Structuring of an individual based evolutive model

Abstract

Individual-based models (IBM) are currently used for the study of evolution since they allow modeling both aspects at the individual, population and community level. Due to these characteristics, this type of modeling establishes a link between micro-evolutionary forces, such as genetic mutations and genetic flow, and the patterns observed at the macroevolutionary level, such as through the structure of phylogenetic trees. Based on the Neutral Biodiversity theory, the model proposed by Aguiar et al. 2009 can be used to study how an initially homogeneous population diversifies into several species due to mutations, sexual reproduction, and structuring of individuals in space. In this model, each individual is characterized by a genome, defined by a binary string. Individuals are separated into so-called species groups depending on the genetic flux between individuals. As it is an evolutionary model, each generation the identification of the species must be made. The computational cost of sexual reproduction and species searching is high when we consider many individuals and/or large genomes since these functions depend on the comparison between the genomes of the individuals. In this work, we will implement such a model, structuring it in a way that is possible the use of large genomes and many individuals. In a next step, we will try to understand how the variation of some parameters of the model, such as the parameter related to genetic flow, influence the formation of species and what patterns can be observed in phylogenetic trees (AU)