Figure 4

Example of incongruency detection in a subtree. The reference species tree is shown in (A), with the names of the taxonomic groups written on the nodes. For each internal node, the distance d to the root is written in red. The subtree containing the incongruency is shown in (B1), with S. aureus being the misplaced taxon. In this subtree, the taxonomic group associated to the grandfather of S. aureus is Bacteria and its distance to the root in the species tree is d=0. In (B2) the father node of S. aureus is removed. The root of this subtree has now two sons E. coli and S. dysenteriae. The new taxonomic affectation of this node becomes Enterobacteria, which corresponds to a distance to the root d=2, in the species tree. Therefore, perturbation induced by the misplacement of S. aureus is equal to 2−0=2.