Table 1. Results of LSD and BEAST for the MTB complex with and without aDNA samples.

With BEAST we performed three different analyses, two using a sub-sample of 300 strains and different priors on the clock rate (1/x and uniform), and one using a sub-sample of 500 strains (Methods, S2 Table).

Data set	Clock rate
MTBC 6,285 + M. canettii (LSD)	5.59E-08 (4.12E-08, 6.17E-08)
MTBC 6,285 + M. canettii + aDNA (LSD)	6.93E-08 (5.48E-08, 8.42E-08)
MTBC 300 (BEAST 1/x)	8.2254E-08 (4.964E-08, 1.141E-07)
MTBC 300 +aDNA (BEAST 1/x)	7.3978E-08 (4.648E-08, 1.019E-07)
MTBC 300 (BEAST unif)	8.26E-08 (4.82E-08, 1.14E-07)
MTBC 300 +aDNA (BEAST unif)	7.1794E-08 (4.157E-08, 9.851E-08)
MTBC 500 (BEAST unif)	6.08E-08 (4.21E-08, 8.07E-08)
MTBC 500 +aDNA (BEAST unif)	5.20E-08 (3.41E-08, 7.12E-08)