Figure 3

Phylogenetic analysis. (A) A total of 168,476 variable sites from a core-gene alignment of 2,103 genes from 65 genomes were used to generate a maximum-likelihood phylogenetic tree of the V. cholerae species, rooted on Vibrio metoecus and Vibrio sp. RC586. Two genomes that are representative of the 7PET lineage were included. The non-toxigenic isolate 48853_F01 clustered together with other non-toxigenic, non-O1/O139 V. cholerae. (B) A maximum-likelihood phylogeny of the 7PET lineage constructed using 1,629 non-recombinant variable sites across 117 V. cholerae genomes, rooted on M66-2. The three toxigenic samples in this study clustered together with other toxigenic O139 genome sequences, all of which form a discrete sub-lineage within 7PET. Hatch marks denote branches that were shortened artificially for illustrative purposes; an unedited tree is presented in Supplementary Fig. S5. Trees were also computed using an ascertainment bias correction model (see Methods). These are presented in Supplementary Fig. S6.