Fig. 1: Phylogeography of Y. pestis in Madagascar.

a Maximum-likelihood phylogeny of Malagasy Y. pestis strains rooted on strain CO92 (isolated in the USA). The tip labels (first circle from the center) are colored according to the color of the subgroup of the strains identified in this study via whole-genome sequencing. The second, third and fourth circles from the center represent the different levels (first, second and third-order) of the hierarchical nomenclature of Y. pestis as established by Wu et al. ³⁹. Colors of the fifth circles represent the host from which the strain was isolated. Numbers on branches represent bootstrap values. b Map of the distribution of the different phylogenetic subgroups across the regions of Madagascar. The pie charts represent the number of Y. pestis strains isolated from a given region and the colors represent the different subgroups (source data is presented in Supplementary Data 5). The subgroup colors are the same as in Vogler et al. ⁷.