Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

Most bacteria engage in gene flow through homologous recombination, and this mechanism may play a crucial role in maintaining species cohesiveness, much like sexual reproduction does in eukaryotes. However, introgression has been reported in bacteria and is associated with fuzzy species borders in some lineages, but its prevalence and impact on the delimitation of bacterial species have not been systematically characterized. Here, we use the term “introgression” to describe gene flow between the genomic backbone of distinct species (i.e., their core genomes)—an analogy to the classical usage in sexual organisms, but distinct in mechanism. We quantified the patterns of introgression across 50 major bacterial lineages. Our results reveal that bacteria present various levels of introgression, with an average of 2% of introgressed core genes and up to 14% in Escherichia–Shigella. Furthermore, our results show that some species are more prone to introgression than others within the same genus, and introgression is most frequent between highly related species. We found evidence that the various levels of introgression across lineages are likely associated with sequence relatedness, but the impact of ecology on this process was less clear. Introgression can occasionally lead to fuzzy species borders, although many of these cases are likely instances of ongoing speciation. Overall, our results indicate that introgression has substantially shaped the evolution and the diversification of bacteria, but this process does not substantially blur species borders.