The coalescent for prokaryotes with homologous recombination from external source

Abstract

The coalescent process for prokaryote species is theoretically considered. Prokaryotes undergo homologous recombination not only with other individuals within the same species (intra-specific recombination) but also with other species (inter-specific recombination). This work particularly focuses the latter because the former has been well incorporated in the framework of the coalescent. We here developed a simulation framework for generating patterns of SNPs (single nucleotide polymorphisms) allowing integration of external DNA out of the focal species, and a simulator named msPro was developed. We found that the joint work of intra- and inter-specific recombination creates a complex pattern of SNPs. The direct effect of inter-specific recombination is to increase the amount of polymorphism. Because inter-specific recombination is very rare in general, it creates a regions with an exceptionally high level of polymorphisms. Following an inter-specific recombination event, intra-specific recombination chop the integrated foreign DNA into small pieces, making a complicated pattern of SNPs that looks as if foreign DNAs were integrated multiple times. This work with the msPro simulator would be useful to understand and evaluate the relative contribution of intra- and inter specific recombination to creating complicated patterns of SNPs in prokaryotes.