Gallet-et-al-2018-RawData-1

This data file contains all the flow cytometry data used to estimate cell concentrations, fitness measures etc

Doumayrou et al_Arabidopsis_thaliana_data

This data file contains mortality measures and proxy data (i.e. mortality rate, reduction of leaf area and visual qualitative symptoms) of nine natural isolates of Cauliflower mosaic virus infecting Arabidopsis thaliana to study the effect of CaMV infection on A. thaliana and the relationship between the mortality rate and different proxies discussed in the manuscript

Doumayrou et al_evolution_traits_data

This data file contains life history data (i.e. virulence, transmission rate and within-host accumulation) of four natural isolates of Cauliflower mosaic virus infecting Brassica rapa to test the evolution of the virulence, transmission and viral accumulation of isolates with low and high within-host accumulation discussed in the manuscript

Doumayrou et al_trade-off_data

This data file contains life history data (i.e. virulence, transmission rate and within-host accumulation) of nine natural isolates of Cauliflower mosaic virus infecting Brassica rapa to test the virulence-transmission trade-off hypothesis discussed in the manuscript

Theoretical evolutionary epidemiology.

<p>(A) change in prevalence (proportion of infected bacteria). (B) change in the λcI857/λ ratio in the provirus stage. (C) change in the λcI857/λ ratio in the free virus stage. The initial value of the λcI857/λ ratio in the provirus was 1∶1, and two initial prevalence values were considered: 1% (red) and 100% (blue). We ran 10000 simulations of our model (see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003209#ppat.1003209.e019" target="_blank">equations (1)</a> and <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003209#ppat.1003209.e034" target="_blank">(2)</a>) allowing some variation over the phenotypic values ( and ) of the two virus strains. The gray envelopes show the range of variation among all simulation runs and colored lines show the median of these simulations (see section S1.3 in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003209#ppat.1003209.s009" target="_blank">Text S1</a>). See Table S1 in <b>supporting <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003209#ppat.1003209.s009" target="_blank">Text S1</a></b> for other parameter values.</p

Doumayrou et al_Brassica_rapa_data

This data file contains mortality measures and proxy data (i.e. mortality rate, reduction of leaf area and visual qualitative symptoms) of twenty natural isolates of Cauliflower mosaic virus infecting Brassica rapa to study the effect of CaMV infection on B. rapa and the relationship between the mortality rate and different proxies discussed in the manuscript

Effect of initial prevalence on transient virulence evolution, in the two life stages of the virus.

<p>We plot the maximal value of the λcI857/λ ratio from our theoretical model (crosses, same parameter values as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003209#ppat-1003209-g002" target="_blank">Figure 2</a>) and from the second experiment (dots and vertical bars are the means and their 95% confidence intervals over two chemostats of the log transformed data, see supplementary information). The λcI857/λ ratio is shown for both the provirus (black) and the free virus (gray) stages. The λcI857/λ ratio is significantly higher among free viruses than among proviruses, and decreases significantly as the initial prevalence increases (maximal λcI857/λ ratio in the first 15 hours of the second experiment, see also <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003209#ppat.1003209.s006" target="_blank">Figure S6</a>).</p

Schematic representation of the bacteriophage λ life cycle.

<p>Free viral particles of the wild type virus (green) and the virulent mutant (red) infect susceptible cells . A proportion of successful infections leads to genome integration at rate and to produce infected cells and or results in cell lysis at rate and . Infected cells lyse through spontaneous reactivation of the provirus at rate and for and , respectively. (See Table S1 in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003209#ppat.1003209.s009" target="_blank">Text S1</a> for the definition and the values of all the parameters of this model).</p

Experimental evolutionary epidemiology.

<p>(A) change in prevalence (proportion of infected bacteria). (B) change in the λcI857/λ ratio in the provirus stage. (C) change in the λcI857/λ ratio in the free virus stage. The initial value of the λcI857/λ ratio in the provirus was 1∶1, and competition was started from two initial prevalence values: 1% (red) and 100% (blue). The data was obtained from the first experiment. The lines are the mean over four chemostats (2 marker/virulence combinations with 2 independent replicates), and the envelopes show the 95% confidence intervals of the log transformed data.</p

analyses

R codes and data files