Figure 3

Hierarchical clustering of phylogenetic profiles of nucleolar proteins. Phylogenetic profiles of all 501 nucleolar or ribosome-associated proteins. Organisms vary along the horizontal axis, proteins along the vertical axis. Presence of a gene is indicated by dark blue, absence by light blue. Organisms from the three domains of life are separated by black bars. The dendrogram resulting from protein-wise hierarchical clustering is given on the left. Several evolutionarily meaningful clusters emerged, which are colored in the dendrogram: red, proteins of archaeal origin; yellow, ubiquitous proteins; green, proteins of (eu-)bacterial origin. Note that the eukaryote-only genes constitute the largest group, followed by the archaea/eukaryote group. There is a considerable number of genes with orthologs only in bacteria and eukaryota, but not in archaea.