Mtb, as well as non-tuberculous Mycobacteria, differ from other bacteria in several key respects of DNA repair [ [39] [40] [41] [42] . Within the host, Mtb must combat damage to its DNA from macrophage-generated reactive oxygen and nitrogen intermediates. The mechanisms by which this is accomplished are not fully understood [43, 44] . Although genes implicated in DNA repair have not expanded in the Mtb lineage, we note that the set of genes showing positive selection on the Mtb lineage in our d N /d S analysis is enriched for genes involved in the COG category for DNA replication, recombination, and repair (Additional file 1: Table S2 ). Several of the genes in this set with highest d N /d S values are known DNA repair genes (including recA, recB, and dnaE2), and several additional genes are helicases (dnaB, helZ, and gyrB).