Figure 2

Tree recovered by both ML and Bayesian inference (both using JTT + Γ + I) from an alignment of 30 RPB1 sequences containing little or no missing data. Support values above or to the right of nodes indicate, from top to bottom, Bayesian inference, ML bootstrap, NJ bootstrap. Values supporting the Glaucocystis/Acanthamoeba/Dictyostelium clade are highlighted in red. Red stars indicate that all three values were 100% and dashes that the value was below 50%. The CTD-clade is highlighted in light blue. To the right is comparative phylogeny showing where the RPB1 tree disagrees with generally accepted views of eukaryotic phylogeny, following the review of Baldauf [10]. Those discrepancies are highlighted in color: green shows the hypothesis of a monophyletic kingdom Plantae, comprising all eukaryotes with primary plastids, yellow the "Chromalveolate hypothesis," and blue the hypothesis of a monophyletic Amoebozoa. Branch lengths are from ML analysis. The specific tree with branch lengths recovered by Bayesian inference is included as a supplement (see additional file 2).