FIG. 4.

M. tuberculosis strain phylogeny based on a combination of LSPs, SNPs, and selected phenotypic traits. The tree shown is a consensus of the most parsimonious trees found using the heuristic search algorithm. Character state boxes are shown at the top (for LSPs, a blue box indicates presence and a yellow box indicates absence; for SNPs and other characters, colors correspond to different character states). Characters 1 to 12 are SNPs, characters 13 to 28 are LSPs, character 29 belongs to the Musser group, character 30 is Smear positive or negative, and character 31 is Site (pulmonary or extrapulmonary). Unresolved branching patterns are collapsed.