Statistics on mutations accumulated in hypermutable sub-lineages.

a<p>Branch names are denoted in phylogenetic tree in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen-1003741-g002" target="_blank">Figure 2</a>.</p>b<p>Position of mutations (consequences at the amino acid level is only shown for SNP mutations).</p>c<p>Mutation accumulated in an ancestor shared by clones CF211-1997a and CF211-2006a.</p

Bayesian phylogenetic reconstruction and divergence date estimates of the <i>P. aeruginosa</i> DK2 clones.

<p>Bayesian statistics were used to estimate the divergence times of predicted ancestors. The tree was based on 736 unique SNPs identified from whole-genome sequencing. Circles labeled A1, A2, B1, B2, C1, and C2, respectively, denotes the position of the first and last genotype of each of the DK2 sub-lineages A, B, and C which were observed to have infected patient CF173. The position of CF173-1991 (A2) is approximated from an equivalent Bayesian phylogenetic analysis including the hypermutator isolates (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen.1003741.s003" target="_blank">Figure S3</a>).</p

Increased pressures of selection for mutations in the top most mutated genes.

<p>Measures of the selection pressures were plotted for genes acquiring ≥<i>X</i> mutations during the evolution of the DK2 lineage. Plot A shows the dN/dS ratio, and plot B shows the ratio of indels relative to silent SNPs.</p

Maximum-parsimonious reconstruction of the phylogeny of the <i>P. aeruginosa</i> DK2 clones.

<p>The phylogenetic tree is based on 7,326 SNPs identified from whole-genome sequencing, and lengths of branches are proportional to the number of mutations. Outlier isolate CF510-2006 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen.1003741-Rau1" target="_blank">[9]</a> (not shown) was used as an outgroup to determine the root of the tree. Branches leading into <i>mutS</i>, <i>mutL</i>, or, <i>mutY</i> hypermutable isolates are named as indicated by italic letters. Statistics on mutations accumulated in the specific branches are summarized in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen-1003741-t001" target="_blank">Table 1</a>. Circles labeled A1, A2, B1, B2, C1, and C2, respectively, denotes the position of the first and last genotype of each of the DK2 sub-lineages A, B, and C which were observed to have infected patient CF173.</p

Pathoadaptive genes.

<p>Genes identified from parallel evolution to be involved in host adaptation. Colors of squares denotes if the gene was mutated relative to the MRCA of the DK2 clones. Only genes mutated in any of the isolates from CF173 are shown (see full list of pathoadaptive genes in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen.1003741.s006" target="_blank">Table S2</a>). The presence of mutations is shown for the first and last genotypes of each of the DK2 sub-lineages A, B, and C, which were observed to have infected patient CF173. The total sum of mutations observed within each of the genotypes is indicated at the top. Genes are grouped by function. Details about specific mutations and their fixation in the DK2 isolates are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen.1003741.s009" target="_blank">Table S5</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen.1003741.s010" target="_blank">Table S6</a>, and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003741#pgen.1003741.s004" target="_blank">Figure S4</a>.</p

Total number of SNPs accumulated in each DK2 isolate.

<p>The number of SNPs accumulated in each of the isolates since their most recent common ancestor (MRCA) is plotted against isolate sampling year.</p

Bacterial growth in the absence and presence of different enemies.

<p>The growth of bacteria isolated from patients with intermittent colonisation (a) or chronic (b) CF-lung infection; panels show mean values averaged over time (91 hours). Panels (c) and (d) show bacterial phage resistance (c) and ability to kill ciliate protist (d) for patients suffering from intermittent colonisation or chronic CF-lung infection. Error bars denote ± 1 SEM.</p

Protist and phage species used in this study.

<p>Protist and phage species used in this study.</p

Bacterial trait measurements.

<p>Bacterial virulence measured <i>in vivo</i> for patients with intermittent colonisation or chronic CF-lung infection (a): virulence is defined as less hours to larval death, more virulent the bacterial strain. Panel (b) shows difference in bacterial protease expression, panel (c) difference in biofilm formation and panel (d) difference in motility for patients suffering from intermittent colonisation or chronic CF-lung infection. Error bars denote ± 1 SEM.</p

Bacterial strains used in this study.

<p>Bacterial strains used in this study.</p