Tree of eukaryotes based on Eukaryotic Dataset. Trees were inferred with PhyloBayes and rooted following a previous suggestion [69, 70]. The values at branches indicate bootstrap support (BS) values (upper value, BI/CAT model; lower value ML/WAG model). Values below 60% are indicated by a hyphen; when BS values are equal only one is indicated. The posterior probability values using PhyloBayes are 1.0 for all except two branches (0.98 for the branch uniting Viridiplantae and Haptophyceae; 0.90 for the clade indicted by *). The analyses using ML (RAxML, WAG+Gamma; four categories, see additional file 1) support the alternative grouping of Malawimonadozoa and JEH with a BS of 77%. Other minor differences include Plantae relationships and the placement of Haptophyceae, which receive no solid support in both BI and ML analyses.