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Phylogenetic diversity of Y. pestis strains from CIS plague foci, revealed by core genome SNP analysis. Red triangles mark phylogenetic branches, the strains of which circulate in the plague foci of the CIS countries. Small blue triangles mark strains, sequenced by us. Maximum likelihood tree of 207 Y. pestis genomes, based on 1708 SNPs, is constructed using PHYML 3.1 with the HKY85 model and 500 bootstrap replications.
