Phylogenetic placement of the urancestor in trees of proteomes reconstructed from molecular functions. A. Box plot describing the distribution of the numbers of functional sub-categories (maximum is 49) that are associated with FSF repertoires in urancestral min_set and max_set and the 420 FL proteomes analyzed. The box was delimited by lower, median, and upper quartiles. Whiskers encompass 5% to 95% values, and crosses 1% and 99% percentiles. Lines on the top and bottom of the plot indicate maximum and minimum numbers. Organisms associated with these values are labeled. The mean is indicated with a rectangle. B. Trees of proteomes and urancestors generated directly from the number of individual functional subcategories. A single most parsimonious tree of proteomes that included the urancestral min_set (46 parsimoniously informative sites; 5,269 steps; CI = 0.121; RI = 0.815; g1 = -0.069) or the max_set (46 parsimoniously informative sites; 5,270 steps; CI = 0.121; RI = 0.814; g1 = -0.133) as artificial taxa was recovered from a maximum parsimony analysis of diversity of molecular functions in proteomes. The matrix contained 421 taxa (i.e. 420 FL proteomes and the urancestral set) and 49 functional sub-categories as characters, with character states describing numbers of functional sub-categories. These trees were identical to each other. Cladograms and subtrees containing the urancestor and a set of 10 taxa that were the most basal in the trees show that urancestral sets are more ancient than any of the 420 FL proteomes that were analyzed. Phylogenetic relationships with BS > 50% are displayed above branches.
Kim and Caetano-Anollés BMC Evolutionary Biology 2011 11:140 doi:10.1186/1471-2148-11-140