Sympatric speciation simulation for recombining microbial populations
symsim Symsim is a discrete generations model implemented in MatLab, with varying population size, designed to investigate the colonization of a new ecological niche. Each generation consists of resource competition, population growth and recombination in a sympatric pool. Symsim models a microbial population growing in an environment composed of two distinct niches, one ancestral (niche 0) and one derived (niche 1). Genotypes consist of L unlinked adaptive loci, each with two allelic states, 0 or 1, conferring adaptation to niche 0 or 1, respectively.

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The symsim model is described in detail in the paper:
Friedman J, Alm EJ, Shapiro BJ. (2012) Sympatric speciation: when is it possible in bacteria? PLOS ONE. (accepted Dec. 2012)
Summary of the paper: It has been theorized for some time that sexual animal populations diverge more readily into new species when a small number of genes are sufficient to initiate and complete the speciation process. Some of these genes may promote sexual isolation between species (important in 'sympatric' speciation, where there are no physical barriers to mating) and others may confer adaptation to different ecological niches. Bacteria, like sexual organisms, adapt to diverse ecological niches. Yet they reproduce clonally, exchanging genes occasionally by recombination, potentially with distant relatives, such that sexual isolation between species is never complete. Despite these differences from sexual organisms, we show that bacteria are also more likely to form new species when just a few genes are involved in niche adaptation. The reason for this is an evolutionary tradeoff: frequent genetic exchange (recombination) is required to generate adaptive combinations of multiple adaptive alleles, but without mechanisms for sexual isolation these adapted species tend to merge back together rather than diverging into separate species. This tradeoff imposes a simple constraint on the speciation process in bacteria, and may explain certain aspects of bacterial biology such as the clustering of genes into operons (effectively reducing the number of genes involved in speciation) and variable recombination rates over time.