Trees of life generated from the structure of RNA and protein molecules congruently show a rooting in Archaea. (a) A rooted phylogenetic tree of 5S rRNA reconstructed from both the sequence and the structure of the molecules (from [105]). (b) Global most-parsimonious scenario of organismal diversification based on tRNA (from [107]). A total of 571 tRNA molecules with sequence, base modification, and structural information were used to build a ToL, which failed to show monophyletic groupings. Ancestries of lineages were then inferred by constraining sets of tRNAs into monophyletic groups representing competing (shown in boxes) or noncompeting phylogenetic hypotheses and measuring tree suboptimality and lineage coalescence (illustrated with color hues in circles). (c) A ToL reconstructed from the genomic abundance counts of 1,510 FSFs as phylogenetic characters in the proteomes of 150 free-living organisms sampled equally and randomly from the three domains of life (data taken from [122, 123]). Taxa were labeled with circles colored according to superkingdom. CI = consistency index, RI = retention index, and = gamma distribution parameter.
