Figure 5: Bayesian phylogeny and population dynamics of 165 genotypes from Lineage 4, calibrated with four high-coverage eighteenth-century genotypes. | Nature Communications

Figure 5: Bayesian phylogeny and population dynamics of 165 genotypes from Lineage 4, calibrated with four high-coverage eighteenth-century genotypes.

From: Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

Figure 5

SNPs in the non-repetitive core genome (Supplementary Data 1) were analysed with BEAST17 using UCLD clock rate and a Bayesian Skyline with 30 steps (details in Supplementary Table 4). (a) Maximum clade credibility tree with nodes (boxes) labelled according to the hierarchical nomenclature of Coll et al.15, with two additional nodes 4.a and 4.b. Supplementary Table 2 summarizes the dating estimates for nodes. Short branches corresponding to four historical genotypes are labelled by name and highlighted by asterisks. Coloured boxes show broad spoligotype groupings for modern isolates, illustrating the paraphyletic nature of these groups (details in Supplementary Fig. 3). (b) Bayesian skyline plot showing changes over time in effective population size, Ne (in black) since 396 CE, with 95% confidence intervals in grey.

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