Supplementary Information for Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750) Marcel Keller, Maria A. Spyrou, Christiana L. Scheib, Andreas Kröpelin, Brigitte Haas- Gebhard, Bernd Päffgen, Jochen Haberstroh, Albert Ribera i Lacomba, Claude Raynaud, Craig Cessford, Peter Stadler, Kathrin Nägele, Gunnar U. Neumann, Jessica S. Bates, Bernd Trautmann, Sarah Inskip, Joris Peters, John E. Robb, Toomas Kivisild, Michael McCormick, Kirsten I. Bos, Michaela Harbeck, Alexander Herbig, Johannes Krause Corresponding authors: Marcel Keller,
[email protected] Michaela Harbeck,
[email protected] Alexander Herbig,
[email protected] Johannes Krause,
[email protected] This PDF file includes: Supplementary Information text SNP Evaluation of the Aschheim Genome and SNP Effect analysis Phylogeographical Analysis Archaeological Context Information Sources for mapping plague outbreaks between 541 and 650 CE Figs. S1 to S6 Tables S1 to S9 References for SI reference citations 1 1 Supplementary Information Text 2 3 SNP Evaluation of the Aschheim Genome and SNP Effect Analysis 4 5 The Aschheim genome was evaluated separately, given its peculiarly high number of false 6 positive SNPs described previously (1). Our systematic evaluation verified previous 7 classifications: all SNPs potentially unique to Aschheim that passed the criteria show a 8 coverage lower than 5-fold, which was the threshold of their SNP calling. However, the high 9 number of presumably shared SNPs that did not pass our stricter criteria underlines again the 10 high ‘heterozygosity’ of the genome (see Table S8) that might be explained not only by 11 contamination by soil bacteria or sequencing errors but presumably also by PCR and capture 12 artefacts, as previously discussed (1).