Figure 5

Dynamics of speciation. (a) Evolutionary dynamics of the G-parasite. The abscissa is time in simulation steps. There are three kinds of ordinate: (1) The ordinate labeled as distance (black) is the Hamming distance between the C-catalyst and non-catalytic molecules that have a stronger affinity to the C-catalyst than to the A-catalyst (for each of the chosen non-catalytic genotypes, the catalytic genotype that gives the strongest affinity to it is used to calculate the distance). The affinity is measured in the G score. The distinction between the C- and A-catalyst was done from the sequence composition of their 5-'dangling-end. Gray scale represents the frequency (occurrence) of phenotypes (the more frequent, the darker). The frequency was averaged over ca. 2000 time steps (100 bins). The plots are based on the top 1000 most abundant phenotypes chosen each from catalytic and non-catalytic replicators at every 500 time steps (this is also the case in (b); for the definition of phenotypes, see "Construction of phylogenies"). (2) The ordinate labeled as max(-G) (red) is the average of the theoretical maximal affinity of G-parasites (the sequences in the upper branch of the Hamming distance distribution are the G-parasites). (3) The ordinate labeled as best(-G) (blue) is the average of the maximal affinity G-parasites can gain from the C-catalyst. (b) Evolutionary dynamics of the A-catalyst. The abscissa is time. The ordinate is the frequency of C's minus that of A's in the 5'-dangling-end of catalytic molecules. Gray scale represents the number of occurrence of phenotypes. The frequency was averaged in the same way as in the Hamming distance in (a).