The numbers of group-specific domains and combinations. Summarized are the specific domains and combinations for respective groups of eukaryotes. We consider two additional phylogenetic groups: *Deuterostomes and **Opisthokonta. Some eukaryote genome sequences are still in draft and the number of proteins was smaller than estimated (such as C. familiaris). However, our method to define group specificity using the multifurcated phylogenetic tree can reduce effects of incompleteness of genome sequences. Additional information is provided in Additional data file 7 (Supplementary Table 2).