Fig. 2
From: Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague
Y. pestis genomic characterisation and maximum likelihood phylogeny. a pMT1 coverage plots made with the Circos80 software. The plots were constructed to a maximum coverage of three-fold, and average coverage was calculated over 100-bp windows. The presented strains are in the following order starting from the outmost: CO92 pMT1 (reference) in grey, the oldest (RISE509) and youngest (RISE505) isolates from the LNBA lineage are shown in purple, RT5 and RT6 are shown in green, the Iron Age RISE397 isolate is shown in brown, a Justinianic isolate from Altenerding (Germany) is shown in blue and a London Black Death isolate is shown in red. The position of the ymt gene within the pMT1 plasmid is indicated on the plot. b A worldwide dataset of Y. pestis ancient and present-day chromosomal genomes (n = 179) was used to reconstruct the phylogenetic tree, considering 1054 SNP positions (see Supplementary Fig. 3 for a phylogeny using all sites). The main branches were collapsed to enhance the clarity of the phylogeny, and branch lengths are shown as number of substitutions per site. The newly sequenced RT5 strain (green) was included in the phylogeny alongside eight Bronze Age strains belonging to the LNBA lineage (purple), a single Justinianic strain (blue), and nine second pandemic strains (red). Asterisks denote bootstrap values >95 (1000 bootstrap iterations carried out). The two-sigma (95.4%) radiocarbon or archaeological dates of Bronze Age and historical strains are shown. Country or geographical region abbreviations are as follows: CHN (China), USA (United States of America), MDG (Madagascar), IND (India), IRN (Iran), MNM (Myanmar), RUS (Russia), GB (Great Britain), DE (Germany), FRA (France), MNG (Mongolia), NPL (Nepal), FSU (Former Soviet Union), CGO (Congo), UGA (Uganda), LTU (Lithuania), EST (Estonia) and CRO (Croatia). See also Supplementary Fig. 4 for the inferred phylogenetic positioning of RISE397. c Timeline spanning radiocarbon and archaeological dates, from which Y. pestis genomic data have been included in this study. Points on the timeline indicate median dates
