Figure 1

Alternative views of the eukaryotic phylogeny and the design of phylogentic analysis. (a) The 'crown-stem' topology of eukaryotic phylogeny. The topology shown is adopted from Sogin [18] and Sogin and Silberman [20]. (b) The 'six supergroups' classification of eukaryotes; the topology shown was reported by Hampl et al. [24]. Different hypotheses about the root position of the eukaryotic tree are indicated by numbered arrows: 1, the unikont-bikont hypothesis [26, 27]; 2, the photosynthetic-nonphotosynthetic scenario [29]; 3, Excavata as basal group [28]. The branch lengths are arbitrary. (c) Hypothetical phylogenetic tree showing the definition of orthogroups in analyses I and III (see Results). Four possible orthogroup topologies are highlighted by colors: 1 (green), eukaryotic genes with prokaryotic outgroup and early eukaryotic duplication; 2 (red), eukaryotic genes with prokaryotic outgroup but no early eukaryotic duplication; 3 (blue), eukaryotic genes without prokaryotic outgroup but show early eukaryotic duplication; 4 (black), eukaryotic genes without prokaryotic outgroup nor early eukaryotic duplication. (d) Hypothetical phylogenetic tree showing an example of a eukaryote-specific gene cluster with duplication. The stars indicate gene duplications.