Fig 1.
PVY infected lyophilized tobacco tissue was used to mechanically inoculate a single founding potato plant. Virus from the founding plant was used to mechanically inoculate three potato plants (source plants, designated number 3, 4 and 5). Each source plant was considered a replication and used as virus source for each transmission mode: AT—aphid transmission (represented by the aphid cartoon), MI—mechanical inoculation (represented by mortar and pestle cartoon), and IT—infected tuber (represented by the potato tuber cartoon). Each time the virus was transmitted to a new plant it was counted as a passage. A leaf and a tuber (represented by the red circle) were sampled, at harvest, from designated plants to compare the virus populations in those locations and among each transmission mode over time. The same procedure was conducted for each of the three PVY strains, PVYO, PVYN, and PVYN-Wi.
Fig 2.
Temporal changes in PVY nucleotide diversities in leaves during experimental evolution using three different transmission modes.
Thin lines connect PVY nucleotide diversities (π) in leaves for separate lineages over the course of the experiment. Colors represent the three different transmission modes (AT–aphid transmission, IT–transmission through infected tubers and MI–mechanical transmission). Line types represent the three different PVY strains used in the experiment. Thick translucent lines connect average values for all of the lineages within the same transmission mode over the course of the experiment. Below the plot, the arrows connect time points with significant increase in nucleotide diversity for specific transmission modes (based on Bonferroni-corrected post hoc pairwise comparisons of the estimated marginal means). Only the data obtained by the analysis of leaf samples is presented in this figure.
Table 1.
Analysis of factors using GLMM analyses for the PVY nucleotide diversity, π, data (leaves).
Fig 3.
Comparison of nucleotide diversities (π) in leaves and tubers.
(a) π in leaves (abscissae) are plotted against π in tubers (ordinates) for the same plants. Different colors represent different transmission modes, different symbols represent different strains. (b) Histograms show distributions of decimal log-transformed ratios of nucleotide diversities in tubers and leaves; dotted lines designate the null hypothesis of equal diversities πtuber/πleaf = 1, colored lines represent medians of the separate distributions. Colors correspond to the different transmission modes as given in the legend above the histograms.
Fig 4.
Estimations of effective population sizes (Ne) for different lineages.
(a) Kernel density plots (posterior distributions) for the estimation of the Ne values for each of the lineages in the experiment; lineages originated from the same source plant (designated number 3, 4 and 5) are plotted on the same plot, line colors represent transmission modes. (b) Modes of the Ne posterior distributions with colors corresponding to transmission modes. Statistically significant differences between medians of modes of Ne posterior distributions of the three transmission modes are designated on the plot.
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: PVYO, PVYN-Wi or PVYN, plus lineage designation within the strain: 3, 4 or 5). Lineages transmitted by the same transmission mode are grouped vertically (AT, MI, IT).
Fig 6.
Temporal changes in nucleotide diversities for synonymous (πs) and nonsynonymous (πN) sites of different PVY cistrons (for the viral populations in leaves) during experimental evolution using three different transmission modes.
Lines connect PVY nucleotide diversities for separate lineages over the course of the experiment. Colors represent three different transmission modes; line types represent three different PVY strains used in the experiment. F–Founding, S–Source.
Fig 7.
Summary of observed patterns in the PVY populations’ dynamics for different transmission modes.
In black, on the left side of potato plant drawings are the representations of the population dynamics' patterns. Suggested mechanisms explaining the observed patterns are highlighted in red, blue, and grey on potato plant drawings and on their right side. (a) Aphid transmission mode, (b) mechanical transmission mode, and (c) tuber transmission mode.