Populations of RNA Molecules as Computational Model for Evolution
We consider populations of RNA molecules as computational model for molecular evolution. Based on a large body of previous work, we review some recent results. In the first place, we study the sequence–structure map, its implications on the structural rep
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Populations of RNA Molecules as Computational Model for Evolution Michael Stich, Carlos Briones, Ester La´zaro, and Susanna C. Manrubia
Abstract We consider populations of RNA molecules as computational model for molecular evolution. Based on a large body of previous work, we review some recent results. In the first place, we study the sequence–structure map, its implications on the structural repertoire of a pool of random RNA sequences and its relevance for the RNA world hypothesis of the origin of life. In a scenario where template replication is possible, we discuss the internal organization of evolving populations and its relationship with robustness and adaptability. Finally, we explore how the effect of the mutation rate on fitness changes depends on the degree of adaptation of an RNA population.
4.1
Introduction
Molecular evolution covers a huge area of research, ranging from prebiotic chemistry and questions on the origin of life, through many aspects related to the origin of and the relationships among species, the study of viral and bacterial evolution and their medical implications up to the artificial design and in vitro selection of molecules, with all their applications in nano- and biotechnology. In this chapter, we do not aim to give a complete overview of that wide research field, but focus on the use of populations of RNA molecules as a model to understand evolution of prebiotic replicators in the RNA world. As RNA viruses share many characteristics with primitive RNA molecules with replicative ability, these studies can also be used to tackle many aspects of viral evolution. Although a large body of our work is inspired by experiments, in this chapter we focus on theoretical approaches for understanding evolutionary processes. M. Stich, C. Briones, E. La´zaro, and S.C. Manrubia Dpto de Evolucio´n Molecular, Centro de Astrobiologı´a (CSIC-INTA), Ctra de Ajalvir, km 4, 28850 Torrejo´n de Ardoz (Madrid), Spain e-mail: [email protected]
P. Pontarotti (ed.), Evolutionary Biology – Concepts, Molecular and Morphological Evolution, DOI 10.1007/978-3-642-12340-5_4, # Springer-Verlag Berlin Heidelberg 2010
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RNA molecules are a very well suited model for studying evolution because they incorporate, in a single molecular entity, both genotype and phenotype. While errors in the replication process introduce mutations in the RNA sequence (genotype), selection acts upon the function (phenotype) of the molecule. Since in many cases the spatial structure of the molecule is crucial for its biochemical function, the structure of an RNA molecule can be considered as a minimal representation of the phenotype. In current biology, RNA viruses are the paradigmatic example for evolving populations: replication is fast, it takes place with a relatively high error rate, and population sizes are large. This has made RNA viruses an often used example for quasispecies, a concept originally proposed by Eigen (1971) and developed over the last decades in the context of virology (Domingo 2006). It st
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