Figure 3. Phylogeny of modern and eighteenth-century M. tuberculosis Lineage 4 genotypes.

(a) Maximum-likelihood tree of 1,582 modern Lineage 4 genotypes and four high-coverage historical genotypes (B68-1, B68-2, B80 and B92-1; blue lines with dots at the tips; details in Supplementary Data 2). The tree was rooted using a Beijing genotype (not shown). Ten additional low-coverage historical genotypes were mapped to the tree with MGplacer (red nodes). Lineages and sub-lineages used for dating (Supplementary Table 3) are indicated by black nodes and coloured segments. (b) Topological representation of phylogenetic paths through nodes outwards from the root (top) for ten low-coverage historical genotypes; pie-charts show SNVs recovered per node (coloured segment) from each low-coverage genome as a proportion of all polymorphic sites defining that node according to MGplacer.