Table 1.

Major phylogenetic lineages within human-adapted MTBC members^a

Lineage	MTBC species	Presence/absence of TbD1	Gagneux's nomenclature (LSP based)	PGG (SNP based)	SCG (SNP based)	Spoligotype-defined families
1	M. tuberculosis	Intact	Indo-Oceanic lineage	1b	1	EAI
2	M. tuberculosis	Deleted	East Asian lineage	1b	2	Beijing
3	M. tuberculosis	Deleted	East African-Indian lineage	1b	3a	CAS
4	M. tuberculosis	Deleted	Euro-American lineage	2, 3	3b, 3c, 4, 5, 6a, 6b	H, LAM, X, T, S, others
5	M. africanum	Intact	West African lineage I	1b	Not described	AFRI2
6	M. africanum	Intact	West African lineage II	1a	Not described	AFRI1

^aTbD1, M. tuberculosis-specific deletion region 1 described by Brosch et al. (8); PGGs are as defined by Sreevatsan et al. (37); SCG subgroups are as defined by Filliol et al. (14) and Alland et al. (2); EAI, East African-Indian family; CAS, Central Asian family; H, Haarlem family; LAM, Latin American-Mediterranean family.