Fig. 4: Recombination to mutation (r/m) ratio as a function of the ANI of the genome pairs compared.

The r/m ratio (y-axes) was estimated for all genome pairs in our collection for each species (graph title on top) using the empirical approach described in the main text, and is plotted against the ANI value of the genome pair compared (x-axes). The marginal plots outside the two axes show histograms for the density of datapoints on each axis. Graphs on the right are zoomed-in versions of the main graphs on the left in the 0–5 range of the y-axis values. Top graphs (A) show results for Sal. ruber genomes; bottom graphs (B) show E. coli genomes. Note that the ratio is frequently above 1 for genomes sharing between 98.5 and 99.5% ANI (e.g., members of different genomovars of the same phylogroup) for both species and that the estimates above ~99.5% ANI are not reliable due to the inability to detect recombination at this high sequence identity level. A few outlier datapoints (genome pairs) with ratios higher than 100 were also observed in the 98–99.5% ANI range and are due to the high identity of the recombined genes identified (causing the denominator in the r/m ratio to be a small number); the graphs on the right show the majority of datapoints, and thus better represent the average pattern. Also, note that a few E. coli and E. fergusoni genome pairs (left part of the lower graph) show a ratio higher than 1, but this is driven by recombined genes that are localized in a couple of specific regions of the genome and encode specific functions (selection-driven recombination, and not widespread across the genome). See main text for additional details.