Epistasis_KB

Epistasis data for 14 rifampicin-resistant double mutants of Pseudomonas aeruginosa in nutrient-rich KB growth media. Column headers described in the readme file

Epistasis_BIOLOG

Epistasis data for 14 rifampicin-resistant double mutants of Pseudomonas aeruginosa in 41 different single-carbon source (BIOLOG) environments. Column headers described in the readme file

Fitness in the presence of sorangicin.

<p>This figure shows the fitness of beneficial mutations (filled symbols) and the ancestral clone (open symbol) at 64 mg/L rifampicin (n = 18 replicates/genotype) and 20 mg/L sorangicin (n = 6 replicates/genotype). The dashed line is a plot of y = x.</p

Fitness effects of beneficial mutations.

<p>Plotted points show the fitness, <i>r</i>, of the wild-type (open symbol) and beneficial mutations (filled symbols) at different concentrations of rifampicin. Fitness was estimated as the mean growth rate of 12 to 18 cultures of each strain at each concentration of rifampicin (standard errors not shown).</p

Beneficial mutations.

<p>This table shows the beneficial mutations in <i>rpoB</i> that we identified in this study. We used a fluctuation test to isolate a total of 80 independent clones carrying beneficial mutations and sequencing revealed that each one of the clones carried one of 15 non-synonymous mutations in <i>rpoB</i>. We used one representative clone carrying each of these beneficial mutations in our experiments.</p

Phenotypic traits under selection.

<p>Plotted points show the rifampicin resistance and growth rate in media lacking rifampicin of beneficial mutation (filled symbols) and the wildtype (open symbols).</p

Distribution of fitness effects of beneficial mutations.

<p>Plotted points show <i>w_i,j</i>, the difference in fitness between beneficial mutations (i.e. those mutations that give higher fitness than the ancestral clone) and the least-fit beneficial mutation at each concentration of rifampicin. <i>P</i> values show the probability that the observed distribution of fitness effects of beneficial mutations is exponential (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000406#pgen-1000406-t002" target="_blank">table 2</a> for further statistical details).</p

A schematic of the distribution of fitness effects of beneficial mutations.

<p>This figure is a schematic showing how the distribution of fitness effects of beneficial mutations can change depending on the absolute fitness of the wild type (shown with vertical lines) in two different arbitrary distributions of mutational effects on fitness. Note that the distribution of fitness effects of beneficial mutations is very similar in both of these distributions when the fitness of the wild-type is high (short dashed line).</p

D521G rpoB mutant RNA-Seq

BAM files: RNA-Seq data for two biological replicates (BR) of the rifampin-resistant D521G rpoB mutant, which was evolved from the PAO1::mini-Tn7-pLAC-lux ancestral strai

H531R rpoB mutant RNA-Seq

BAM files: RNA-Seq data for 2 biological replicates (BR) of the rifampin-resistant H531R rpoB mutant evolved from the PAO1::mini-Tn7-pLAC-lux ancestral strai