Phage survivorship and bacterial resistance following host bottlenecks

Excel file containing different spreadheets for all plotted graphs/analyses. All labels/factors are explained in the actual Excel file

Vmax Data

Vmax Data.csv, Data description: Data used to create Figure 2: Average growth rate of evolved strains in vitro relative to the ancestral strain. The data gives the growth rate of the evolved strains relative to the ancestral strain from which all strains were derived. There are 6 replicate lines, which were averaged to give “Growth Rate Relative to Ancestor”. Data was collected in the laboratory using a spectrophotometer. Columns correspond to: Strain Replicate; the name allocated to each of the replicate lines, e.g. H1 corresponds to replicate line 1 evolved on hard agar. Vmax Replicate: The Vmax was measured independently twice in order to provide replicates. This value was averaged in statistical analysis. Agar Type on which Strain was Evolved: Strains were either evolved in hard or liquid agar. Vmax Relative to Ancestor: Vmax of evolved strain under each treatment group was divided by Vmax of ancestral strain under the same treatment to give a relative measurement of area dispersed. Averaged Vmax Replicates: Replicate relative Vmax measurements were averaged. Selection Type: Strains were either under positive or neutral artificial selection for dispersal

Relative fitnesses of cheat clones derived from the wild type (panel (a), n = 14) and mutator (panel (b), n = 18) populations described in [16].

<p>Fitness was measured in competition with cooperating bacteria at initially low (c.5%) and high (c.50%) cheat frequency. Diamonds show medians and associated 95% confidence intervals.</p

Figure 3 Relative fitness

Data shows the relative fitness of dispersers to non-dispersers (i.e. CFU disperser/ CFU non-disperser) in Pseudomonas aeruginosa after 48 hours growth and dispersal. Motility variants were tested across three treatment groups: No Phage, Local Phage and Global Phage. Excel was used to create the data file

Biofilm Data

Biofilm Data.csv, Data description: Data used to create Figure 3: Biofilm production of evolved strains. Results show the average biofilm production of 6 isolates evolved in each experimental environment, relative to the ancestral strain from which all evolved strains were derived. Data was collected in the laboratory using a crystal violet staining method. Columns correspond to: Strain Replicate: the name allocated to each of the replicate lines, e.g. H1 corresponds to replicate line 1 evolved on hard agar. Bioflim Replicate: The biofilm production was measured independently eight times in order to provide replicates. This value was averaged in statistical analysis. Agar Type on which Strain was Evolved: Strains were either evolved in hard or liquid agar. Biofilm Relative to Ancestor: Vmax of evolved strain under each treatment group was divided by Vmax of ancestral strain under the same treatment to give a relative measurement of area dispersed. Averaged Biofilm Replicates: Replicate relative biofilm measurements were averaged. Selection Type: Strains were either under positive or neutral artificial selection for dispersal

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

In vivo Growth Data

In vivo Growth Data.csv, Data description: Data used to create Figure 4: Average growth rate of evolved strains within a host (G. mellonella) relative to the ancestral strain. Data was collected in the laboratory. Columns correspond to: Strain Replicate: the name allocated to each of the replicate lines, e.g. H1 corresponds to replicate line 1 evolved on hard agar. In vivo Replicate: The in vivo growth rate production was measured independently four times in order to provide replicates. This value was averaged in statistical analysis. Agar Type on which Strain was Evolved: Strains were either evolved in hard or liquid agar. In vivo Relative to Ancestor: In vivo growth rate of evolved strain under each treatment group was divided by In vivo growth rate of ancestral strain under the same treatment to give a relative measurement of area dispersed. Averaged In vivo Replicates: Replicate relative in vivo growth rate measurements were averaged. Selection Type: Strains were either under positive or neutral artificial selection for dispersal. Caterpillar Fresh Weight: The weight of each caterpillar was measured before inoculation to control for the effects of caterpillar size on bacterial growth

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

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