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Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping

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  • W. Fontana
  • P. Schuster
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    Abstract

    Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness among phenotypes, independently of their similarity. Because of neutrality, phenotypes denote equivalence classes of genotypes. The definition of neighborhood relations among phenotypes relies, therefore, on the statistics of neighborhood relations among equivalence classes of genotypes in genotype space. The folding of RNA sequences(genotypes) into secondary structures (phenotypes) is an ideal case to implement these concepts. We study the extent to which the folding of RNA sequences induces a "statistical topology" on the set of minimum free energy secondary structures. The resulting nearness relation suggests a notion of "continuous" structure transformation. We can, then, rationalize major transitions in evolutionary trajectories at the level of RNA structures by identifying those transformations which are irreducibly discontinuous. This is shown by means of computer simulations. The statistical topology organizing the set of RNA shapes explains why neutral drift in sequence space plays a key role in evolutionary optimization.

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    File URL: http://www.iiasa.ac.at/Publications/Documents/IR-98-004.pdf
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    File URL: http://www.iiasa.ac.at/Publications/Documents/IR-98-004.ps
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    Bibliographic Info

    Paper provided by International Institute for Applied Systems Analysis in its series Working Papers with number ir98004.

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    Date of creation: Feb 1998
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    Handle: RePEc:wop:iasawp:ir98004

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    1. Peter Schuster, 1997. "Genotypes with Phenotypes: Adventures in an RNA Toy World," Working Papers 97-04-036, Santa Fe Institute.
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    Cited by:
    1. Bårbel M. R. Stadler & Peter F. Stadler & Peter R. Wills, 2001. "Evolution in Systems of Ligation-Based Replicators," Working Papers 01-09-052, Santa Fe Institute.
    2. Christian Reidys & Christian V. Forst & Peter Schuster, 2000. "Replication and Mutation on Neutral Networks: Updated Version 2000," Working Papers 00-11-061, Santa Fe Institute.
    3. BŠrbel M. R. Stadler & Peter F. Stadler & Max Shpak & GŸnter P. Wagner, 2001. "Recombination Spaces, Metrics, and Pretopologies," Working Papers 01-02-011, Santa Fe Institute.

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