Fig. 2

Pairwise distances (with losses) for three phylogenetic trees for three gene families in the Tree of Life dataset. COG0466 has 87 leaves, COG0651 has 84 leaves, and COG0703 has 85 leaves. All are reconciled to a species tree with 100 leaves. Each of the three rows corresponds to one gene family and the three columns correspond to the DTL cost parameters (2,3,1), (1,2,1), and (1,1,1), respectively. The entry at index 0 of each vector is omitted. These examples demonstrate that the pairwise distance distributions are sensitive to event costs and may be multimodal, indicating the presence of two or more clusters in MPR space