Fig. 2: Phylogeny of ancient and modern Y. pestis genomes.

Maximum likelihood phylogenetic tree based on the SNP alignment (10,743 positions) of 226 modern genomes, 62 published ancient genomes, the novel genomes Warburg_1 and Warburg_2 (red) and the outgroup Y. pseudotuberculosis. LN strains are highlighted in green and LNBA strains in yellow. Dating of the ancient strains is given as calibrated years before the present (cal BP). Country abbreviation is given in brackets (CH = Switzerland, CG = Congo, CN = China, CZ = Czech Republic, DE = Germany, EE = Estonia, ES = Spain, FR = France, FSU = Former Soviet Union, HR = Croatia, IN = India, IR = Iran, KG = Kyrgyzstan, KZ = Kazakhstan, LT = Lithuania, LV = Latvia, MG = Madagascar, MM = Myanmar, MN = Mongolia, NP = Nepal, PL = Poland, RU = Russia, SE = Sweden, UA = Ukraine, UG = Uganda, UK = United Kingdom, US = United States). Unique positions to the outgroup were excluded to facilitate the visualisation. Bootstrap values were calculated for 1000 replicates and nodes with a support above 90 are marked with an asterisk. The scale corresponds to substitutions per site. Genomes included in the phylogeny are listed in Supplementary Data 5.