Pervasive, genome wide positive selection, leading to functional divergence in the bacterial genus Campylobacter

Abstract

An open question in bacterial genomics is the role which adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for 8 species. We estimate the Campylobacter core genome at 647 genes, with 92.5% of the non-recombinant core genome loci under positive selection on at least one lineage and the same gene frequently under positive selection on multiple lineages. Tests are provided which reject recombination, saturation and variation in codon usage bias as factors contributing to this high level of selection. We suggest this genome wide adaptive evolution, may result from a Red Queen macro-evolutionary dynamic, in which species are involved in competition for resources within the mammalian and/or vertebrate gastrointestinal tract. Much reduced levels of positive selection evident in Streptococcus (Lefebure and Stanhope 2007) may be a consequence of these taxa inhabiting less species rich habitats, and more unique niches. Despite many common loci under positive selection on multiple Campylobacter lineages we found no evidence for molecular adaptive convergence at the level of the same, or adjacent codons, or even protein domains. Taken collectively these results describe the diversification of a bacterial genus that involves pervasive natural selection pressure across virtually the entire genome, with this adaptation occurring in different ways in different lineages, despite the species tendency towards a common gastrointestinal habitat.