Evidence that mutation is universally biased towards AT in bacteria

Abstract

Mutation is the engine that drives evolution and adaptation forward in that it generates the variation on which natural selection acts. Mutation is a random process that nevertheless occurs according to certain biases. Elucidating mutational biases and the way they vary across species and within genomes is crucial to understanding evolution and adaptation. Here we demonstrate that clonal pathogens that evolve under severely relaxed selection are uniquely suitable for studying mutational biases in bacteria. We estimate mutational patterns using sequence datasets from five such clonal pathogens belonging to four diverse bacterial clades that span most of the range of genomic nucleotide content. We demonstrate that across different types of sites and in all four clades mutation is consistently biased towards AT. This is true even in clades that have high genomic GC content. In all studied cases the mutational bias towards AT is primarily due to the high rate of C/G to T/A transitions. These results suggest that bacterial mutational biases are far less variable than previously thought. They further demonstrate that variation in nucleotide content cannot stem entirely from variation in mutational biases and that natural selection and/or a natural selection-like process such as biased gene conversion strongly affect nucleotide content.

Figure 1. Phylogenetic and genomic variation in GC content.

(A) The phylogeny of the four broad clades examined in this study. It was built using the iTOL webpage (http://itol.embl.de/). Average GC content of the different broad clades are indicated on the margins. Small blue triangles represent the five lineages of clonal pathogens used in the analysis. (B) Genomewide observed GC content of synonymous and non-synonymous sites correlate with the intergenic GC content across bacterial genomes.

Figure 2. Relative rates of the six nucleotide pair mutations.

The most common mutation is always G/C to A/T transitions. The rates are normalized for the unequal nucleotide content of the five different lineages (Materials and Methods). (A) non-synonymous SNPs. (B) synonymous SNPs.

Figure 3. Equilibrium GC content (GC_eq ) and the observed GC content in the five studied clonal pathogen lineages.

GC_eq is calculated from the estimated rates AT to GC and GC to AT mutations (r_AT→GC and r_GC→AT) as . GC_eq values are significantly lower than the observed GC content at all site categories (intergenic, synonymous and non-synonymous) and for all four lineages of clonal pathogens with either intermediate or high GC contents. MTBC intergenic SNPs were not available for analysis. Error bars depict 95% confidence intervals for GC_eq. No correlation is observed between GC_eq and current GC for the clonal pathogen lineages (P≤1).

Figure 4. Comparison between GC_eq calculated using data from clonal pathogens and GC_eq calculated using data from more diverged lineages.

GC_eq estimated using more diverged lineages is always more similar to and significantly correlated with current GC content values (P = 0.03).