Individual zoospore production per leaflet (Means+SE) in single and multiple infections for the BP3 reference genotype (grey bars) and BEK (A), P13 (B), P43 (C) and PON05 (D) genotypes (black bars).

<p>Individual zoospore production per leaflet (Means+SE) in single and multiple infections for the BP3 reference genotype (grey bars) and BEK (A), P13 (B), P43 (C) and PON05 (D) genotypes (black bars).</p

Analyses of variance contrasts for global (i) and individual (ii) reproductive strategy.

<p>Non-significant interactions were removed from models before computing F statistics and significance of other factors. Bold typeface indicates significant effects (P-value<0.05).</p

Characteristics of the five <i>Phytophthora infestans</i> genotypes used in the experimental setup.

<p>All isolates were chosen for having the same mating type. The virulence profile corresponds to the ability of pathogen genotype to infect potato genotype containing resistance genes (numbered from 1 to 11). Avr3a genotype is given for the two single nucleotide polymorphisms at the positions 241 and 312 of the avr3a gene, which are responsible for the virulence profile towards the resistance gene number 3 (named R3). A₃₄₁/T₃₁₂ genotype corresponds to a parasite genotype unable to infect a potato genotype containing the R3 resistance gene (see virulence profile of BP3), whereas G₂₄₁/G₃₁₂ genotype corresponds to parasite genotype able to overcome the R3 resistance gene (see virulence profile of all but BP3).</p

Overall zoospore density (Means+SE) in single-site infection (SSI), double-site infection of single genotype (DSI-sg) and double-site infection of multiple genotypes (DSI-mg).

<p>Overall zoospore density (Means+SE) in single-site infection (SSI), double-site infection of single genotype (DSI-sg) and double-site infection of multiple genotypes (DSI-mg).</p

Relative proportion (Means+SE) of zoospores density of BP3 (grey bars) and challenger (black bars) genotypes in double-site infection of multiple genotypes (DSI-mg).

<p>Relative proportion (Means+SE) of zoospores density of BP3 (grey bars) and challenger (black bars) genotypes in double-site infection of multiple genotypes (DSI-mg).</p

Data & scripts_v2

ZIP folder containing all scripts, data and simulation results used in this study

MCC phylogeny of 60 PVY isolates for the R1 region.

<p>The tree was calculated from the posterior distribution of trees generated by Bayesian MCMC coalescent analyses with BEAST <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037853#pone.0037853-Drummond1" target="_blank">[55]</a>. Posterior probabilities are indicated above branches. Branches detected to be under positive selection are shown in green.</p

Susceptible-Exposed-Hidden-Detected-Removed (<i>SEHDR</i>) model of an individual’s epidemiological status.

<p>At <i>T</i>₀, patch <i>i</i> is planted with infectious (<i>I</i>) or susceptible (<i>S</i>) individuals with probabilities <i>p</i>_<i>i</i> and 1-<i>p</i>_<i>i</i>, respectively. An individual passes between compartments at event times <i>T</i>_<i>E</i>, <i>T</i>_<i>H</i>, <i>T</i>_<i>D</i> and <i>T</i>_<i>R</i>. Apart from <i>T</i>₀, only the detection time <i>T</i>_<i>D</i> can be known (yellow); all other event times are censored (blue). Infectious individuals from both within and outside the patch contribute to the force of infection , which is the expected number of infectious events affecting an individual over time interval (<i>t</i>_<i>r</i>−1, <i>t</i>_<i>r</i>]. The probability that a given susceptible (<i>S</i>) individual becomes exposed (<i>E</i>) in this time interval is 1-exp(-), assuming independent infection events. A latent period of duration <i>T</i>_<i>H</i>-<i>T</i>_<i>E</i> follows, after which the individual becomes infectious (<i>H</i>). Infectious individuals are removed (<i>R</i>) only after detection (<i>D</i>) or when the entire patch is removed. For simplicity, the <i>i</i> and <i>t</i>_<i>r</i> subscripts are omitted in the figure.</p

Impact of the number of introduction patches (<i>κ</i>) on the expected Fisher information for the sharka epidemic.

<p>For each <i>κ</i>, the estimation with the highest mean posterior log-likelihood was retained. For <i>κ</i><10 no introduction patch combination returned a finite posterior log-likelihood. The empirical approximation of the Fisher information was maximal at <i>κ</i> = 11.</p

Comparison of simulated and estimated dispersal kernels.

<p>From left to right: kernels with the minimum, lower quartile, median, upper quartile and maximum Kullback-Leibler (KL) distances (posterior mean), as estimated (red) under the most exhaustive scheme (Θ₄), based on simulated epidemics with short-, medium- and long-range kernels (from top to bottom; black). Kernels are represented by their marginal cumulative distribution function <i>F</i>^1<i>D</i> (with distance from the source represented on the log₁₀ scale). The mean KL distance is indicated for each estimation.</p