Fig. 6.

Comparison of REALPHY phylogenies to phylogenies inferred in previous publications. Both REALPHY trees (green) were built using PhyML, with the general time-reversible (GTR) model of nucleotide evolution and gamma distributed rate variation. The annotation on the branch points in black denotes the bootstrap support for the branch points from a total of 100 bootstrap experiments (only shown if <100) for REALPHY trees, Bayesian probabilities for the Baltrus tree (shown if <0.95) and bootstrap values out of 1,000 for the Touchon tree (shown if <1,000). Annotations in gray show the number of REALPHY single-reference trees that support the particular branch points (only shown if <21 for E. coli and <3 for P. syringae). Boxed parts of the trees contain differences to the previously published corresponding tree. (A) E. coli phylogeny reconstructed by Touchon et al. (2009) (left) compared with a phylogeny reconstructed from all 21 merged reference alignments produced by REALPHY. The differences between the two trees are the placements of E. coli 536 and S88. (B) P. syringae phylogeny reconstructed by Baltrus et al. (2011) (left) compared with a phylogeny based on mappings to the three fully sequenced P. syringae strains: P. syringae B728a, P. syringae pv. phaseolicola 1448a and P. syringae pv. tomato DC3000. Right: The root of the tree was arbitrarily selected to facilitate comparison between the two topologies. When inferring trees from single reference genome alignments, two branch points are not supported by all three trees (annotated on the corresponding branches). These branch points concern the placement of Cit7 (P. syringae B728a as reference) and Pae (P. syringae pv. phaseolicola 1448a as reference).