Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting
The major tree is obtained by suppressing all minor hybrid edges (γ < 0.5) to capture the major vertical inheritance pattern. Accuracy is measured as half the Robinson-Foulds distance between the true and estimated tree, i.e. the number of incorrect edges in the estimated tree. A lot fewer genes are needed to accurately estimate the major vertical pattern, compared to the horizontal pattern.