Figure 1

Shigella dysenteriae type 1 phylogeny. a. Maximum likelihood phylogeny of the 56 Shigella dysenteriae type 1 strains, relative to E. coli K12, O157, O55, Shigella flexneri and Shigella sonnei. The root of the tree was determined using the more distant relative E. coli UTI89. The tree was constructed using 78,267 variable positions found over 1,859 genes with 1,000 Bootstrap repetitions (values displayed on the branches). Sd1 strains are framed in orange. A neighbor-joining tree based on the rate of synonymous substitutions (dS) between each pair showed the same topology as the maximum likelihood tree, with similar relative branch lengths (data not shown). b. Maximum likelihood phylogeny based on a concatenation of the 919 polymorphic positions identified between the 56 Shigella dysenteriae type 1 strains in the common genes that are single-copy and not subjected to recombination (see Methods). The root (E. coli ancestor) was approximately placed based on the E. coli outgroups (Figure 1a). Geographic distribution of lineages or sub-lineages: A. Tennessee, B. China, C1. Guatemala, C2. Zambia, C3. Cameroon and an unknown location, D1. Bangladesh, D2. Central African Republic, D3. Bangladesh, D4. Bangladesh and India, D5. Bangladesh and D6. India and Thailand.