Synthetic Performance. (a-c) Effect of model parameters on reconstruction accuracy under three different models. “Prob” in (c) is Pinnovation. (d) Effect of evolutionary distance (number of network modification operations) on the quality of the ancestral network reconstruction. In both plots, boxes show 1st and 3rd quartile over 100 networks with median indicated by a line. Pentagons show the median if interactions incident to nodes lost in both lineages are not considered.