Bursts of reproduction can create genetic structure in frequently recombining bacterial populations

In many bacterial species, strong genetic structure is present, where individuals are clustered into genetically distinct groupings within the species. However, high rates of homologous recombination have also been observed in many of these species, high enough that simple models of evolution predict that such genetic structure should be eliminated. One proposed resolution to this contradiction is the presence of recurrent bursts of reproduction caused by rapid adaptation or microepidemics. We investigate this hypothesis using coalescent simulations of the simplest bursty reproduction model. Our simulations show that bursts of reproduction can indeed create genetic structure even when recombination is so frequent that all structure would be eliminated in the absence of bursts. This genetic structure is only possible when there is a burst of reproduction that is sufficiently large and recent in the population's history. We describe the mechanism by which a burst creates genetic structure and analyze its distinctive effect on the patterns of diversity, focusing on the distribution of pairwise genetic distances and its relationship to the fraction of identical blocks along the genome. Interestingly, genetic structure from bursts of reproduction can appear among pairs of samples which do not share any genetic material by clonal descent, a feature which cannot be observed in populations whose structure is just a consequence of limited recombination. However, we find that for other statistics beyond the distribution of pairwise distances, the simplest model of bursty reproduction cannot entirely reproduce the distributions observed in nature.