Table 1.

Genetic diversity of Old World M.tb across lineages 1–7

	MTBC	L1	L4	L2	L3	L5	L6	L7
Sample
n	552	89	143	181	65	15	31	28
Diversity
ϴ	2.13E‐03	7.56E‐04	7.80E‐04	4.49E‐04	3.88E‐04	1.72E‐04	3.04E‐04	7.99E‐05
Π	2.80E‐04	1.92E‐04	1.54E‐04	7.46E‐05	9.16E‐05	8.77E‐05	1.41E‐04	4.52E‐05
Demographic inference
N/Nanc	91 ± 4	71 ± 5	55 ± 22	112 ± 102	148 ± 2	504 ± 111	50 ± 5	17 ± 4
Generations (Nanc)	0.16 ± 0.01	0.80 ± 0.06	0.65 ± 0.35	0.41 ± 0.94	3.54 ± 0.04	3.94 ± 0.73	1.10 ± 0.09	2.45 ± 0.89
LL expansion	−1,788.4	−424.2	−492.8	−467.1	−108.2	−42.4	−151.9	−64.5
LL neutral	−10,549.2	−3,246.6	−3,474.6	−2,378.9	−1,717.0	−520.7	−912.3	−159.4
p‐value	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Structure UN subregions
Var. between	21	19	4	20	16	NA	NA	NA
Var. within	79	81	96	80	84	NA	NA	NA
p‐value	<0.001	<0.001	0.002	<0.001	0.004	NA	NA	NA
Structure botanical continents
Var. between	14	5	2	9	13	NA	NA	NA
Var. within	86	95	98	91	87	NA	NA	NA
p‐value	<0.001	0.02	0.05	<0.001	0.002	NA	NA	NA
TMRCA
Median	−2,898	−360	77	−20	520	784	100	1,311
Lower	−4,032	−906	−368	−488	177	502	−339	1,152
Upper	−2,172	−10	362	279	739	964	382	1,413
Geographic origin
1st region	W Africa	S Asia	E Africa	SE Asia	S Asia	W Africa	W Africa	E Africa
Probability	54.2%	75.6%	98.9%	81.0%	63.5%	99.9%	99.8%	99.8%
2nd region	E Africa	E Africa	E Europe	E Asia	E Africa	E Africa	E Africa	S Africa
Probability	37.5%	24.1%	0.7%	9.2%	36.2%	0.1%	0.2%	0.0%

TMRCA estimates reflect scaling of results to evolutionary rates calibrated from ancient DNA (median 5.00 × 10⁻⁸ substitutions/ site/year [Kay et al., 2015]) and are written as calendar years. To account for uncertainty in this rate estimate, our lower and upper TMRCA estimates reflect scaling of our results with the low and high bounds of the 95% highest posterior density estimates of the rate reported from ancient DNA analysis (i.e., 4.06 × 10⁻⁸ and 5.87 × 10⁻⁸, respectively).

Abbreviations: MTBC, Mycobacterium tuberculosis complex; NA, not applicable; TMRCA, time to most recent common ancestor.