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. Author manuscript; available in PMC: 2017 Apr 30.
Published in final edited form as: Nat Genet. 2016 Oct 31;48(12):1535–1543. doi: 10.1038/ng.3704

Figure 6. Genome-based phylogeny and diversity by continent of 293 strains of the L4.3/LAM sublineage.

Figure 6

(a) Bayesian phylogeny with label colors indicating continent of strain origin: blue, Europe/Mediterranean; red, Sub-Saharan Africa; yellow, America; pink, Asia. Numbers on nodes indicate posterior probabilities. Pie charts indicate reconstructed ancestral geographical regions of the internal nodes. The hypothetical L4.3/LAM-ancestor is labeled and a European origin for this ancestor was supported using a Bayesian Method (shown) and a Maximum Parsimony method (Supplementary Fig. 14). The pie colors correspond to the colors of the taxa labels. (b) Boxplot of pairwise genetic distances (number of polymorphisms) of L4.3/LAM strains by continent (p-values from Wilcoxon rank sum test). (c) Nucleotide diversity per site (π), measured by continent. Error bars indicate 95% confidence intervals. MTBC isolates from countries of the continent group “Oceania“ (UN category; including Australia and New Zealand, Melanesia, Micronesia and Polynesia) were excluded for the genetic diversity analysis in panels B and C due the low number of samples.