Frequent hybridization and gene sweeps shape evolution of a natural bacterial population

Genetic sequencing of natural bacterial populations often reveal distinct genomic clusters. At the same time, recent studies have shown extensive recombination across a wide range of genetic divergences, raising the question of how can clusters be maintained over time. Previous studies have shown that ecological separation can emerge within highly-recombining bacterial populations. However, whether this mechanism can prevent the hybridization and merging of distinct clusters is not known. Here, we use the evolution of a diverse population of cyanobacteria from the Yellowstone hot springs as natural experiment to address this question.

Earlier work found that Yellowstone cyanobacteria comprise two distinct clusters adapted to different temperatures. Detailed analysis amplicon sequence data from one cluster found high rates of recombination and levels of diversity consistent with evolution over more than half a million years. Building upon previous work, we analyzed a large collection of single-cell genomes that provide a largely unbiased sample of diversity in the whole population. We find that despite their different ecologies, continual hybridization and gene sweeps have gradually eroded the genetic differences between clusters. These results suggest that ecological barriers cannot by themselves maintain genomic clusters over long evolutionary times and highlight the importance of spatial dynamics for maintaining microbial diversity.