Additional file 1.

Figure S1. Inclusion of non-FL proteomes in phylogenomic analyses makes relationships of lineages incorrect. Cladogram of a most parsimonious rooted tree obtained from 1,446 FSFs and 645 proteomes (1,414 parsimoniously informative sites; 177,229 steps; CI = 0.057; RI = 0.780; g1 = -0.065). Terminal leaves of Archaea (A), Bacteria (B), and Eukarya (E) were labeled in red, blue, and cyan, respectively. The dotted lines explicitly display the borders between two superkingdoms. The life-styles of proteomes were displayed using a vertical bar beside their terminal leaves. Free-living (FL), parasitic (O), and obligate parasitic (OP) proteomes were labeled in blue, gray, and red, respectively. The 645 proteomes consist of 420 FL (48 A, 239 B, 133 E), 93 parasitic (0 A, 71 B, 22 E), and 132 obligate parasitic (1 A, 111 B, 20 E) organisms. OP lineages were present at the base of the three superkingdoms. Figure S2. Representative phylogenomic tree of proteomes describing the evolution of 102 FL organisms sampled equally across superkingdoms (34 archaeal, bacterial, and eukaryal proteomes, respectively). One most parsimonious tree was reconstructed based on genomic abundances of 1,370 FSFs in the proteomes (1,311 parsimoniously informative sites; 50,564 steps; CI = 0.194; RI = 0.724; g1 = -0.486). 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. Figure S3. The iterative analysis increases the reliability of FSFs that are positioned in the root nodes of the proteome trees. For the chain that produced the minimum number of LUCA FSFs and the smallest tree length, the ambiguity of character-state changes for the FSFs in the root nodes of the proteome trees was examined. In the plot, the x-axis indicates the number of iterations from 1 to 50, with zero representing the initial proteome tree. The y-axis denotes the number of the FSFs that had ambiguous character-state changes in their root branches of the proteome trees. The dramatic decreases of ambiguous character-state changes in root branches were consistently observed in all of the 30 chains that were examined. Table S1. FSF repertoires in the 352_set and urancestral max_set and min_set. Table S2. FSF molecular functions. Table S3. Functional enrichment.

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Kim and Caetano-Anoll├ęs BMC Evolutionary Biology 2011 11:140   doi:10.1186/1471-2148-11-140