Speciation trajectories in recombining bacterial species

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 that the amount of habitat overlap determines the outcome for a pair of clusters, which may range from fast clonal divergence with little interaction between the clusters to a stationary population structure, where different clusters maintain an equilibrium distance between each other 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.Author summary: Species are conventionally defined as groups of individuals that breed with each other, but not with those of other species. However, this does not apply to bacteria because, even if they reproduce clonally, DNA may be donated between distinct species. Nevertheless, bacterial species do exist, and a fundamental question is how they are created. We present a mathematical model to describe bacterial speciation. The model predicts that two groups of ecologically different bacteria, assumed to live in partially overlapping habitats, may evolve into genetically distinguishable clusters, without being able to proceed to full separation. Analysis of a divergent Streprococcus pneumoniae subgroup shows that such ‘satellite species’ exist and can be distinguished from more rapidly diverging clusters, like the one we detect in Campylobacter jejuni.