Fig. 2.

Contribution of toxigenic V. cholerae O1 environmental isolates to the evolution of the cholera epidemic in Haiti between 2012 and 2014. (A) MCC phylogeny for 116 environmental and clinical toxigenic V. cholerae O1 isolates collected between October 2010 and December 2015 inferred from genome-wide hqSNP data using the Bayesian phylogeography framework implemented in BEAST package version 1.8.4. Branch lengths are scaled in time by enforcing a relaxed molecular clock. Environmental and clinical states are indicated in green and violet, respectively. Circles at internal nodes indicate high posterior probability (PP) support (PP > 0.9). (B) Trunk reward proportion (TRP) at each ancestral location state estimated over time inferred using the continuous-time Markov chain model. Green- and purple-shaded areas represent the trunk proportions over time for environmental and clinical transitions, respectively. (C) Number of jumps (%) of all possible intrastate (clinical-to-clinical, environmental-to-environmental) and interstate transitions (clinical-to-environmental, environmental-to-clinical) normalized by total numbers of transitions obtained from the MCC phylogeny. Internal refers to all internal branches including the backbone path, and external to terminal branches of the tree. (D) Weighted averages of synonymous substitution rate estimates for environmental toxigenic V. cholerae O1 isolates were based on 200 randomly sampled trees from the posterior distribution of molecular clock-calibrated Bayesian phylogenies. Internal refers to estimates based on all internal branches of the tree, while external refers to estimates based on terminal branches. An asterisk indicates a significant (P < 0.001) difference between rate estimates. Error bars indicate standard deviation.