Evolution and recombination of the plasmidic qnr alleles.

qnr is an important and recently emerged plasmidic fluoroquinolone resistance gene. Numerous qnr alleles have been detected, but previous studies have suggested that there is little functional divergence among them. We performed phylogenetic analysis of representative qnr alleles and examined the phylogeny for the occurrence of positive selection (d(N)/d(S)). Positive selection rarely occurred near the tips of the tree, which confirms that the evolution of qnr alleles has not been driven by functional divergence. Interestingly, we also found evidence of recombination events among qnr alleles that may lack any functional relevance but contribute to the sequence variation of qnr alleles. These findings suggest that drift and recombination may be more important contributors to qnr sequence divergence than selection for new functions.