Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences

Abstract

The identification of clones within bacterial populations is often taken as evidence for a low rate of recombination, but the validity of this inference is rarely examined. We have used statistical tests of congruence between gene trees to examine the extent and significance of recombination in six bacterial pathogens. For Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, and Staphylococcus aureus, the congruence between the maximum likelihood trees reconstructed using seven house-keeping genes was in most cases no better than that between each tree and trees of random topology. The lack of congruence between gene trees in these four species, which include both naturally transformable and nontransformable species, is in three cases supported by high ratios of recombination to point mutation during clonal diversification (estimates of this parameter were not possible for Strep. pyogenes). In contrast, gene trees constructed for Hemophilus influenzae and pathogenic isolates of Escherichia coli showed a higher degree of congruence, suggesting lower rates of recombination. The impact of recombination therefore varies between bacterial species but in many species is sufficient to obliterate the phylogenetic signal in gene trees.

Figure 1

Maximum likelihood analysis of congruence in H. influenzae. The ML tree of each locus is compared with the ML trees from the other four loci. The differences in likelihood (Δ-ln L) are shown between loci (squares) and between each locus and 200 trees of random topology (diamonds). The 99th percentile of the likelihood differences between the ML tree for each gene and the 200 random tree topologies is indicated by the dotted line.