Hybridization driven by selection is a major source of genetic diversity in a natural bacterial population

The traditional view of bacterial evolution is that populations form distinct genetic clusters within a narrow ecological niche, with limited recombination between closely related individuals. However, recent evidence from deep sequencing of microbial populations suggests an alternative view in which frequent recombination leads to bacteria evolving as large quasi-sexual populations [1]. Which of these views best approximates natural bacterial populations remains unresolved.

To address this question, we used single cell genomics to sequence a large, unbiased sample from a population of thermophilic cyanobacteria. Consistent with previous results, we find that coarse genomewide measures of diversity suggest the population comprises two main, highly distinct, sequence clusters [2]. Despite this, diversity patterns on finer scales are fundamentally incompatible with the view that clusters represent distinct species with recombination mainly limited to closely-related cells. Instead, we find evidence that selection leads to extensive hybridization between highly diverged strains on genome scales ranging from tens to thousands of base pairs. These results suggest that hybridization may play a major and previously unrecognized role in maintaining diversity in bacterial populations.