On the Evolution of Redundancy in Genetic Codes |
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Authors: | David H Ardell Guy Sella |
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Institution: | Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyv?gen 18C, 752 36 Uppsala, Sweden, SE Department of Biological Sciences, Stanford University, Stanford CA 94305, USA, US
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Abstract: | We simulate a deterministic population genetic model for the coevolution of genetic codes and protein-coding genes. We use
very simple assumptions about translation, mutation, and protein fitness to calculate mutation-selection equilibria of codon
frequencies and fitness in a large asexual population with a given genetic code. We then compute the fitnesses of altered
genetic codes that compete to invade the population by translating its genes with higher fitness. Codes and genes coevolve
in a succession of stages, alternating between genetic equilibration and code invasion, from an initial wholly ambiguous coding
state to a diversified frozen coding state. Our simulations almost always resulted in partially redundant frozen genetic codes.
Also, the range of simulated physicochemical properties among encoded amino acids in frozen codes was always less than maximal.
These results did not require the assumption of historical constraints on the number and type of amino acids available to
codes nor on the complexity of proteins, stereochemical constraints on the translational apparatus, nor mechanistic constraints
on genetic code change. Both the extent and timing of amino-acid diversification in genetic codes were strongly affected by
the message mutation rate and strength of missense selection. Our results suggest that various omnipresent phenomena that
distribute codons over sites with different selective requirements—such as the persistence of nonsynonymous mutations at equilibrium,
the positive selection of the same codon in different types of sites, and translational ambiguity—predispose the evolution
of redundancy and of reduced amino acid diversity in genetic codes.
Received: 21 December 2000 / Accepted: 12 March 2001 |
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Keywords: | : Evolution — Origin — Code-message coevolution — Redundancy — Amino acid — Wobble — Mutation-selection balance — Codon usage |
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