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Modeling of Evolving RNA Replicators

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Nonlinear Dynamics in Biological Systems

Part of the book series: SEMA SIMAI Springer Series ((SEMA SIMAI,volume 7))

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Abstract

Populations of RNA replicators are a conceptually simple model to study evolutionary processes. Their prime applications comprise molecular evolution such as observed in viral populations, SELEX experiments, or the study of the origin and early evolution of life. Nevertheless, due to their simplicity compared to living organisms, they represent a paradigmatic model for Darwinian evolution as such. In this chapter, we review some properties of RNA populations in evolution, and focus on the structure of the underlying neutral networks, intimately related to the sequence-structure map for RNA molecules.

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References

  1. Manrubia, S.C., Cuesta, J.A.: Neutral networks of genotypes: evolution behind the curtain. ARBOR 186, 1051–1064 (2010)

    Article  Google Scholar 

  2. Eigen, M.: Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58, 465–523 (1971)

    Article  ADS  Google Scholar 

  3. Fontana, W., Schuster, P.: A computer model of evolutionary optimization. Biophys. Chem. 26, 123–47 (1987)

    Article  Google Scholar 

  4. Huynen, M.A., Konings, D.A.M., Hogeweg, P.: Multiple coding and the evolutionary properties of RNA secondary structure. J. Theor. Biol. 165, 251–267 (1993)

    Article  Google Scholar 

  5. Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L.: From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B 255, 279–284 (1994)

    Article  ADS  Google Scholar 

  6. Schuster, P.: Genotypes with phenotypes: adventures in an RNA toy world. Biophys. Chem. 66, 75–110 (1997)

    Article  Google Scholar 

  7. Takeuchi, N., Hogeweg, P.: Evolutionary dynamics of RNA-like replicator systems: a bioinformatic approach to the origin of life. Phys. Life Rev. 9, 219–263 (2012)

    Article  ADS  Google Scholar 

  8. Schuster, P.: Prediction of RNA secondary structures: from theory to models and real molecules. Rep. Prog. Phys. 69, 1419 (2006)

    Article  ADS  Google Scholar 

  9. Stadler, P.F.: Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. THEOCHEM 463, 7–19 (1999)

    Article  Google Scholar 

  10. Kimura, M.: Evolutionary rate at the molecular level. Nature 217, 624–626 (1968)

    Article  ADS  Google Scholar 

  11. Holland, J.J., De la Torre, J.C., Steinhauer, D.A.: RNA virus populations as quasispecies. Curr. Top. Microbiol. Immunol. 176, 1–20 (1992)

    Google Scholar 

  12. Briones, C., Stich, M., Manrubia, S.C.: The dawn of the RNA world: toward functional complexity through ligation of random RNA oligomers. RNA 15, 743–9 (2009)

    Article  Google Scholar 

  13. Ancel, L.W., Fontana, W.: Plasticity, evolvability, and modularity in RNA. J. Exp. Zool. Mol. Dev. Evol. 288, 242–283 (2000)

    Article  Google Scholar 

  14. Fontana, W.: Modelling ‘evo-devo’ with RNA. BioEssays 24, 1164–77 (2002)

    Article  Google Scholar 

  15. Aguirre, J., Buldú, J.M., Stich, M., Manrubia, S.C.: Topological structure of the space of phenotypes: the case of RNA neutral networks. PLoS ONE 6, e26324 (2011)

    Article  ADS  Google Scholar 

  16. Anderson, P.C., Mecozzi, S.: Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline. J. Am. Chem. Soc. 127, 5290–1 (2005)

    Article  Google Scholar 

  17. Stich, M., Briones, C., Manrubia, S.C.: On the structural repertoire of pools of short, random RNA sequences. J. Theor. Biol. 252, 750–63 (2008)

    Article  MathSciNet  Google Scholar 

  18. Fontana, W., Konings, D.A.M., Stadler, P.F., Schuster, P.: Statistics of RNA secondary structures. Biopolymers 33, 1389–404 (1993)

    Article  Google Scholar 

  19. Gan, H.H., Pasquali, S., Schlick, T.: Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res. 31, 2926–43 (2003)

    Article  Google Scholar 

  20. Grüner,W., Giegerich, R., Strothmann, D., Reidys, C., Weber, J., Hofacker, I.L., Stadler, P.F., Schuster, P.: Analysis of RNA sequence structure maps by exhaustive enumeration II. Structures of neutral networks and shape space covering. Monatsh. Chem. 127, 375–389 (1996)

