Extended Data Fig. 5: Posterior densities of the times of the most recent ancestors (tMRCAs) of the T. pallidum subspecies and major lineages as estimated by the molecular clock dating under different relaxed clock models and the results of the Bayesian date randomization test (DRT). | Nature

Extended Data Fig. 5: Posterior densities of the times of the most recent ancestors (tMRCAs) of the T. pallidum subspecies and major lineages as estimated by the molecular clock dating under different relaxed clock models and the results of the Bayesian date randomization test (DRT).

From: Redefining the treponemal history through pre-Columbian genomes from Brazil

Extended Data Fig. 5: Posterior densities of the times of the most recent ancestors (tMRCAs) of the T. pallidum subspecies and major lineages as estimated by the molecular clock dating under different relaxed clock models and the results of the Bayesian date randomization test (DRT).The alternative text for this image may have been generated using AI.

a) TPE, b) TPA, c) TPA SS14, d) TPA Nichols, e) TEN and f) T. pallidum. Vertical lines inside the density curves in panels a-f indicate the upper and lower limits of the 95% HPD intervals. g) Posterior distributions for the mean clock rate, using the true, unpermuted sampling dates (far left) and 50 replicates with sampling dates permuted among tips under a UCED model with a narrow mean clock-rate prior. Distributions are truncated at the upper and lower limits of the 95% HPD intervals and horizontal red lines indicate the median estimates. The red dashed lines indicate the median and the limits of the 95% HPD interval of the mean clock rate estimated under the true sampling dates.

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