Fig. 1

Distribution of pseudogenes across African MU strains. (a) Number of pseudogenes identified in the whole genome. (b) Distribution of the number of pseudogenes per country of isolate origin. The red dotted line indicates a boundary between the lineages based on the number of pseudogenes. Density is the frequency at which pseudogene numbers occurred. (c) Correlation between sample collection date and the number of pseudogenes in lineage 1 African strains. The blue line is a regression line with a negative Pearson’s rank correlation, r (156) = 0.022 (p-value = 0.78), and a gradient of -0.04 pseudogenes per year. Points are coloured by the source (country) of the strains. (d) Locally weighted scatterplot smoothing regression of the percent pseudogenes per MU genome. Strains were ordered starting with the closest isolate to the M. marinum reference to the farthest isolate according to their order in a maximum likelihood phylogenetic tree, and this is surrogate to for the root-to-tip distance. Black, purple, and brown- bounded lines represent lineage 1, the smaller sublineage of lineage 1 and lineage 2 respectively