Speciation trajectories in recombining bacterial species

While speciation in eukaryotes is well-studied, a controversy over the nature of bacterial species due to recombination between distant strains continues. It is generally agreed that bacterial diversity can be classified into genetically and ecologically cohesive units, but what produces such variation is a topic of intensive research. Recombination may maintain coherent species of frequently recombining bacteria, but the emergence of distinct clusters within a recombining species, and the impact of habitat structure in this process are not well described, limiting our understanding of how new species are created. Here we present a model of bacterial evolution in overlapping habitat space. We show three different outcomes are possible for a pair of clusters, depending on the size of their habitat overlap: fast divergence with little interaction between the clusters, slow divergence with frequent recombination between the clusters, and stationary or near stationary population structure, where the clusters remain at an equilibrium distance for an indefinite time. We fit our model to two data sets. In Streptococcus pneumoniae, we find a genomically and ecologically distinct subset, held at a relatively constant genetic distance from the majority of the population through frequent recombination with it, while in Campylobacter jejuni, we find a minority population we predict will continue to diverge at a higher rate. This approach may predict and define speciation trajectories in multiple bacterial species.