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. 2022 Apr 12;119(17):e2116722119. doi: 10.1073/pnas.2116722119

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Copyright © 2022 the Author(s). Published by PNAS.

This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).

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Fig. 2. — Y. pestis molecular dating using BEAST. (A) Maximum-clade credibility tree summarizing the results of divergence dating analysis between all extant Y. pestis lineages and the LNBA− lineage based on the coalescent skyline tree prior in BEAST v2.6.6. The maximum-clade credibility tree was produced using TreeAnnotator and visualized using FigTree v1.4.4 (https://github.com/rambaut/figtree/releases/tag/v1.4.4). Newly generated genomes are shown in purple (LNBA−) and green (I2470). (B) Posterior estimates of the time to the most recent common ancestor (TMRCA) for the divergence of all known Y. pestis as well as the divergence of the LNBA− clade are shown for the coalescent skyline tree prior. Density plots were produced using the ggplot2 package (39) in R v3.6 (43).