Phylogenetic Analysis of 2009 Plague Isolates.

<p>The phylogenies of the 2009 isolates were inferred from MLVA data (Panels A and B) or the SNP/Indel data (panels C and D). In all cases, the Pestoides F strain was utilized as an outgroup. <b>Panels A and B</b>: Reconstruction of relationships from MLVA data. (<b>A</b>) Neighbor Joining Analysis of MLVA data. Numbers above branches represent NJ analysis bootstrap proportions, greater than 50%, based on 1000 replications; numbers below branches represent MP analysis bootstrap support. (<b>B</b>) Maximum Parsimony analysis. Numbers above branches represent bootstrap proportions, greater than 50%, based on 1000 replications; numbers below branches represent Majority Rule consensus values. <b>Panels C and D</b>: Phylogenetic analysis using newly identified SNPs/Indels using the (<b>C</b>) Maximum Likelihood method. The tree with the highest log likelihood (−411.0996) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. (<b>D</b>) Phylogenetic analysis using the Maximum Parsimony method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Additional details for the methods employed in phylogenetic reconstructions can be found in Materials and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031604#s2" target="_blank">Methods</a>.