All type A strains emerged from node 4, whereas all type B strains emerged from node 50. The type A strains were divided into two primary sub-nodes, node 39 and node 5, corresponding to clades A2 and A1 respectively. A1 strains further subdivided into node 8, node 23, and node 5, corresponding to clades A1a and A1b and the MA00-2987 strain, respectively (Table 1). SCHU S4, the laboratory type A strain, JPH203 fell within the A1a clade (node 8). Type B strains also divided into two clades based on nodes 52 and 64; these clades are referred to here as B1 and B2, respectively. The Japanese holarctica
isolate FRAN024 formed its own phylogenetic group. Subsections of the phylogenetic tree at higher resolution, representing the type A1 (excluding MA00-2987), A2 and B strains (excluding FRAN024) are shown in Figure 3. Figure 2 Whole genome SNP based phylogenetic analysis of Francisella strains. Phylogenetic analysis of resequenced Francisella strains. The whole-genome resequencing data was pared down to those base positions at which a SNP call occurred in one or more of the forty strains.
These sequences were used to generate a phylogenetic BIRB 796 tree using the MrBayes program as described in methods. This tree was then displayed as a cladogram (A) and as a phylogram (B) using the TreeView program http://taxonomy.zoology.gla.ac.uk/rod/treeview.html. Distinct clustering of type A and type B strains was observed. Both type A and B strains were further discriminated within the clusters. In the cladogram, the percentage values on the branches are the probabilities of the partitions indicated
by each branch. The numbers shown in red are node numbers of significant nodes that are referenced in the manuscript. In the phylogram, the branch lengths are proportional to the mean of the posterior probability density, and a scale bar is given to relate unless the branch lengths to their selleck inhibitor numeric values. Figure 3 Expanded phylogram for F. tularensis A1, A2 and type B strains. Expanded sections of the phylogram (Figure 2B) containing the F. tularensis A1 strains except MA00 2987 (A), A2 strains (B) and type B strains except FRAN024 (C). The three subtrees are shown at different scales. The scale bars below each subtree are given to relate the branch lengths to their numeric probability values. Within type A nodes, strains originating from distinct geographic locations (WY96 3418, CA02 0099, UT02 1927, KS00 1817, MA00 2987, AR01 1117, OK00 2732) with no known link to one another were clearly resolved by whole genome SNP based phylogenetic clustering (Figure 3, Table 1). This method also showed high potential for differentiating between closely related F. tularensis strains. The A1a strains, SCHU S4, FRAN023, FRAN031, FRAN032, FRAN026, FRAN030, and FRAN033 all originate from the same temporal location (Ohio) in the 1940′s (Figure 3, Table 1).