Gain and loss of domains and domain promiscuity during the evolution of eukaryotes. The number of domains gained and lost in each branch, inferred using Dollo parsimony, is shown on the bar plot to the left of the branch, and the number of gained and lost promiscuous domains, inferred using DNAPARS, is shown on the bar plot to the right of the branch. (Green bars) gain; (red bars) loss. The bars are normalized to the highest gain (green bars) or highest loss (red bars) of all the nodes. Additionally, each edge is colored to indicate (green) the greater number of gained promiscuous domains, (red) the greater number of lost promiscuous domains, and (black) equal contributions of gain and loss of promiscuity. The root node represents the Last Eukaryotic Common Ancestor (LECA). As gain and loss cannot be inferred for LECA, the presence of domains and the number of domains ascertained to be promiscuous are given by numbers. The major branches of eukaryotes are labeled. The tree has the “crown group” topology (Hedges 2002). For additional information, see Supplemental Figure S2. The species abbreviations are as described in Methods.
