A timeline of domain appearance in the protein world. (A) Phylogenomic tree of FF domain structures (tree length = 177,864; CI = 0.030; RI = 0.749; g
= -0.070) reconstructed from a genomic census of 2,397 FFs in 420 proteomes of free-living organisms (all 420 characters were parsimoniously informative). Terminal leaves are not labeled because they would not be legible. The Venn diagram shows diversity of FFs in the three superkingdoms. (B) Five phases in the evolutionary timeline of appearance of FFs in all three superkingdoms (top), and in Archaea, Bacteria, and Eukarya. Individual plots show the relationships of f (distribution index) and nd values (age of FFs). (C) The seven horizontal bars indicate nd ranges for taxonomic groups of FFs that are unique to individual superkingdoms (A, B, E) or shared by two (AB, BE, AE) or all (ABE) superkingdoms. The total number of FFs emerging in each phase is indicated in parentheses. The numbers labeled above bars indicate diversity of FFs belonging to taxonomic groups in each phase. (D) Cumulative frequency distribution of FFs along the timeline of domain structures.