Hypothesis-specific constraint tree for the rhomboid family. (a) Hypothesis 1, polyphyletic origin of eukaryotic rhomboids from prokaryotic progenitors. The RHO and PARL subfamilies are denoted; the remaining clusters include prokaryotic rhomboids designated as in Figure 2 (with 'a' added to the GI number). Within each cluster, the branches were collapsed into a multifurcation. (b) Hypothesis 2, monophyletic origin of eukaryotic rhomboids. All eukaryotic and prokaryotic sequences were collapsed into the two respective clusters. The trees are unrooted, although shown in a pseudorooted form.