Fig 1. SNP and MLVA phylogenies depicting 18 major phylogenetic subgroups identified among 773 Malagasy Yersinia pestis samples.

(A) SNP phylogeny based on 212 informative SNPs identifying 100 individual nodes (circles and stars) among 770 Malagasy Y. pestis samples (only the lineage could be identified for the remaining 3 samples, and not the specific node). Stars indicate terminal nodes defined by a sequenced strain. Circles indicate intermediary nodes (i.e., collapsed branch points) along the lineages containing groups of samples. Branch points that did not contain any samples are labeled in black italics. A dashed arrow indicates a branch leading to a single, previously identified, terminal node not represented among the samples in this analysis. Lineages (lower case letters) and nodes within lineages (numbers within circles and stars) were named as in [17–19], with new letters and numbers assigned to newly identified lineages and nodes, respectively. Basal nodes d and k are represented by pie charts, indicating the presence of multiple MLVA identified subgroups within these nodes. Color shading indicates the 18 identified phylogenetic subgroups and, to the extent possible, corresponds to the subgroup colors used in reference [19]. Solid pale green and striped pale green, respectively, indicate the new SNP lineage (w) and remaining subset of samples within basal node d that were split in this analysis from a single previously identified subgroup. The number of SNPs on branches with >1 SNP are indicated in red. The single SNP differentiating between Groups I and II is indicated by a perpendicular red line on the branch between nodes d and k. (B) MLVA phylogenies of 10 and 38 Malagasy Y. pestis samples from basal SNP nodes d and k, respectively. The MLVA phylogenies consist of neighbor-joining dendrograms constructed in MEGA6 [35] using mean character based distance matrices. Bootstrap values ≥50 (generated in PAUP 4.0b10 (D. Swofford, Sinauer Associates, Inc., Sunderland, MA) based upon 1,000 simulations) supporting MLVA phylogeny branches are indicated. One and four additional phylogenetic subgroups consistent with previous analyses [19] were identified within the MLVA phylogenies of nodes d and k, respectively. In addition, 1 and 3 samples within nodes d and k, respectively, did not fall into any identified phylogenetic subgroup and were labeled with a “+” or an “*”, and classified as II.NONE and I.NONE, respectively.