EcoSim

EcoSim is an individual-based predator-prey ecosystem simulation in which agents can evolve. It has been designed to investigate several broad ecological questions, as well as long-term evolutionary patterns and processes such as speciation and macroevolution. EcoSim has been designed by Robin Gras at the University of Windsor in 2009 and it is still currently used for research in his Bioinformatics and Ecosystem Simulation Lab. EcoSim is an individual-based predator-prey ecosystem simulation in which agents can evolve. It has been designed to investigate several broad ecological questions, as well as long-term evolutionary patterns and processes such as speciation and macroevolution. EcoSim has been designed by Robin Gras at the University of Windsor in 2009 and it is still currently used for research in his Bioinformatics and Ecosystem Simulation Lab. The agents have a behavior model which allows the evolutionary process to modify the behaviors of the predators and prey. Furthermore, there is a speciation mechanism which allows to study global patterns as well as species-specific patterns. In EcoSim, an individual's genomic data codes for its behavioral model and is represented by a fuzzy cognitive map (FCM). The FCM contains sensory concepts such as foodClose or predatorClose, internal states such as fear or hunger, and motor concepts such as escape or reproduce. The FCM is represented as an array of floating-point values which represent the extent to which one concept influences another. For example, it would be expected that the sensory concept predatorClose would positively affect the internal concept fear, which would then positively affect the escape motor concept. These relationships among concepts evolve over time, sometimes giving a new meaning to a concept. Furthermore, the FCM is heritable, meaning that a new agent is given an FCM which is a combination of that of its parents with possible mutations. EcoSim subscribes to the “genotypic cluster” definition of a species. Speciation has been implemented using a 2-means clustering algorithm technique designed to allow the splitting of an existing species into two species, by clustering the individuals that initially belonged to the first species into one of the new two species, each one of them containing the agents that are mutually the most similar. Since EcoSim has the capacity to allow speciation events to occur, it is possible to track speciation events throughout a run of the simulation and construct the actual phylogenetic tree.