Figure 1.
A global phylogenetic tree of tRNA molecules reconstructed from sequence and structure.
MP analyses of data from 571 tRNA molecules resulted in the preset limit of 20,000 minimal length trees, each of 10,083 steps. Consistency index (CI) = 0.069 and 0.069, with and without uninformative characters, respectively; Retention index (RI) = 0.681; Rescaled consistency index (RC) = 0.047; g1 = −0.107. Terminal leaves are not labeled since they would not be legible. Nodes labeled with closed circles have BS values >50%. tRNA molecules belonging to different superkingdoms and viruses and coding for Sec, Ser, Tyr, and Leu are labeled with colors. Note several of these tRNAs have short variable arms and are derived in the tree.
Figure 2.
Timeline of organismal diversification.
Constraints representing non-competing hypotheses of organismal relationship (white circles) are used to define a timeline for the appearance of lineages in a universal tree derived from the sequence and structure of tRNA. Blue circles represent constraints representing competing hypotheses. They illustrate both the most parsimonious lineage relationship and their coalescence. Areas colored in light green, salmon, and light yellow are delimited by lineage coalescence and describe three evolutionary epochs. The timeline is given in a scale of additional steps (S) needed to fulfill constraints. S values were not normalized.
Table 1.
Origins of the tripartite world
Table 2.
Origins of the viral world
Table 3.
The numbers of additional steps (S) required to force molecules into monophyly based on tRNA category, amino acid specificity, and organismal constraints using MP analyses of combined tRNA structure and sequence data
Table 4.
Rates of evolution in the three superkingdoms and viruses derived from strict consensus trees