FIGURE 1.

Phylogeny of all TPA complete genome sequences determined to date. Maximum likelihood bootstrapping method was used to generate the phylogenetic tree based on 2273 variable positions found exclusively in the whole genome sequences available to date (Table 2). The bootstrap values, when above 60, are given next to the branches in red. SS14-like strains are represented by red squares, Nichols-like strains by blue squares. The year of isolation is given next to the branches. Strains designated CW30-CW88 are the whole genome sequences determined in this study by DpnI enrichment while Phi-1 and Grady were established in this study by PSGS. These represent 65% of all whole genome sequences of TPA to date. tpr genes, repetitive regions and inter- and intra-recombinant loci were excluded from this analysis (Supplementary Table S2 and Figures 2, 5). We used the genome of Samoa D (T. pallidum subsp. pertenue) as an outgroup.