Figure 3. Phylogenetic tree for Yersinia pestis.
(A) Maximum likelihood phylogeny of Y. pestis genomic SNPs showing the position of the Observance (OBS) lineage (red) relative to those of 130 modern (black) and three ancient strains (Black Death in green and Justinian Plague in blue). Modern strains from the third pandemic are shown in purple to highlight their close genetic relatedness. Monophyletic groups of sequences have been collapsed to improve clarity and are shown as triangles. The tree is rooted using single strain of Y. pseudotuberculosis (IP32953), with all derived SNPs removed to assist scaling, with branch lengths reflecting the number of nucleotide substitutions/SNP site. The length of the branch leading to the 0.PE3_Angola (AFR) lineage was reduced because its excessive length adversely affected the scaling of the tree. Location abbreviations are as follows: CNH (China), GEO (Georgia), FSU (Former Soviet Union), MNG (Mongolia), NPL (Nepal), IRN (Iran), AFR (Africa), USA (United States of America), MDG (Madagascar), IND (India). (B) Expanded phylogeny schematic to show the relative positions of the Black Death and the Observance lineages. Numbers on branches correspond to SNPs.