Phylogenetic tree of the rhomboid family. The sequences and their regions used to construct the tree are exactly those shown in Figure 1. The color coding and abbreviations are as in Figure 1. The two major eukaryotic subfamilies are denoted as RHO and PARL (see text) and four clusters containing unexpected (from a phylogenetic viewpoint) sets of species are denoted 1-4. The clades that were investigated in the KH test are denoted A through D. Although the tree is shown in a pseudorooted form for convenience, this is an unrooted tree. Internal nodes with at least 70% RELL bootstrap supported are denoted by black circles and nodes with a 50-70% support by blue circles. The posterior probabilities reported by the MRBAYES program are indicated for some key internal branches. Domain architectures are connected to the respective proteins by brackets or lines. The domain key is shown at the bottom of the figure.