Bayesian unrooted phylogeny of eukaryotes, with a basal trichotomy representing uncertainties in the relationships between the three groups. The tree was obtained from the consensus between two independent Markov chains, run under the CAT model implemented in Phylobayes. The species colour code corresponds to the type of plastid pigments, as follows: purple, chlorophyll a; green, chlorophyll a+b; and red, chlorophyll a+c. The asterisks represent primary, secondary or tertiary endosymbiosis. Underlined numbers at nodes represent PP of the analysis performed with the constant sites removed/analysis performed with all sites; other numbers represent the result of the ML bootstrap analysis (BS)—Node 1 below the line: ML analysis of the full-length alignment//ML analysis with category 7 removed/ML analysis with catergories 6+7 removed. Black dots correspond to 1.0 PP and 100% BS; black squares correspond to 1.0 PP and the specified values of BS. The scale bar represents the estimated number of amino acid substitutions per site.