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. 2010 Oct 7;6(10):e1001134. doi: 10.1371/journal.ppat.1001134

Figure 3. Analysis of aDNA from human remains with 18 markers (glpD, napA and 16 SNPs [11]) that define the three main branches of the Y. pestis evolutionary tree.

Figure 3

The upper part shows the Y. pestis codons that were either similar to the Y. pseudotuberculosis ancestor strain (in blue) or exhibited a SNP (in green). These codons were used here to describe the various branches and sub-branches of the Y. pestis microevolutionary tree, as defined in [11]. The lower part of the figure shows the codons obtained at each specific position in the aDNA from individuals originating from three different archeological sites (Bergen op Zoom [Ber], Hereford [Her], and Saint-Laurent-de-la-Cabrerisse [SLC]). Samples which failed to give an amplification product are indicated in grey. Yellow indicates sequencing results that did not unambiguously resolve a SNP. n.t.: not tested. *: Probably CGT, which could give rise to TGT by deamination.