Evidence for natural selection on the <i>Staphylococcus aureus</i> genome during asymptomatic carriage.

<p>A) The relative number of synonymous versus non-synonymous SNPs on all branches of the within-host genealogies relating colonies sampled from hosts A-M. Each pie represents a branch in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061319#pone-0061319-g001" target="_blank">Figure 1</a>, divided into segments according to the proportion of synonymous (green) and non-synonymous (orange) mutations on that branch. The area of the pie is proportional to the number of synonymous and non-synonymous mutations on that branch. The solid line is the uncorrected <i>dN</i>/<i>dS</i> ratio estimated from SNPs within hosts, which was significantly greater than the uncorrected <i>dN</i>/<i>dS</i> ratio estimated from SNPs between hosts (dashed line, McDonald-Kreitman test <i>p</i><0.001). B) The sample frequency of SNPs, represented by the minor (less frequent) allele. Bars are color-coded according to SNP type: synonymous (green), non-synonymous (orange), nonsense (red) and intergenic (grey). C) The expected and observed number of within-host mutations per gene (solid and hatched bars respectively), combined across participants A–M, Q and R.