Additional file 3.

Supplemental Figure S2. Cladograms used to determine root placement of B. pseudomallei/mallei clade. Trees on left were drawn with the same 17,718 SNPs used to draw the tree in Additional file 2. Trees on right were drawn using a more inclusive set of 67,644 SNPs that were at least two nucleotides away from the nearest polymorphism. Top trees are Maximum Likelihood (ML) trees with likelihood settings from the best fit model selected by AIC in Modeltest 3.7 shown. ML trees were not bootstrapped due to the computational time required. All other trees are 50% majority-rule consensus trees with 1,000 bootstrap replicates. Middle row of trees are Maximum Parsimony trees with consistency indices labeled. The distance based Neighbor Joining algorithm was used to draw the bottom trees. Note that while most trees suggest that the first lineage to diverge from the B. pseudomallei/mallei clade is the Bp668 lineage, all trees suggest an Australian root to this clade. Bayesian analyses were not performed on these data as the number of SNPs exceeded the capacity of Mr. Bayes 3.

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Pearson et al. BMC Biology 2009 7:78   doi:10.1186/1741-7007-7-78