Fig. 3: Molecular dating of Y. pestis branches 1–4.
From: The source of the Black Death in fourteenth-century central Eurasia
a, Maximum clade credibility time-calibrated phylogenetic tree. The tree is based on 167 genomes (historical and modern) and was estimated using the coalescent skyline tree prior and a log-normal relaxed clock. Collapsed branches contain modern and ancient isolates dating after AD 1400 (post-Black Death). The coloured arrows mark the nodes, for which equivalent posterior age distributions are shown in b. The estimated divergence dates (95% HPD intervals) of modern branches are shown on each corresponding node. b, Estimated posterior distributions based on the coalescent Bayesian skyline tree prior for the divergence of Y. pestis branches 1–4 (blue), for the estimated divergence of BSK001/003 (purple) and for the entire dataset used for this analysis (time to the most recent common ancestor of branches 1–4 and 0.ANT3, shown in grey). The dotted lines indicate mean posterior estimates and are annotated with the corresponding 95% HPD intervals.
