Figure 6.

Fitch and Dollo parsimony. Difference between reconstruction of the gain/loss-labeling for a tree using Fitch parsimony versus Dollo parsimony. The black circles are (ancestral) species that display a certain feature (have a certain TFBS), the white circles are (ancestral) species that do not show the feature. Red circles or lines symbolize a parsimony-based reconstructed loss event and blue circles are a gain event respectively. Fitch parsimony [30] minimizes the total number of changes that must be assumed to explain the tree labeling. In the example Fitch parsimony assumes only 3 changes but includes one re-gain event. Because we consider re-gain of a TFBS that was lost at exactly the same position rather unlikely we also offer Dollo parsimony [31,32], that prohibits re-gain. This results in fewer events at the inner nodes.