Fig. 4

Homologous recombination in human- and animal-derived S. aureus isolates detected by ClonalFrameML. a Comparison of the ρ/θ ratios between human and animal isolates. b Comparison of the number of recombination events detected in human and animal isolates. In panels a and b, colored dots represent genomes in each category. c Total length of recombined DNA per genome and the number of recombination events detected (box shading) per genome. The tree is identical to that in Fig. 1a. The list of all recombination events are presented in Supplementary Table S4. d Comparison of the pairwise core genome SNP distance before and after recombined DNA was removed. In panel d, each dot represents comparison between a pair of genomes. In the violin plots, the mean value is represented by the red dot, box represents the interquartile range, horizontal line in the middle of the box represents the median, and the lower and upper whiskers represent the lowest data point without the outliers and the highest data point without outliers, respectively