Figure 3

Reanalysis of the 1070-gene yeast data set of [35]. Top: the species tree inferred by maximum pseudo-likelihood when no reticulations are allowed during the search. It is identical to the tree reported in [35]. The two black numbers for every internal node are gene-support frequency (left) and internode certainty (right) reported in [35]. Bottom: the species network inferred by maximum pseudo-likelihood with 2 reticulations. The red solid edge is the reticulation edge in the optimal species network with 1 reticulation. Blue and red numbers are branch lengths and inheritance probabilities, respectively, inferred by the method.