Relationships among sequenced E. histolytica strains. Relationships were estimated using 3,696 polymorphic sites and two phylogenetic approaches, distance-based analysis (neighbor-joining) and maximum likelihood (ML), both as implemented in MEGA 5 . ML used the General Time Reversible model of evolution, selected as best using the model testing function in MEGA 5, while neighbor-joining used the maximum composite likelihood model. Statistical support for distance and ML trees was evaluated using bootstrapping (1,000 replicates). The ML tree is shown. The tree is rooted by comparison with orthologous positions in E. dispar (data not shown) along the branch to the PVBM08B and PVBM08F strains. Bootstrap values from both types of phylogenetic analysis are shown in the following order: Distance/ML. An asterisk indicates where the bootstrap value is under 50%.