Phylogenomic trees of proteomes and domain structures. A. Phylogenomic tree of proteomes describing the evolution of 420 FL organisms. One most parsimonious tree was recovered from an analysis of the abundances of 1,420 FSFs in the proteomes of the FL organisms (1,388 parsimoniously informative sites; 130,844 steps; CI = 0.075; RI = 0.774; g1 = -0.199). Taxa are proteomes and characters are FSFs. Non-parametric bootstrap values that have more than 50% supports were shown above or below branches that cluster the superkingdoms or much higher groups. Terminal leaves of Archaea, Bacteria, and Eukarya were labeled in red, blue, and cyan, respectively. B. A phylogenomic tree of protein domain structure describing the evolution of 1,420 FSFs. One most parsimonious tree was recovered from analysis of genomic abundances of FSFs in 420 FL proteomes (420 parsimoniously informative sites; 201,838 steps; CI = 0.046; RI = 0.806; g1 = -0.0187). Taxa are FSFs and characters are proteomes. Terminal leaves were not labeled, since they would not be legible. INSET: A timeline was unfolded from the tree of FSFs using a PERL script that calculates the relative age (node distance; nd) of individual FSFs by counting the number of internal nodes along a lineage from the root to a terminal node on a relative 0-1 scale. The bar diagram shows ranges of age (nd) for FSFs that are unique to superkingdoms (A, B, or E) or are shared by two (AB, AE, or BE) or all (ABE) superkingdoms. The basal_set represents the set of FSFs that appeared before the first appearance of an FSF not shared by all superkingdoms, a BE FSF.