Figure 1

Overall evaluation of support for nodes in 105 and 92 taxon sets. Support for nodes using different taxon datasets, algorithms and evolutionary models. The top portion lists taxa with clear ultrastructural identities [1] whereas taxa below the line represent putative eukaryotic supergroups. As described in the text, two datasets were examined (105 and 92 taxa). R:n = RAxML analysis of 4 genes as nucleotides, with third codon positions removed; B:n = Bayesian analysis of 4 genes as nucleotides, with third codon positions removed; B:S-A = Bayesian analysis of the SSU-rDNA gene and the remaining three genes as amino acids; B:A = Bayesian analysis of three genes as amino acids; PhyML = Likelihood analysis under PHYML of three genes as amino acids. The 'Rhizaria' are indicated by grey boxes for the 92 taxon analysis as there were insufficient taxa to address this hypothesis; instead, we report support for the nested group 'Cercozoa.'