As an alternative approach to identify potential admixture (and possible HGT), we created phylogenies for all gene families and then screened for phylogenies where there was an absence of congruity with the general pattern for the genome (see methods; Fig. 7). We screened for clade monophyly using the monophyletic function of the R ape package42 as well as the TOPD/FMTS43 tree congruence tool. Potentially incongruent trees were verified by manual inspection. For rapid processing, we used UPGMA distance based trees as we were comparing features of the gross topology44. Of the 1140 core genes, only 66 were found to have phylogenies with the whole genome (Supplementary Figure 4a). All of the inconsistencies fell in Clades 2 and 3: there was no evidence of an allele from another clade within the Lp species. For accessory genes, the rate was higher but these were still a relatively small proportion of the whole (145/2379) (Supplementary Figure 4b). In this case, 31 genes had a polyphyletic distribution. These were either genes that encoded hypothetical proteins, or functions associated with plasmids and phages.