Fig. 1.

Guide tree used to produce the simulated gene evolution datasets. Two long-branch assemblages (the outgroups and the Lineage C) are placed on both extremes of the tree. Fifty different cases of this general topology were considered, and they differed according to the taxa in Lineage C to which the long and short branches were assigned. These 50 cases represented all possible combinations of two to four fast-evolving taxa in the Lineage C, with all other branch lengths equal. For each of the 50 cases, 200 simulations were performed, and a total of 10,000 trees were produced. Branch length units are substitutions per site.