Nucleotide sequence analysis was performed on 12 natural isolates of Escherichia coli in four loci located in close proximity on the chromosome. A comparison of gene genealogies indicated that three recombination events have occurred in a subset of the strains (ECOR group A) in the time since their divergence from a common ancestor, while during the same time, no mutational divergence has occurred. The common ancestor of this subset existed no more than 2400 years ago, and recombination was shown to occur at a rate of 5.0 x 10(-9) changes per nucleotide per generation-50-fold higher than the mutation rate. Thus, recombination has been the dominant force driving the clonal divergence of the ECOR group A strains and must be considered a significant factor in structuring E. coli populations.