Fig. 2

Phylogenetic tree constructed with SNPs. a pe/ppe genes (5,404 SNPs, 10 % of the genome); the pe_pgrs3 gene was identified as having SNPs leading to the lineages not perfectly clustering, potential evidence of recombination affecting these loci. b pe/ppe genes excluding pe_pgrs3 (5,572 SNPs, ~10 % of the genome). Clear clustering according to lineage can be seen (Lineage 1 (Indo-Oceanic, green), lineage 2 (East-Asian (Beijing), blue), lineage 3 (East-African-Indian, purple), lineage 4 (Euro-American, red)). Reference genomes are labelled. M. canetti is annotated in cyan