    Google Scholar 

  21. Reidys, C., Stadler, P.F., Schuster, P.: Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bull. Math. Biol. 59, 339–97 (1997)

    Article  MATH  Google Scholar 

  22. Bull, J.J., Meyers, L.A., Lachmann, L.: Quasispecies made simple. PLoS Comput. Biol. 1, 450–460 (2005)

    Article  Google Scholar 

  23. van Nimwegen, E., Crutchfield, J.P., Huynen, M.: Neutral evolution of mutational robustness. Proc. Natl. Acad. Sci. U. S. A. 96, 9716–20 (1999)

    Article  ADS  Google Scholar 

  24. Aguirre, J., Buldú, J., Manrubia, S.: Evolutionary dynamics on networks of selectively neutral genotypes: effects of topology and sequence stability. Phys. Rev. E 80, 066112 (2009)

    Article  ADS  Google Scholar 

  25. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., Schuster, P.: Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125, 167–188 (1994)

    Article  Google Scholar 

  26. Sabeti, P.C., Unrau, P.J., Bartel, D.P.: Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem. Biol. 4, 767–74 (1997)

    Article  Google Scholar 

  27. Gevertz, J., Gan, H.H., Schlick, T.: In vitro RNA random pools are not structurally diverse: a computational analysis. RNA 11, 853–63 (2005)

    Article  Google Scholar 

  28. Knight, R., De Sterck, H., Markel, R., Smit, S., Oshmyansky, A., Yarus, M.: Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res. 33, 5924–35 (2005)

    Article  Google Scholar 

  29. Kim, N., Gan, H.H., Schlick,T.: A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA 13, 478–92 (2007)

    Google Scholar 

  30. Stich, M., Lázaro, E., Manrubia, S.C.: Phenotypic effect of mutations in evolving populations of RNA molecules. BMC Evol. Biol. 10, 46 (2010)

    Article  Google Scholar 

  31. Stich, M., Lázaro, E., Manrubia, S.C.: Variable mutation rates as an adaptive strategy in replicator populations. PLoS ONE 5, e11186 (2010)

    Article  ADS  Google Scholar 

  32. Stich, M., Manrubia, S.C.: Motif frequency and evolutionary search times in RNA populations. J. Theor. Biol. 280, 117–26 (2011)

    Article  MathSciNet  Google Scholar 

  33. Cowperthwaite, M., Economo, E., Harcombe, W., Miller, E., Meyers, L.: The ascent of the abundant: how mutational networks constrain evolution. PLoS Comput. Biol. 4, e1000110 (2008)

    Article  ADS  MathSciNet  Google Scholar 

  34. Greenbury, S.F., Johnston, I.G., Louis, A.A., Ahnert, S.E.: A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure. J. R. Soc. Interface 11, 20140249 (2014)

    Article  Google Scholar 

  35. Schaper, S., Louis, A.A.: The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima. PLoS ONE 9, e86635 (2014)

    Article  ADS  Google Scholar 

  36. Manrubia, S., Cuesta, J.: Evolution on neutral networks accelerates the ticking rate of the molecular clock. J. R. Soc. Interface 12, 20141010 (2015)

    Article  Google Scholar 

  37. Stich, M., Manrubia, S.C.: Topological properties of phylogenetic trees in evolutionary models. Eur. Phys. J. B 70, 583–92 (2009)

    Article  ADS  MathSciNet  MATH  Google Scholar 

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Acknowledgements

The authors are indebted to S. Manrubia for useful discussions and comments on the manuscript. JA acknowledges financial support from Spanish MICINN (projects FIS2011-27569 and FIS2014-57686). MS acknowledges financial support from Spanish MICINN (project FIS2011-27569).

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Correspondence to Michael Stich .

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Aguirre, J., Stich, M. (2016). Modeling of Evolving RNA Replicators. In: Carballido-Landeira, J., Escribano, B. (eds) Nonlinear Dynamics in Biological Systems. SEMA SIMAI Springer Series, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-319-33054-9_1

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