Evolutionary dynamics in molecular populations of ligase ribozymes

The emergence of life depended on the ability of the first biopolymer populations to thrive and approach larger population sizes and longer sequences that could store enough information, as required for a cellular type of life. The evolution of these populations very likely occurred under circumstances under which Muller's Ratchet in synergism with random drift could have caused large genetic deterioration of the biopolymers. The genetic deterioration of the molecules caused by the accumulation of mutations occurred during the copying process, can drive the populations to extinction unless there is a mechanism to counteract it. To test the effect of the mutation rate and the effective population size on the time to extinction, we used clonal populations of B16-19 ligase ribozymes, evolved with the continuous evolution in vitro system. The experiments were done using populations of 100, 300, 600 and/or 3000 molecules, and at low and high mutation rates. The error-prone Moloney Murine Leukemia virus reverse transcriptase was used with and without the addition of Mn(II). Populations evolved without Mn(II) were of four effective sizes. The times to extinction for those populations were found to be directly related to the effective size of the population. The small populations approached extinction at an average of 24.3 cycles; while the large populations did so at an average of 44.5 cycles. Genotypic characterization of the populations showed the presence of deleterious mutations in the small populations, which are the likely cause of their genetic deterioration and extinction via mutational meltdown. These deleterious mutations were not observed in the large populations; in contrast an advantageous mutant was present. Populations of 100 and 3000 molecules were evolved with Mn(II). None of the populations showed signs of genetic deterioration nor did they become extinct. Genotypic characterization of the 100-molecule population indicated the presence of a cloud of mutants forming a "quasispecies" structure. The high error rate used generated an extended class of closely genetically-related mutants, as indicated by their Hamming distance. The close connectedness of the mutants facilitates the recovery of one from another in the event of being removed from the population by random genetic drift. Thus, quasispecies shift the target of selection from the individual to the group and through cooperative behavior the populations stay extant. The fitness of the six most abundant molecules evolved was measured. The total fitness of the molecules was measured by identifying the fitness component of the system that affect the ligase replication cycles: the ligation, the reverse transcription and the transcription reactions. It was found that the strength of the three components of fitness varied in different chemical environments, and each has a differential effect in the total absolute fitness of the ligases. The ligase molecules evolved have different total absolute fitness values, and ranged above and below the fitness of B16-19.