Figure 3.

Sequence logos and typical secondary structures for each sequence classes. Genotypes were categorized into sequence classes through the phylogenies shown in Fig. 2 (see Methods for mode details). Sequence logos were produced by using WebLogo [45]. The typical secondary structures were produced as follows. For a set of aligned structures represented by dot-bracket notation, the frequencies of bound and unbound bases (i.e., '(', ')' and '.') are counted for each structure position. For each position, if the frequency of '(' or of ')' exceeds 20%, then the corresponding bracket is drawn; otherwise, '.' is drawn. The color of the brackets represents its frequency: the more frequent, the more red. Physical complexity C [40] was calculated from the sequence logos (see Discussion for details). For μ = 0.004, C_C = 41.3 for the C-catalyst; C_G = 22.5 for the G-parasite; C_A = 26.5 for the A-catalyst; C_U = 13.0 for the U-parasite; and C_∀ = 13.4 if all sequence classes are grouped together. For μ = 0.008, C_C = 41.5; C_G = 19.9; C_A = 20.9; and C_∀ = 15.7. For μ = 0.013, C_C = 37.9; C_G = 21.0; and C_∀ = 27.5. For μ = 0.015, C_C = 38.2 (C_C = C_∀ by definition).