Phylogenetic analysis of ancient and modern <i>M</i>. <i>leprae</i> strains.

<p>(<b>A</b>) Maximum parsimony tree reconstructed from 3124 informative SNP positions. The tree is drawn to scale, with branch lengths representing number of substitutions. <i>M</i>. <i>lepromatosis</i> was used as outgroup. The novel strains from this study are labelled in red, and the previously published ancient strains are labelled in blue. Animal symbols indicate strains isolated from red squirrels, armadillos and non-human primates. The main branches are color-coded, and the SNP subtypes are marked with dotted vertical bars. Bootstrap values (500 replicates) are shown next to each node. (<b>B</b>) Bayesian phylogenetic tree based on 2371 SNP positions calculated with BEAST 1.8.1. Median divergence times in years B.C.E. and C.E. are shown on the main nodes (the 95% Highest Posterior Density ranges are given in square brackets). Tip labels for each sample show the name, the country of origin and the isolation date, or the radiocarbon dates. The novel strains from this study are labelled in red, and the previously published ancient strains are labelled in blue. Posterior probabilities for each node are shown in grey. The main branches are color-coded. The hypermutator strains 85054, Amami, S15, Br14-3, Br2016-15, Zensho-4, Zensho-5 and Zensho-9 (as described in [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006997#ppat.1006997.ref014" target="_blank">14</a>]) were excluded from this analysis.