Figure 2.

Phylogeny for various mutation rates. Phylogenies are constructed from 2000 genotypes selected from a simulation for various values of the mutation rate (μ). They were constructed through maximum likelihood method by using PHYML [43]. Due to great divergence among sequences and the procedure in genotype selection, the phylogeny depicts only the patterns in the population of sequences, but not necessarily the evolutionary relationship among them (see Methods for details). The leaves of the phylogenies were colored according to the sequence composition of a genotype's dangling-end. For catalytic genotypes, the 5'-dangling-end of the catalytic strand (which is to recognize templates) is chosen. If the dangling-end has more C's, the color becomes more cyan, whereas, if it contains more A's, then the color becomes more magenta. For non-catalytic genotypes, the 3'-dangling-end (which is to be recognized by catalysts) with the most extreme sequence composition among a pair of complementary sequences is chosen. If the dangling-end has more G's, the color becomes more red, whereas, if more U's, then more green. In this coloring scheme, the C-catalyst tends to appear cyan; the A-catalyst, magenta; the G-parasite, red; the U-parasite, green. However, it should be noted that the red leaves appearing in the clades of the C-catalyst are not the G-parasite (e.g., see (a)). Instead, these represent the mutants of the C-catalyst that have lost the catalytic structure, and they are members of the C-catalyst quasi-species (see also "Evolution of the ecological organization" in main text). This is also the case for the green leaves in the clades of the A-catalyst. Finally, for more precise color coding, insets indicate the colors as a function of nucleotide frequencies, where it reads 0.1 on scales (the frequency more than 0.5 are joined). The left (resp. right) inset is for catalytic (resp. non-catalytic) genotypes.