Results of covariation analysis.

<p>For P1, HC-Pro and P3 ORFs, two groups of covariation were detected (indicated in different rows). Positions falling into the PIPO region codifying for the P3N-PIPO cistron are indicated in bold.</p

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

Results of the codon selection analyses.

<p>For each gene, the total number of codons, as well as those detected to be under negative, neutral or positive selection with both FEL and IFEL methods are given. The last column indicates the location of positively selected sites.</p>*<p>partial genes;</p>**<p>sites detected to be under positive selection by both FEL and IFEL methods;</p>***<p>FEL method detected position 2981, whereas the other two positively selected positions at the CP gene were detected with IFEL method.</p

Results of selection analyses per branches.

<p>For each region under study, branches showing positive selection, location of amino acid subregions involved and ORFs are indicated. For terminal branches, the name of the corresponding isolate is shown, whereas for internal branches the strain subjected to the selection event is indicated. Covarying positions detected in the previous analyses falling into the subregions providing a positive selection signature are shown in the last column. (<i>P</i><0.0001 for all subregions).</p

Schematic representation of the PVY genome, including UTR regions and gene distribution.

<p>The three regions (R1, R2 and R3) defined to perform the present study are indicated above and numbered ignoring the 5′ UTR.</p