Fig. 1.

Sampling locations, phylogeny and radiocarbon date ranges of newly reported and relevant published Y. pestis genomes. (A) Archeological sites where Y. pestis genomes have been recovered dating to the LNBA period. A list of the site names and abbreviations can be found in SI Appendix, Table S1. (B) ML tree computed from all variable positions (SNPs) in Y. pestis (n = 7,506); the uncollapsed tree can be seen in SI Appendix, Fig. S1. Unique positions to the outgroup (Y. pseudotuberculosis) were excluded from the SNP alignment to improve visibility. The scale represents the expected number of substitutions per site. Numbers on the tree indicate the deletions detected in the genomes displayed in SI Appendix, Fig. S5. Colored are ancient branches that appear to be extinct today: blue indicates the preLNBA− lineages, purple the LNBA− lineage, green the LNBA+ flea-adapted genomes from the Bronze Age, and red the genomes from the first plague pandemic. Nodes marked with asterisks have a bootstrap support of at least 90. The plotted date interval on the right corresponds to radiocarbon 2σ date ranges (C14; dark orange) or 95% HPD dates intervals (light orange) inferred by BEAST of the genomes from the LNBA period aligned to the corresponding tips in the ML tree. Symbols and colors correspond to those in A. Plots were produced with ggplot (39), ggmap (40), ggalt (41), and ggpubr (42) packages with R v3.6 (43); the phylogenetic tree was plotted with FigTree v1.4.4 (https://github.com/rambaut/figtree/releases/tag/v1.4.4) and Inkscape (44) was used for the final figure.