Figure 1: Signatures of recombination in the S. aureus core genome.

(a) Maximum likelihood phylogeny of 95 isolates from Oxfordshire, England and 15 reference isolates, based on 2,114,882 core invariant and biallelic sites. The reference genomes represent international strains (Australia: JKD6159; Japan: Mu50, N315; UK: EMRSA15, MSSA476, TW20; USA: JH1, USA300), animal-associated strains (bovine: RF122; ovine: ED133; poultry: ED98, swine: SO385), and historic strains (1943: NCTC 8325; 1952: Newman; 1960s: COL). Branches are colour coded by the proportion of homoplasious substitutions. Isolates are labelled by ST or reference genome and colour coded by clonal complex. Group 1 and group 2 S. aureus, as previously defined⁴², are indicated. (b) Alternative, phylogenetically incongruent, relationships among CCs supported by some core biallelic sites but not others. (c) Decay in LD with increasing physical distance between pairs of core biallelic sites. LD is quantified by r², the squared correlation coefficient. (d) Relationship between allele frequency, LD and number of substitutions at core biallelic sites. Each circle represents all the biallelic sites sharing a particular phylogenetic pattern, with the area proportional to the number of sites with that pattern. Circles are colour coded by the number of substitution events reconstructed along the phylogeny by maximum likelihood at each site with that pattern. Black circles correspond to the sites consistent with a unique mutation on a single branch of the phylogeny, while non-black circles represent homoplasious BiPs.