A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

Table 3 Model comparison for L4 dataset

Model	Marginal likelihood	Mean rate (95% HPD)	Mean rate variance (95% HPD)	Mean tree height (95% HPD)	Origin (BDSKY only)
BDSKY+UCLD	− 6033864.2003	3.1885E−8 (1.9488E−8, 4.4007E−8)	4.991E−17 (1.0674E−17, 8.9835E−17)	1444.5416 (929.3966, 2083.7636)	NA
BDSKY+UCLD+origin	− 60327945.1483	3.4761E−8 (2.447E−8, 4.5029E−8)	5.5123E−17 (1.9718E−17, 9.4555E−17)	1319.2463 (952.8702, 1761.4382)	2310.916 (1165.2155, 3372.9253)
CC+UCLD	− 6043356.1504	3.1068E−8 (1.988E−8, 4.1624E−8)	4.3865E−17 (1.3291E−17, 7.806E−17)	1569.0512 (1054.607, 2225.4758)	NA
SKY+UCLD	− 6034698.3620	2.8097E−8 (1.5329E−8, 3.9927E−8)	3.7609E−17 (6.0593E−18, 7.1919E−17)	1690.536 (1016.2712, 2646.5163)	NA
CC+strict	− 6034091.5119	2.9299E−8 (2.2173E−8, 3.6637E−8)	NA	1567.544 (1186.1186, 1978.6488)	NA

Selected parameter estimates from five models applied to the Lineage 4 dataset: constant coalescent with uncorrelated lognormal clock (CC+UCLD), constant coalescent with strict clock (CC+strict), Bayesian skyline coalescent with uncorrelated lognormal clock (SKY+UCLD), birth-death skyline with uncorrelated lognormal clock and tree conditioned on the root (BDSKY+UCLD), and birth-death skyline with uncorrelated lognormal clock with origin parameter estimate (BDSKY+UCLD+origin). Marginal likelihoods obtained through path sampling (see the “Methods” section)