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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Manrubia, S.C., Cuesta, J.A.: Neutral networks of genotypes: evolution behind the curtain. ARBOR 186, 1051–1064 (2010)
Eigen, M.: Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58, 465–523 (1971)
Fontana, W., Schuster, P.: A computer model of evolutionary optimization. Biophys. Chem. 26, 123–47 (1987)
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)
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)
Schuster, P.: Genotypes with phenotypes: adventures in an RNA toy world. Biophys. Chem. 66, 75–110 (1997)
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)
Schuster, P.: Prediction of RNA secondary structures: from theory to models and real molecules. Rep. Prog. Phys. 69, 1419 (2006)
Stadler, P.F.: Fitness landscapes arising from the sequence-structure maps of biopolymers. J. Mol. Struct. THEOCHEM 463, 7–19 (1999)
Kimura, M.: Evolutionary rate at the molecular level. Nature 217, 624–626 (1968)
Holland, J.J., De la Torre, J.C., Steinhauer, D.A.: RNA virus populations as quasispecies. Curr. Top. Microbiol. Immunol. 176, 1–20 (1992)
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)
Ancel, L.W., Fontana, W.: Plasticity, evolvability, and modularity in RNA. J. Exp. Zool. Mol. Dev. Evol. 288, 242–283 (2000)
Fontana, W.: Modelling ‘evo-devo’ with RNA. BioEssays 24, 1164–77 (2002)
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)
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)
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)
Fontana, W., Konings, D.A.M., Stadler, P.F., Schuster, P.: Statistics of RNA secondary structures. Biopolymers 33, 1389–404 (1993)
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)
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)
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)
Bull, J.J., Meyers, L.A., Lachmann, L.: Quasispecies made simple. PLoS Comput. Biol. 1, 450–460 (2005)
van Nimwegen, E., Crutchfield, J.P., Huynen, M.: Neutral evolution of mutational robustness. Proc. Natl. Acad. Sci. U. S. A. 96, 9716–20 (1999)
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)
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)
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)
Gevertz, J., Gan, H.H., Schlick, T.: In vitro RNA random pools are not structurally diverse: a computational analysis. RNA 11, 853–63 (2005)
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)
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)
Stich, M., Lázaro, E., Manrubia, S.C.: Phenotypic effect of mutations in evolving populations of RNA molecules. BMC Evol. Biol. 10, 46 (2010)
Stich, M., Lázaro, E., Manrubia, S.C.: Variable mutation rates as an adaptive strategy in replicator populations. PLoS ONE 5, e11186 (2010)
Stich, M., Manrubia, S.C.: Motif frequency and evolutionary search times in RNA populations. J. Theor. Biol. 280, 117–26 (2011)
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)
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)
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)
Manrubia, S., Cuesta, J.: Evolution on neutral networks accelerates the ticking rate of the molecular clock. J. R. Soc. Interface 12, 20141010 (2015)
Stich, M., Manrubia, S.C.: Topological properties of phylogenetic trees in evolutionary models. Eur. Phys. J. B 70, 583–92 (2009)
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).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
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
Download citation
DOI: https://doi.org/10.1007/978-3-319-33054-9_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-33053-2
Online ISBN: 978-3-319-33054-9
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)