Impact of recombination on bacterial evolution

Abstract

Genetic exchange plays a defining role in the evolution of many bacteria. The recent accumulation of nucleotide sequence data from multiple members of diverse bacterial genera has facilitated comparative studies that have revealed many features of this process. Here we focus on genetic exchange that has involved homologous recombination and illustrate how nucleotide sequence data have furthered our understanding of: (i) the frequency of recombination; (ii) the impact of recombination in different parts of the genome; and (iii) patterns of gene flow within bacterial populations. Summarizing the results obtained for a range of bacteria, we survey evidence indicating that the extent and nature of recombination vary widely among microbiological species and often among lineages assigned to the same microbiological species. These results have important implications in studies ranging from epidemiological investigations to examination of the bacterial species problem.

Figure I. Illustration of the ClonalFrame model.

The top part shows the clonal genealogy in black and recombination events in distinct colors. The bottom part shows the genotypes of the isolates, with fragments unaffected by recombination shown in black and fragments affected by recombination colored according to the recombination events whereby they originated.

Figure I. Illustration of the STRUCTURE model.

The top part shows the ancestral populations in distinct colors. The bottom part shows the genotypes of the isolates, with fragments colored according to their ancestral population of origin.

Figure 1. Effect of recombination on the discrepancy of phylogenetic signals.

Three isolates (1, 2 and 3) and two genes (A and B) are considered. In the first scenario, no recombination occurred so that the phylogenies of genes A and B are identical to the clonal genealogy and they exhibit congruence. In the second scenario, a recombination event in gene B of isolate 3 resulted in a different phylogeny for that gene and the phylogenies of genes A and B are incongruent.

Figure 2. Comparison of three inter-species studies on recombination rates.

The results of Hanage et al. [13], Perez-Losada et al. [14] and Vos and Didelot [15] are shown for the six species considered by all three studies, namely S. aureus, B. cereus, N. meningitidis, H. pylori, S. pneumoniae and S. pyogenes.