File S1 - The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus

Figures S1–S5 & Tables S1–S2. Figure S1. Phylogenetic evidence for recombination among Cauliflower mosaic virus from the Europe, Japan, Middle East (Iran and Turkey) and USA. ORFs I–V (A) and ORF VI (B). Neighbor-Net network analysis was performed using SplitsTree4. Horseradish latent virus is used as the outgroup. Formation of a reticular network rather than a single bifurcated tree is suggestive of recombination. The isolates obtained in this study are listed in Table S1 in File S1. Figure S2. Recombination analysis by RAT plot. Each blue line represents a pairwise sequence comparison. The red curve represents the estimated proportion of recombinants at each position in the alignment. The red vertical lines denote estimated positions of recombination breakpoints, which approximately match the boundaries of the ORF VI region. The estimated nucleotide positions of the recombination sites are shown relative to the 5′ end of the genome, using numbering of the gapped aligned sequences with gaps removed (see Materials and methods). Recombination sites in parentheses are shown relative to the 5′ end of the genome using numbering of the sequence of the Xinjing isolate. Figure S3. Maximum-likelihood tree estimated from ORF VI of 105 non-recombinant Cauliflower mosaic virus isolates. Nodes are labelled with bootstrap support percentages. Figure S4. Regression of root-to-tip distance (inferred from Maximum-likelihood trees) against year of isolation for the gene with the smallest number of sequences in each ORF region. Figure S5. Estimates of nucleotide substitution rates. Mean estimates and 95% credibility intervals are shown. These were estimated from 66 ORFs I–V and 97 ORF VI (see text). In each set of estimates, the first is based on the original data, whereas the remaining ten values are from date-randomized replicates. The 95% credibility intervals of the estimates from the date-randomized replicates do not overlap with the mean posterior estimate from the original data set. In addition, the lower tails of the credibility intervals are long and tend towards zero. These features suggest that there is sufficient temporal structure in the original data sets for rate estimation. Table S1. Cauliflower mosaic virus isolates analyzed in this study. Table S2. Detailed results from BEAST analyses of Cauliflower mosaic virus. (PDF)