We use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the oil spill with fisheries independent data. The model suggests that recruitment effects and fishery closures had little influence on biomass dynamics. However, at the assumed level of oil concentrations and toxicity, impacts on fish mortality and growth rates were large and commensurate with observations. Sensitivity analysis suggests the biomass of large reef fish decreased by 25% to 50% in areas most affected by the spill, and biomass of large demersal fish decreased even more, by 40% to 70%. Impacts on reef and demersal forage caused starvation mortality in predators and increased reliance on pelagic forage. Impacts on the food web translated effects of the spill far away from the oiled area. Effects on age structure suggest possible delayed impacts on fishery yields. Recovery of high-turnover populations generally is predicted to occur within 10 years, but some slower-growing populations may take 30+ years to fully recover.

Calibration of complex, process-based ecosystem models is a timely task with modellers challenged by many parameters, multiple outputs of interest and often a scarcity of empirical data. Incorrect calibration can lead to unrealistic ecological and socio-economic predictions with the modeller's experience and available knowledge of the modelled system largely determining the success of model calibration. Here we provide an overview of best practices when calibrating an Atlantis marine ecosystem model, a widely adopted framework that includes the parameters and processes comprised in many different ecosystem models. We highlight the importance of understanding the model structure and data sources of the modelled system. We then focus on several model outputs (biomass trajectories, age distributions, condition at age, realised diet proportions, and spatial maps) and describe diagnostic routines that can assist modellers to identify likely erroneous parameter values. We detail strategies to fine tune values of four groups of core parameters: growth, predator-prey interactions, recruitment and mortality. Additionally, we provide a pedigree routine to evaluate the uncertainty of an Atlantis ecosystem model based on data sources used. Describing best and current practices will better equip future modellers of complex, processed-based ecosystem models to provide a more reliable means of explaining and predicting the dynamics of marine ecosystems. Moreover, it promotes greater transparency between modellers and end-users, including resource managers.Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site. Highlights► Best practices for calibrating complex process-based ecosystem models are described. ► We emphasize the importance of understanding the model structure and data sources. ► Strategies to estimate core parameters for an Atlantis ecosystem model are defined. ► Key diagnostic routines to help modelers identify erroneous parameters are outlined. ► A pedigree to evaluate ecosystem model confidence and data quality is proposed.

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In spite of considerable effort to predict wildland fire behaviour, the effects of firebrand lift-off, the ignition of resulting spot fires and their effects on fire spread, remain poorly understood. We developed a cellular automata model integrating key mathematical models governing current fire spread models with a recently developed model that estimates firebrand landing patterns. Using our model we simulated a wildfire in an idealised Pinus ponderosa ecosystem. Varying values of wind speed, surface fuel loading, surface fuel moisture content and canopy base height, we investigated two scenarios: (i) the probability of a spot fire igniting beyond fuelbreaks of various widths and (ii) how spot fires directly affect the overall surface fire’s rate of spread. Results were averages across 2500 stochastic simulations. In both scenarios, canopy base height and surface fuel loading had a greater influence than wind speed and surface fuel moisture content. The expected rate of spread with spot fires occurring approached a constant value over time, which ranged between 6 and 931% higher than the predicted surface fire rate of spread. Incorporation of the role of spot fires in wildland fire spread should be an important thrust of future decision-support technologies.