Table 1.
Synonymous (Ks) and non-synonymous (Ka) substitutions.
Fig 1.
Maximum likelihood phylogenetic analysis of six putatively non-recombinant gene regions.
Alignment positions are indicated. Isolates are coloured according to group, as indicated, and NY-1 (NC 004667), subject to topological conflicts between trees is indicated with larger font.
Fig 2.
Phylogenetic analysis of the whole genomes under partitioned ML.
(a) Multi-labelled ‘genome’ tree and (b) the corresponding rooted network inferred using Dendroscope.
Fig 3.
Summary of RAxML phylogenetic analysis.
(a) 392 GLRaV-3 sequences of 602nt or more in length was used for the analysis. The tree is rooted, but the outgroups have been removed for ease of presentation; the scale indicates branchlengths in substitutions per site. Values at nodes are ML bootstrap support: first, given this tree, thereafter (within parentheses) support for the equivalent clade given the analysis including sequences of 4761nt or more in length. Groups and supergroups proposed here are indicated. Further details, including support values and tip labels are presented in supporting information S2 Fig. (b) A grapevine (Vitis vinifera cv. Cabernet Sauvignon) showing typical symptoms of Grapevine leafroll disease.
Fig 4.
Bayesian phylogenetic inference and molecular dating analysis.
BEAST was used for estimation of node ages and rooting of the GLRaV-3 tree, independent of the outgroup. a. Exponential relaxed clock. b. Lognormal relaxed clock. Variant groups are indicated and colour coded following Figs 1–3. For the major clades, posterior probability (PP) clade support is indicated above the branches; 0.95 PP age ranges at the nodes. The extent of 0.95 PP age ranges for nodes within groups I-IV is indicated by grey boxes.