PMID: 7520506Jul 1, 1994Paper

Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes

Journal of Molecular Evolution
M Huynen, Paulien Hogeweg

Abstract

Evolution of RNA secondary structure is studied using simulation techniques and statistical analysis of fitness landscapes. The transition from RNA sequence to RNA secondary structure leads to fitness landscapes that have local variations in their "ruggedness." Evolution exploits these variations. In stable environments it moves the quasispecies toward relatively "flat" peaks, where not only the master sequence but also its mutants have a high fitness. In a rapidly changing environment, the situation is reversed; evolution moves the quasispecies to a region where the correlation between secondary structures of "neighboring" RNA sequences is relatively low. In selection for simple secondary structures the movement toward flat peaks leads to pattern generation in the RNA sequences. Patterns are generated at the level of polynucleotide frequencies and the distribution of purines and pyrimidines. The patterns increase the modularity of the sequence. They thereby prevent the formation of alternative secondary structures after mutations. The movement of the quasispecies toward relatively rugged parts of the landscape results in pattern generation at the level of the RNA secondary structure. The base-pairing frequency of the sequences...Continue Reading

Citations

Oct 24, 2007·Journal of Molecular Evolution·Nobuto Takeuchi, Paulien Hogeweg
Apr 12, 2003·Bio Systems·Tom SmithMichael O'Shea
Apr 1, 1997·Current Opinion in Structural Biology·P SchusterA Renner
Aug 18, 1999·Proceedings of the National Academy of Sciences of the United States of America·E van NimwegenM Huynen
Apr 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·C Kappen
Jan 1, 1996·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A HuynenP F Stadler
Aug 16, 2000·Artificial Life·P Hogeweg
Jan 1, 1997·Evolutionary Computation·L Pagie, P Hogeweg
Feb 26, 2014·BMC Bioinformatics·Chris A Nasrallah
Feb 1, 2012·PloS One·Folkert K de Boer, Paulien Hogeweg
May 21, 2008·Mathematical Biosciences·Gergely J Szöllosi, Imre Derényi
Aug 12, 2006·Journal of Theoretical Biology·Robert ForsterClaus O Wilke
Jun 26, 2012·Physics of Life Reviews·Nobuto Takeuchi, Paulien Hogeweg
Aug 16, 2019·PLoS Computational Biology·Alexander KlugJoachim Krug
Aug 16, 2017·Nature Communications·Nobuto TakeuchiKunihiko Kaneko
Oct 6, 2021·Journal of the Royal Society, Interface·Nora S Martin, Sebastian E Ahnert

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