Appendix 1—table 2. Number of substitutions and phylogeny changes within sub-alignments corresponding to known phylogroups.

Starting from the full 5% homoplasy-corrected core genome alignment we extracted, for each phylogroup, the sub-alignment of all strains belonging to that phylogroup and determined the number of bi-allelic SNPs M and number of phylogeny changes C. Each row of the table corresponds to one of the known phylogroups and shows the number of our strains in that phylogroup, the SNP rate within the clade $M/L$, the lower bound C on the number of phylogeny changes, the ratio $C/M$, and the estimated average number of times each position in the genome has been overwritten by recombination $T_{\mathrm{est}}$. Note that the phylogroup ’O’ stands for the outgroup. See Figure 1—figure supplement 1 for the phylogroup annotation of our strains.

Phylogroup	No. of strains	SNP rate $M\mathrm{/}L$	Phyl. changes C	$C/M$	$T_{\mathrm{est}}$
A	6	0.0024	178	0.027	0.65
B1	35	0.013	4540	0.130	16.5
B2	6	0.011	2664	0.088	9.7
D	29	0.017	5426	0.114	19.7
E	1	-	-	-	-
F	3	0.007	-	-	-
O	9	0.003	2	0.0002	0.007