Fig. 3.

Maximum likelihood reconstruction of whole genome phylogeny of ocular Chlamydia trachomatis sequences from the Bijagós Archipelago (Guinea-Bissau). Maximum likelihood reconstruction of the whole genome phylogeny of 81 Ct sequences from the Bijagós Islands and 54 Ct reference strains. Bijagós Ct sequences (n = 81) were mapped to Ct A/HAR-13 using SAMtools [55]. SNPs were called as described by Harris et al. [4]. Phylogenies were computed with RAxML [62] from a variable sites alignment using a GTR + gamma model and are midpoint rooted. The scale bar indicates evolutionary distance. Bijagós Ct sequences in this study are coloured black, and reference strains are coloured by tissue localization (red = Ocular, green = Urogenital, blue = LGV). Branches are supported by > 90% of 1000 bootstrap replicates. Branches supported by 80–90% (orange) and < 80% (brown) bootstrap replicates are indicated