Y. pestis microevolution tree with the steps at which the specific regions are predicted to have been acquired or to have undergone various mutations. The 21 Y. pestis strains for which a complete genome sequence was available were positioned on the microevolutionary tree based on the presence or absence of a set of 16 SNPs (indicated inside white ovals) shown to characterize the various Y. pestis phylogenetic branches (1). To position strain Pestoides A, additional SNPs defining branch 0.PE4 were examined. Among them, some were present (sA [s95, s96, s97, s99, s102, s104, s105, s114, s116, and s120]), while others were absent (sB [s94, s98, s100, s101, s106, s107, s108, s109, s110, s111, s112, s113, s115, s117, s118, and s119]). The hatched rectangle corresponds to the position in the tree where the Y. pestis-specific regions are predicted to have been acquired. The various mutations in specific regions that characterize phylogenetic branches are indicated by an arrow and a gray rectangle in which the type of mutation (SNP or partial deletion [ΔP]) and the locus involved are indicated. A more detailed description of these mutations is presented in Table S6 in the supplemental material.