Templated assembly of the remaining strains were mapped to the 1942 finished sequence using the GSMapper tool in Newbler (Roche). High-confidence mutations were selected from Newbler ''HCDiffs'' calls (Table S1 ) by applying additional selection criteria that mandated high quality scores in both reference and templated assemblies with .80% of the sequencing reads differing from the reference, elimination of mutation calls associated with homopolymer tracts (with the exception of tracts that were formed by a deletion -see below), and a minimum coverage depth of 56 with bidirectional sequence reads. Finally, the raw 454 reads from the 1942 isolate were mapped to the finished sequence to assess error bias in the 454 process and to correct for residual sequencing errors in the finished sequence. Accession numbers of the relevant wholegenome shotgun sequences are found in Table 3 . Phylogeny was calculated using PAUP 4.0b10. Fifty-eightnucleotide positions were used with gaps being treated as a ''5th base'' and all characters assuming equal weight. One thousandbootstrap replicates were computed using a heuristic search with the optimal criterion set to ''parsimony''. The tree was created using stepwise addition.