfish mature, and rockfish biomass. Two alteernate management scenarios are scored against these metrics (forming hexagrams), one plotted in red and the other in blue.

The Atlantis ecosystem modeling platform has been developed by Dr. Beth Fulton and collaborators at CSIRO Australia. Atlantis is a spatially explicit simulation model that includes ecology, oceanography, and fisheries. We are applying Atlantis as a strategic tool for ecosystem based management in the California Current and the Gulf of California. The work has been supported by both NOAA and the Gordon and Betty Moore Foundation. Our models for the California Current are available here:

Kaplan, I.C., and P.S. Levin. 2009. Ecosystem based management of what? An emerging approach for balancing conflicting objectives in marine resource management. In R.J. Beamish and B.J. Rothschild, eds. The Future of Fisheries In North America. Springer, NY 736 pages.

Horne et al. (2010) California Current Atlantis Model

Brand et al. (2007) California Current Atlantis Model

Dufault et al. (2009) Supporting research related to fish, marine mammal, and bird diets in the California Current

Several applications of Atlantis are described below, and in a recent review article (Fulton et al. 2011). Much of my current work related to identifying ecosystem indicators and testing policy scenarios is a part of NOAA's Integrated Ecosystem Assessments, as described in Levin et al. (2009) and shown in the figure below:

Schematic of Integrated Ecosystem assessment, linking the follosign components: Monitorign, Identyifying goals, developing indicators, Risk Analysis, Assessmsent of EBM status relative to goals, and Management Strategy Evaluation.

Ocean Acidification and Food Webs

Overlaid dome-shaped plots of English sole landed value vs. fishign mortality rate. In both cases, peak is around x= 0.11, but top plot (no acidification) peaks at $2.25 million, while lower plot (with acidification) peaks at about $250,000

Catch shares, or individual fishing quotas (IFQs), are a promising fisheries management method that allocates individual fishers a set portion of the total catch, and may reduce overcapitalization and promote sustainable fishing practices. Any management scheme, including catch shares, should be robust to potential shifts in the biophysical system. In this work we coupled possible catch scenarios under an IFQ scheme with ocean acidification impacts on shelled benthos and plankton, using an Atlantis ecosystem model for the US West Coast.

IFQ harvest scenarios alone in most cases did not have strong impacts on the food web, beyond the direct effects on harvested species. However, when we added impacts of ocean acidification, the abundance of commercially important groundfish such as English sole (Pleuronectes vetulus), arrowtooth flounder (Atheresthes stomias), and yellowtail rockfish (Sebastes flavidus) declined up to 20-80% due to the loss of shelled prey items from their diet. English sole exhibited a tenfold decline in potential catch and economic yield when confronted with strong acidification impacts on shelled benthos. Therefore, it seems prudent to complement catch shares with careful consideration of potential climate change effects such as acidification. Our analysis provides an example of how new ecosystem modeling tools that evaluate cumulative impacts can be integrated with established management reference points and decision mechanisms.


Kaplan, I.C., M. Burden, P.S. Levin, and E.A. Fulton. 2010. Fishing Catch Shares in the Face of Global Change: A Framework for Integrating Cumulative Impacts and Single Species Management. Canadian Journal of Fisheries and Aquatic Sciences 67: 1968-1982.

Fishing Fleet Dynamics and Catch Shares (ITQs)

Two maps of US WEst Coast, divided into Atlantis 62 model cells, with spatial effort concentration of the Moss Landing Trawl Fleet plotted on a red to blue color scale, with blue the highest intensity. Left plot is from 2004 data (logbooks), right plot is from model simulation; both apear approximately similar, with effort concentrated in cetnral CA and off San francisco, but small amounts of effort as far N as Cape Mendocino and as far S as Pt Conception

This project provides West Coast fisheries managers with a tool to test the efficiency and robustness of alternative fishery management strategies in a holistic ecosystem framework. We augment a well developed ecological simulator (Atlantis) of the US West Coast marine ecosystem with fleet dynamic models that are consistent with the economic incentives created by the current and anticipated fishery management system for the West Coast groundfish fishery. The simulation model is used to evaluate alternative policies for setting total allowable catch (TACs) under different management systems including cumulative catch limits (i.e., status quo strategy), and a variety of individual transferable quotas options (ITQs). These ITQ options include alternative schemes for leasing quota, and penalties for quota overages. The model, which is spatially explicit, allows us tofor evaluate evaluation of the effects of area closures. In addition to providing insights into how alternative fishery management policies will affect the profitability and sustainability of primary fisheries, the model illustrates the wider ecosystem impacts of fishery management policies.

Ecosystem Modeling for Artisanal Fisheries in the Gulf of California

Gulf of California Shrimp Trawler  Atlantis model geometry for Northern Gulf of California, showing area divided into 62 polygons based on depth zones, fishing zones, and latitudinal regions

With modeling by Dr. Cameron Ainsworth and policy application by Dr. Hem Nalini Morzaria Luna, we have developed an Atlantis ecosystem model for strategic management simulations in the Northern Gulf of California, Mexico. We developed the model in collaboration with the PANGAS research consortium, with support from the David and Lucille Packard Foundation.

Published products to date include:

Ainsworth, C., Morzaria-Luna, H., Kaplan, I.C., Levin, P.S., Fulton, E. 2012. Full compliance with harvest regulations yields economic and ecological benefits: Northern Gulf of California case study. Journal of Applied Ecology 49(1) 63-72.

Download PDF - Diet compositions of fish species in the Northern Gulf of California (English) View

Descargar PDF - Composición de las dietas de peces en el Golfo Norte de California (Espanol) View

Ainsworth et al. (2011) Gulf of California Atlantis Model. NOAA Technical Memorandum NMFS-NWFSC-110

Stock Assessment

Kaplan and Helser (2007) Stock Assessment for Arrowtooth Flounder

Image of arrowtooth flounder
Photo courtesy of Dan Kamikawa, NOAA