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Hearing silence: non-neutral evolution at synonymous sites in mammals

Key Points

  • Synonymous mutations in mammals are often assumed to be free from natural selection, not only because such mutations do not alter the encoded protein, but also because neutral theory predicts that when population sizes are small, as they are in mammals, selection should be too weak to act on changes that have relatively small effects on fitness.

  • Recent evidence indicates that synonymous sites in mammals are not always neutrally evolving and numerous examples of disease-associated synonymous mutations now exist.

  • Selection might act on synonymous codon usage to maximize the efficiency of translation, to promote mRNA stability and/or to improve splicing efficiency. In mammals, there is good support for the latter two models, but less for the first possibility.

  • Although non-neutral evolution at synonymous sites means that the genomic mutation rate has been underestimated, it is unlikely to be a source of error that exceeds the uncertainties inherent in the other parameters that are used to estimate the mutation rate.

  • As synonymous sites can be subject to purifying selection, a high Ka/Ks ratio cannot be assumed to indicate positive selection on a protein. Preliminary studies indicate that the method might be misleading as often as it is correct.

  • Knowing why some synonymous sites are functional allows us to better understand how codon choice might be manipulated to increase the efficacy of transgene expression, especially when transgenes have most of their introns removed.

Abstract

Although the assumption of the neutral theory of molecular evolution — that some classes of mutation have too small an effect on fitness to be affected by natural selection — seems intuitively reasonable, over the past few decades the theory has been in retreat. At least in species with large populations, even synonymous mutations in exons are not neutral. By contrast, in mammals, neutrality of these mutations is still commonly assumed. However, new evidence indicates that even some synonymous mutations are subject to constraint, often because they affect splicing and/or mRNA stability. This has implications for understanding disease, optimizing transgene design, detecting positive selection and estimating the mutation rate.

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Figure 1: The effect of isochores on synonymous codon usage and codon-usage bias.
Figure 2: Usage of certain codons is more biased near intron–exon junctions, owing to synonyms being differentially common in exonic splicing enhancers.
Figure 3: Fluctuation in rates of evolution across the BRCA1 gene.

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Acknowledgements

The authors wish to thank K. Wolfe, F. Kondrashov and an anonymous reviewer for helpful comments on the manuscript. J.V.C. and J.L.P. were funded by the UK Biotechnology and Biological Sciences Research Council.

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Glossary

Effective population size (Ne)

The number of individuals in a population that contribute to the next generation.

Codon usage

The relative frequency at which alternative codons specifying a particular amino acid are used.

Positive selection

Also known as Darwinian selection. Natural selection that promotes the spread of a new mutation through the population, resulting in a fixed difference between species.

Molecular clock

A model of sequence evolution in which the number of changes that occur between two lineages accumulate at a constant rate, therefore allowing the estimation of the time since lineage divergence from the number of changes that have occurred.

Biased gene conversion

Gene conversion is a process by which similar genomic fragments become identical. If, after the DNA-repair system recognizes GC:AT mismatches in a heteroduplex (for example, arising during recombination between paired sister chromosomes), mismatches are resolved in favour of certain bases, the process is considered to be biased. Typically, biased gene conversion favours GC over AT in GC:AT mismatches.

Expression breadth

The proportion of tissues in which a given gene is expressed.

Expression rate

The average level of gene expression across all tissues in which a given gene is expressed.

Synonymous substitution rate (Ks)

The ratio of the number of synonymous differences (corrected for multiple hits) between two orthologous genes to the number of sites in the gene at which synonymous mutations could occur.

Intronic substitution rate (Ki)

The number of differences per site (corrected for multiple hits) between orthologous introns.

Purifying selection

Also known as negative selection. Selection that eliminates a new mutation from the population, therefore removing changes from the population and maintaining the status quo.

Iso-acceptor tRNA

Any tRNAs molecule that is charged by the single aminoacyl-tRNA synthetase which is specific to a given amino acid. The entire complement of tRNAs is divided into 20 iso-accepting groups, with each group being associated with a particular synthetase.

MicroRNAs

Short non-coding RNAs (22 nucleotides long) that can repress gene expression by base pairing to target mRNAs.

Non-synonymous substitution rate (Ka)

The ratio of the number of non-synonymous differences (corrected for multiple substitutions at the same site) between two orthologous genes to the number of sites at which non-synonymous mutations could occur.

Sliding-window plot

A graphical representation of a sequence in which subsections, sometimes overlapping, of a given size (a window) are successively analysed.

Synergistic epistasis

The interaction between mutations that causes their combined effect on fitness to be greater than would be expected from their individual (multiplicative) effects.

Transgene

Foreign DNA that is experimentally inserted into totipotent embryonic cells or into unicellular organisms.

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Chamary, J., Parmley, J. & Hurst, L. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7, 98–108 (2006). https://doi.org/10.1038/nrg1770

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