学会抄録

Genome annotation. (XLSX 9 kb

Phytophthora infestans genotypes

21 isolates of Phytophthora infestans were genotyped at 12 microsatellite loci: D13, PinfSSR8, PinfSSR4, PinfSSR11, PinfSSR6a, PinfSSR3, Pi4B, Pi70, Pi63, Pi04, G11 and PinfSSR2. Binary data indicate presence (1) or absence (0) of alleles

Virulence level of the different G. pallida lineages

Virulence level of the different G. pallida lineage

Life-history traits of the virulent and avirulent lineages

Life-history traits of the virulent and avirulent lineage

Models description and selection criteria.

a<p>Six models are obtained by crossing 2 hypotheses regarding the genetic differentiation of virus populations between plants (D₁ and D₂) with 3 hypotheses regarding the competition issue between virus variants (C₁ to C₃). They include four to 14 parameters and were compared using Akaike information criterion (AIC) and Bayesian information criterion (BIC) to identify the model that is best supported by the data.</p>b<p>The process of genetic differentiation of the virus populations between plants, described by the scale parameter <i>θ</i> of a Dirichlet-multinomial distribution, was allowed either to be constant (<i>θ^s</i> = <i>θ</i>) or time varying (, for the five sampling dates ).</p>c<p>The process of virus competition within plants included the intrinsic rates of variant increase (given that ) as parameters but might undergo one of three hypotheses specifying the type of Lotka-Volterra competition coefficients .</p>d<p>−2log(Likelihood).</p

Parameter estimates of the model that is best supported by the data (model

<p><b>). </b><b>A</b>: Relative fitness of the four PVY variants (NN, NH, DN and DH) estimated by their intrinsic rates of increase <i>r</i>. The mean fitness of the population was arbitrarily set to 1 due to identifiability constraints (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002654#ppat.1002654.s004" target="_blank">Text S1</a>). In both graphs, dots indicate the mean values of the parameter whereas segments stand for the 95% confidence interval. Arrows indicate the most likely pathway leading to the resistance-breaking variant. <b>B</b>: <i>F</i>_ST indices as a function of time (dpi). <i>F</i>_ST characterizes the degree of genetic differentiation of the virus populations between plants. For each sampling date , was assessed as where is the scale parameter of a Dirichlet-multinomial distribution. For illustration purposes, a spline function (full line) is fitted to data.</p

Observed intra-host dynamics of four PVY variants.

<p><b>A</b>: Description of the four PVY variants used (NN, NH, DN and DH). Variants are named according to the amino acids at positions 119 and 121 of the VPg pathogenicity factor. All variants infect the pepper genotype Yolo Wonder (YW) but only DH infects the genotype Florida VR2 which carries the <i>pvr2²</i> resistance gene. <b>B–F</b>: Frequencies of the four PVY variants in the eight plant samples collected 6, 10, 15, 24 and 35 dpi. Additionally, for each date, a bar with the mean frequencies of the variants for the eight samples is provided. <b>G</b>: Mean (± standard deviation) frequencies of the four PVY variants as a function of time (dpi). <b>H</b>: Standard deviation of the frequencies of the four PVY variants as a function of time (dpi).</p

Goodness of fit of the model that is best supported by the data (model

<p><b>). </b><b>A</b>: Correlation between the 20 (4 variants×5 dates) observed mean frequencies of the four PVY variants and their estimated mean values. <b>B</b>: Correlation between the 20 observed standard deviations of the frequencies of the four PVY variants and their estimated standard deviations. The full line is the first diagonal (<i>i.e.</i> line <i>y</i> = <i>x</i>).</p

GenepopData_Glais-et-al

SSR data for isolate

PhenotypicData_Glais-et-al

Pathogenicity data for the isolates included in pape