Evolution of bacterial genomes under horizontal gene transfer

Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in gene content. This huge variation in gene content led to the concepts of the distributed genome of bacteria and their pangenome (Tettelin et al.,2005; Ehrlich et al.,2005). We present a population genetic model for gene content evolution which accounts for several mechanisms. Gene uptake from the environment is modeled by events of gene gain along the genealogical tree relating the population. Pseudogenization may lead to deletion of genes and is incoporated by gene loss. These two mechanisms were studied by Huson and Steel (2004) using a fixed phylogenetic tree. Taking the random genealogy given by the coalescent (Kingman, 1982; Hudson, 1983), we studied the resulting genomic diversity already in Baumdicker et al. (2010). In the present paper, we extend the model in order to incorporate events of interspecies horizontal gene transfer. Within this model, we derive expectations for the gene frequency spectrum and other quantities of interest.