How recombination and clonal evolution shape bacterial lineages and genomes

Abstract Homologous recombination is a key process in bacterial genome evolution. By analyzing sequencing collections of 12 bacterial species encompassing >100,000 genomes, we determine how recombination and clonal evolution shape bacterial lineages and genome structures. Previous analyses proposed that for some bacterial species recombination is so dominant that almost no clonal genomic fraction remains. Further, it has been suggested that bacterial phylogenies are entirely structured by scale-free distributions of recombination rates, based on measurement of private SNP distributions that exhibit power-law tails. Using a coalescent model of populations that recombine with different gene pools, we find a substantial clonal signal in all global bacterial populations analyzed, and infer recombination rates that typically vary by less than an order of magnitude within species. Additionally, for a local population of Escherichia coli isolates that exhibit power-law private SNP distributions, we infer narrowly-distributed recombination rates and a substantial clonal signal, and show that their clonal genealogy exhibits a distribution of coalescence times spanning several orders of magnitude. Using simulations and theory, we demonstrate that power-law SNP distributions are not indicative of widely-varying recombination rates and can be generated by a clonal genealogy recombining with an external pool at a constant rate. We use regression analysis to quantify the relative impact of recombination and clonal evolution on the diversity and lineage structure of local and global populations. Our findings have implications for how bacterial phylogeny is interpreted and lays key groundwork for understanding which evolutionary forces determine species diversity.