Figure 5

Evolutionary history for the 6th fragment in the coalescent simulation. Evolutionary tree for the sixth fragment in the coalescent simulation. The leaf node labels are as in Figure 1. This tree was used as the left-side tree in the repetitive phylogenetic simulation experiments. The right-side trees corresponding to the different recombination types were obtained as follows: 1) (recent recombination with a distant relative) strain 27 was moved to the same branch with strain 19. 2) (recent recombination with a close relative) strain 27 was moved to the same branch with strain 7. 3) (old recombination) the branch containing all the cyan strains was moved to become a part of the branch containing the red strains. 4) (recombination involving a miniature cluster) strain 11 was moved to the same branch with strain 19. 5) (recombined fragment obtained from outside of the populations in data) strain 27 was moved to its own branch, which joins the rest of the tree close to the root.