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Table 3 Model comparison for L4 dataset

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

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
  1. 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)