Defining urancestral FSFs by serial and iterative phylogenetic and character state reconstruction analysis. A. Venn diagrams with seven cells describing the distribution of FSFs in the three superkingdoms of life, Archaea (A), Bacteria (B), and Eukarya (E), in sets derived from iterative refinement. The Venn diagram in the top shows the taxonomic occurrence of the modern set of 1,420 FSFs in the 420 FL organisms analyzed in this study. The Venn diagram of the 352_set describes the distribution of 352 FSFs that are plesiomorphic and positioned at the root branch of the proteome tree of Figure 1A. The Venn diagram of the urancestral max_set describes the distribution of a minimal set of 152 FSFs that was recovered by serial and iterative phylogenetic and character state reconstruction analysis (see B). The set was defined by identifying a tree of proteomes with minimal length, extracting FSF that are plesiomorphic and basal, and updating the character set of FSFs for further phylogenetic analysis in 30 chains of 50 rounds of iterations each. The Venn diagram of the min_set describes the distribution of 70 FSFs identified by the intersection of the max_set and a basal_set of 130 FSFs that are present in the three superkingdoms and are placed at the base of the tree of domain structure described in Figure 1B. B. Change in the length of trees and number of FSFs recovered in individual iterations of chain number 26. For the ith iteration, the left y-axis indicates the number of distinct FSFs that appear in the root branch of the (i-1)th proteome tree and the right y-axis represents the lengths of the reconstructed tree. The numbers of FSFs converged into a single value after the 35th iteration. The arrow points to the iteration that generates the most parsimonious trees with the minimal tree length in the chain. C. Correlation between mean of G and f indexes for the different sets of FSFs.
Kim and Caetano-Anollés BMC Evolutionary Biology 2011 11:140 doi:10.1186/1471-2148-11-140