Atlantis: A spatially explicit end‐to‐end marine ecosystem model with dynamically integrated physics, ecology and socio‐economic modules

Abstract

Marine ecosystem management is increasingly expected to take into account a wide range of ecological and socio‐economic factors. Decision‐making is helped by end‐to‐end ecosystem models that allow exploration of alternative management scenarios given a complex range of interacting factors. We present Atlantis – a spatially structured largely deterministic end‐to‐end marine ecosystem model written in C, available for all major operating systems, based on dynamically interacting physics, biology, fisheries, management, assessment and economics submodels. A detailed installation guide and example application files are also provided. One of the main features of Atlantis is its modularity. At the simplest level Atlantis can have uniform forcing of oceanographic processes, a single primary producer and a consumer. At the most complex level, Atlantis can be used with a range of environmentally driven ecological responses, complex and habitat‐dependent food web, dynamic assessment, management and fishing effort driven by market forces and human behaviour. The combination chosen should be guided by the available data and the questions to be answered. Atlantis provides a large and customizable list of output files and summary statistics that can be analysed and plotted using a number of dedicated r packages. When applying the Atlantis package, the users should be aware of the caveats associated with complex models, such as parameter and structural model uncertainty and challenges interpreting interactions of multiple processes.

Fisheries management tools to support coastal and marine spatial planning: A case study from the Northern Gulf of California, Mexico

“…The modeling platform summarizes biological components as functional groups aggregated by trophic, life history, or niche similarities. Further information on Atlantis can be found in the User's Guide [6] , the Atlantis Wiki ( https://research.csiro.au/atlantis/home/links/ ), and recently published Atlantis applications [29 , 49 , 50] . The Atlantis model for the Northern Gulf of California, which includes the Coastal Corridor, extends over 57,800 km 2 , represents ecosystem structure and function in 2008, current fishing effort, and provides a detailed representation of the Northern Gulf's oceanography, historical fishing patterns, migration and movement of key species, and variability in diet compositions [2 , 3] .…”

The impact of fishing on a highly vulnerable ecosystem, the case of Juan Fernández Ridge ecosystem

“…Hence, Atlantis can be implemented with different levels of complexity, from a simple model with few interactions to a complicated model with multiple biological connections and a complex structure of fishing fleets [43]. A detailed description of the Atlantis model and all its options and equations can be found in the model’s manual [45–47].…”

Ecosystem-Based Harvest Control Rules for Norwegian and US Ecosystems

“…To evaluate the implications of alternative harvest rules on the broader ecosystem, we implement the end-to-end Atlantis C++ code framework (Fulton et al, 2004(Fulton et al, , 2011Audzijonyte et al, 2019). As an end-to-end model, Atlantis simulates oceanography, nutrient cycling, food web dynamics, fisheries, and other human uses on a three-dimensional domain.…”