Fig. 2
Phylogenetic positioning of second pandemic strains. A maximum likelihood phylogeny was generated allowing for up to 3% missing data (97% partial deletion) and considering a total of 6,058 single nucleotide polymorphisms (SNPs). The image shows a graphical representation of Branches 1–4 (see Supplementary Fig. 12 for a complete phylogeny), to emphasise the phylogenetic positioning of the new and previously published second pandemic strains (labels of new 14th- to 17th-century strains appear in bold). Dashed branches denote uncertainty in the private SNP calls of the respective genomes. Sub-clades of published genomes are collapsed to enhance tree visibility. Numbers (n) in brackets indicate the number of strains represented in each collapsed branch. Node support was estimated using 1,000 bootstrap iterations. Nodes that have bootstrap values of ≥95 are indicated by asterisks (*). Scale denotes substitutions per site. Geographic abbreviations of modern strain isolation locations are as follows: China (CHN), United States of America (USA), Madagascar (MDG), India (IND), Myanmar (MNM), Congo (COG), Uganda (UGA), Mongolia (MNG), Nepal (NPL), Iran (IRN), Kazakhstan (KAZ), Kyrgyzstan (KGZ), Tajikistan (TJK), Armenia (ARM), Georgia (GEO), Azerbaijan (AZE), Uzbekistan (UZB), Turkmenistan (TKM), Russia (RUS) and unspecified regions of the Former Soviet Union (FSU)
