Fig. 5.

Coding sites in epitope encoding regions are enriched for evidence of directional selection influenced by HIV-1 coinfection. Episodic directional selection in M. tuberculosis strains isolated from HIV-1 uninfected and HIV-1 coinfected individuals was evaluated using the MEDS method (Murrell et al. 2012). Sites that showed evidence of directional selection associated with phylogenetic branches separating HIV-1 uninfected and HIV-1 coinfected individuals (i.e., with an associated MEDS P value < 0.05, without Bonferroni multiple testing correction) were assigned to essential, nonessential and epitope encoding gene categories (Sassetti et al. 2003). The percentage of sites falling in each category is indicated by the bars. The site counts used to calculate these percentages can be seen in supplementary table 3, Supplementary Material online.