Journal of Molecular Evolution

, Volume 43, Issue 3, pp 165–169 | Cite as

Exploring phenotype space through neutral evolution

  • Martijn A. Huynen
Article

Abstract

RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can play a role in adaptation.

Key words

RNA secondary structure Neutral Evolution Adaptive evolution Genotype-phenotype relation Sequence space Fitness landscape 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Ekland EH, Szostak JW, Bartel DP (1995) Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269:364–370PubMedGoogle Scholar
  2. Fontana W, Konings DAM, Stadler PF, Schuster P (1993) Statistics of RNA secondary structures. Biopolymers 33:1389–1404CrossRefPubMedGoogle Scholar
  3. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster PA (a) Vienna RNA Package. pub/RNA/ViennaRNA-1.03 ftp.itc.univie.ac.at (Public Domain Software)Google Scholar
  4. Huynen MA, Konings DAM, Hogeweg P (1993) Multiple coding and the evolutionary properties of RNA secondary structures. J Theor Biol 165:251–267CrossRefPubMedGoogle Scholar
  5. Huynen MA, Stadler PF, Fontana W (1996a) Smoothness within ruggedness: the role of neutrality in adaptation. Proc Natl Acad Sci USA 93:397–401CrossRefGoogle Scholar
  6. Huynen MA, Perelson A, Vieira W, Stadler PF (1996b) Base pairing probabilities in a complete HIV-1 genome. J Comp Biol 3:253–274Google Scholar
  7. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeGoogle Scholar
  8. Konings DAM, Hogeweg P (1989) Pattern analysis of RNA secondary structures, similarity and consensus of minimal-energy folding. J Mol Biol 207:597–614CrossRefPubMedGoogle Scholar
  9. Maynard-Smith J (1970) Natural selection and the concept of a protein space. Nature 255:563–564Google Scholar
  10. Provine WB (1986) Sewall Wright and evolutionary biology. University of Chicago Press, ChicagoGoogle Scholar
  11. Schuster P, Fontana W, Stadler PF, Hofacker IL (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proc R Soc Lond (Biol) 255:279–284Google Scholar
  12. Tacker M, Stadler PF, Bornberg-Bauer E, Hofacker IL, Schuster P (1996) Robust properties of RNA secondary structure folding algorithms. Working Paper 96-04-016, Santa Fe InstituteGoogle Scholar
  13. Waterman MS (1978) Secondary structure of single-stranded nucleic acids. Studies on foundations and combinatories. Adv Math Suppl Studies 1:167–212Google Scholar
  14. Wright S (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution. In: Jones DF (ed) Proceedings of the sixth international congress on genetics, vol 1. pp 356–366, Brooklyn Botanic Garden, New YorkGoogle Scholar
  15. Zuker M, Stiegler P (1981) Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133–148PubMedGoogle Scholar

Copyright information

© Springer-Verlag New York Inc 1996

Authors and Affiliations

  • Martijn A. Huynen
    • 1
    • 2
    • 3
  1. 1.Theoretical Biology and BiophysicsLos Alamos National LaboratoryLos AlamosUSA
  2. 2.Center for Nonlinear StudiesLos Alamos National LaboratoryLos AlamosUSA
  3. 3.Santa Fe InstituteSanta FeUSA

Personalised recommendations