Fig. 1.

Phylogeny and population structure of B. pseudomallei . A core SNP-based maximum likelihood phylogeny of 1654 genomes, with geographic origins highlighted. Differences in the levels of bacterial diversity across different geographic origins: Australasia (purple), Hainan, China (red), Thailand (green), Vietnam (orange), Singapore (blue), Malaysia (yellow), America (cyan), and other (grey). Outer ring represents population clusters based on Bayesian Analysis of Population Structure (BAPS) hierarchical clustering (groups 1–16) and six subgroups of the five major groups based on a threshold of 5000 pairwise SNP distances (PSDs; see Methods). Except for group 8, which is paraphyletic and marked by three black arrowheads, each group forms a monophyletic branch. One hundred iterations of bootstrap were performed and red asterisks indicate bootstrap values of major nodes that are greater than 80 in the five major groups.