  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.
