Assessing the Likelihood of Recurrence during RNA Evolution in Vitro
- 1 January 2004
- journal article
- Published by MIT Press in Artificial Life
- Vol. 10 (1), 1-22
- https://doi.org/10.1162/106454604322875887
Abstract
Recurrence is the possibility of resulting in the same endpoint multiple times when a living system is allowed to evolve repeatedly starting from a given initial point. This concept is of concern to both evolutionary theoreticians and molecular biologists who use nucleic acid selection techniques to mimic biotic and computorial processes in the test tube. Using the continuous in vitro evolution methodology, many replicate experimental evolutionary lineages with populations of catalytic RNA were performed to gain insight into the parameters that could affect recurrence. The likelihood that the same genotype will result in parallel trials of an evolution experiment in vitro depends on several factors, including the phenotype under selection, the size and composition of the initial diverse pool of nucleic acids used in the experiment, the degree of mutation possible during the experiment, the shape of the fitness landscape through which the population evolves, and the strategies used to invoke selection and to search the landscape, among others. By considering these factors, it can be predicted that recurrence is more likely when a small, wild-type-based starting pool is used with efficient selection and search strategies involving little online mutagenesis within a rugged adaptive landscape with a strong local optimum. The recurrence experiments performed here on the 150-nucleotide ligase ribozyme demonstrate that it repeatedly jumps from one peak in a fitness landscape to another, apparently hurdling a deep fitness valley. These predictions can and should be tested by additional multiple replicates of actual evolution experiments in the laboratory.Keywords
This publication has 37 references indexed in Scilit:
- Error catastrophe and antiviral strategyProceedings of the National Academy of Sciences, 2002
- Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7Molecular Biology and Evolution, 1997
- Inventing and improving ribozyme function: Rational design versus iterative selection methodsTrends in Biotechnology, 1994
- What would be conserved if "the tape were played twice"?Proceedings of the National Academy of Sciences, 1994
- Isolation of New Ribozymes from a Large Pool of Random SequencesScience, 1993
- Statistics of RNA secondary structuresPeptide Science, 1993
- Directed Evolution of an RNA EnzymeScience, 1992
- Uniform Selection as a Diversifying Force in Evolution: Evidence from DrosophilaThe American Naturalist, 1989
- Selforganization of matter and the evolution of biological macromoleculesThe Science of Nature, 1971
- The Effect of Variation of FitnessThe American Naturalist, 1937