Fig 5. SNPs dynamics in different lineages.

Each heatmap represents the dynamics of SNPs frequencies in each lineage during the experiment. Within each heatmap, lines represent specific SNPs; rows represent passage numbers. SNPs frequencies are represented by color according to the color key at the bottom of the figure. The dendrograms in front of the heatmaps represent clustering of SNPs trajectories (SNPs that have similar frequency changes in time and thus may be linked are clustered together). Black rectangles at the end of each heatmap designate nonsynonymous mutations; positions and corresponding changes for fixed nonsynonymous mutations are given below the corresponding heatmap. Lineages started from the same source plant are grouped vertically (designated by strain name: PVY^O, PVY^N-Wi or PVY^N, plus lineage designation within the strain: 3, 4 or 5). Lineages transmitted by the same transmission mode are grouped vertically (AT, MI, IT).