(A) The cumulative distribution of pairwise divergences is shown as a different colored line for each species (see legend in panel B). Both axes are shown on logarithmic scales. The vertical lines in corresponding colors show the critical divergences at which half of the genome is recombined for each species. (B) Cumulative distributions of clonal fractions across the pairs of strains for each species, with the blue, yellow, and green shaded regions indicating the fully recombined, partially recombined, and mostly clonal regimes, respectively, that is analogous to Figure 2I (C) For each species, the height of the bar shows the fraction of SNPs that fall in recombined regions for pairs of strains for which half of the genome is recombined, that is see Figure 2H. (D) The violin plots show, for each species, the distribution of branch support, that is the relative ratio of SNPs supporting versus clashing with each branch split, analogous to the right panel of Figure 4. The blue lines correspond to the medians of the distributions. (E) Box-whisker plots showing the 5, 25, 50, 75, and 95 percentiles of the distributions of nucleotide distances between consecutive SNPs (green) and phylogeny breakpoints (blue, that is analogous to Figure 5C), for each species. The axis is shown on a logarithmic scale. (F) Box-whisker plots of the distributions of the number of consecutive SNPs in tree-compatible segments, that is analogous to Figure 5B.