Dendrograms for Group I (A) and Group II (B) are indicated. The SNP phylogeny from Figure 1 is also indicated (C) for comparison. Subclades within Groups I and II are collapsed in the full phylogenies (dotted boxes) for those groups (colored triangles) and are then individually expanded to show the structure within each subclade. The expanded subclades are labeled based upon their membership in Group I or II and by a capital letter (e.g., I.A) and are indicated by colored bars. Bootstrap values ≥50 supporting individual subclades are indicated on the expanded subclade phylogenies. SNP locations are indicated by vertical red lines. These red lines are labeled with the SNP ID numbers presented in Table S2 on the full phylogenies for unaffiliated isolate-specific SNPs and on the expanded phylogenies for all other SNPs. The years of isolation for isolates within each full and expanded phylogeny are indicated beside the panel label and underneath the individual phylogeny, respectively. The gray subcluster marked by the gray arrow in subclade I.A represents the “Mahajanga I.A subcluster,” a subcluster containing most of the isolates from the Mahajanga plague focus. Seven isolates from the central highlands that also fell within this subcluster are labeled with a “CH.” Five Mahajanga isolates that did not belong in this subcluster are labeled with a gray “M” (A). Black stars indicate the locations of the two sequenced Malagasy strains, MG05-1020 in subclade I.B and IP275 in subclade I.H.