First Advisor

Niles Lehman

Date of Publication


Document Type


Degree Name

Doctor of Philosophy (Ph.D.) in Biology






RNA -- Evolution, Molecular evolution, Mutation (Biology)



Physical Description

1 online resource (vii, 145 p.) : ill. (some col.)


The emergence of life depended on the ability of the first biopolymer populations to thrive and approach larger population sizes and longer sequences. The evolution of these populations likely occurred under circumstances under which Muller's Ratchet in synergism with random drift could have caused large genetic deterioration of the biopolymers. This deterioration can drive the populations to extinction unless there is a mechanism to counteract it. The effect of the mutation rate and the effective population size on the time to extinction was tested on clonal populations of B16-19 ligase ribozymes, evolved with the continuous evolution in vitro system. Populations of 100, 300, 600 and/or 3000 molecules were evolved with and without the addition of Mn(II). The times to extinction for populations evolved without Mn(II) 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 closely genetically-related, forming a "quasispecies" structure.. 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 individual to group. The total fitness of the molecules was measured by identifying the fitness component of the system that effect the ligase replication cycles: ligation, reverse transcription and transcription. It was found that the strength of the three components of fitness varied and that each one has a differential effect in the total absolute fitness of the ligases.


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Portland State University. Dept. of Biology

Persistent Identifier