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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Kreitman, M. The neutral theory is dead — long live the neutral theory. Bioessays 18, 678–683 (1996).
Kimura, M. Evolutionary rate at the molecular level. Nature 217, 624–626 (1968).
Wolfe, K. H., Sharp, P. M. & Li, W. H. Mutation rates differ among regions of the mammalian genome. Nature 337, 283–285 (1989).
Smith, N. G. C. & Hurst, L. D. The causes of synonymous rate variation in the rodent genome: can substitution rates be used to estimate the sex bias in mutation rate? Genetics 152, 661–673 (1999).
Keightley, P. D. & Eyre-Walker, A. Deleterious mutations and the evolution of sex. Science 290, 331–333 (2000).
Shabalina, S. A., Ogurtsov, A. Y., Kondrashov, V. A. & Kondrashov, A. S. Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17, 373–376 (2001).
Lewontin, R. C. The Genetic Basis of Evolutionary Change (Columbia Univ. Press, New York, 1974).
Gillespie, J. H. Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155, 909–919 (2000).
Ohta, T. & Gillespie, J. H. Development of neutral and nearly neutral theories. Theor. Pop. Biol. 49, 128–142 (1996).
Ohta, T. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J. Mol. Evol. 40, 56–63 (1995).
Nielsen, R. Robustness of the estimator of the index of dispersion for DNA sequences. Mol. Phyl. Evol. 7, 346–351 (1997).
Rodriguez-Trelles, F., Tarrio, R. & Ayala, F. J. Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH. Proc. Natl Acad. Sci. USA 98, 11405–11410 (2001).
Gillespie, J. H. The Causes of Molecular Evolution (Oxford Univ. Press, Oxford, 1991).
King, J. L. & Jukes, T. H. Non-Darwinian evolution. Science 164, 788–798 (1969).
Kimura, M. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267, 275–276 (1977).
Clarke, B. Darwinian evolution of proteins. Science 168, 1009–1011 (1970).
Ikemura, T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2, 13–34 (1985). A review of how skews in tRNA abundance correspond to biased codon usage in E. coli and S. cerevisiae . This relationship showed that synonymous sites can be functional, with selection in this model promoting efficient protein synthesis.
Akashi, H. & Eyre-Walker, A. Translational selection and molecular evolution. Curr. Opin. Genet. Dev. 8, 688–693 (1998).
Duret, L. Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12, 640–649 (2002). An excellent review of evolution at synonymous sites in D. melanogaster, C. elegans and vertebrates, with particular emphasis on the effects that make it difficult to disentangle the neutral and selective forces that impinge on codon usage, particularly in mammals.
Wright, S. I., Yau, C. B., Looseley, M. & Meyers, B. C. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol. Biol. Evol. 21, 1719–1726 (2004).
Keightley, P. D., Lercher, M. J. & Eyre-Walker, A. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3, e42 (2005).
Woolfit, M. & Bromham, L. Population size and molecular evolution on islands. Proc. Biol. Sci. 272, 2277–2282 (2005).
Sharp, P. M., Averof, M., Lloyd, A. T., Matassi, G. & Peden, J. F. DNA sequence evolution: the sounds of silence. Philos. Trans. R. Soc. Lond. B 349, 241–247 (1995).
Eyre-Walker, A. An analysis of codon usage in mammals: selection or mutation bias? J. Mol. Evol. 33, 442–449 (1991).
Bernardi, G. et al. The mosaic genome of warm-blooded vertebrates. Science 228, 953–958 (1985).
Eyre-Walker, A. & Hurst, L. D. The evolution of isochores. Nature Rev. Genet. 2, 549–555 (2001).
Eyre-Walker, A. Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152, 675–683 (1999).
Lercher, M. J., Smith, N. G., Eyre-Walker, A. & Hurst, L. D. The evolution of isochores: evidence from SNP frequency distributions. Genetics 162, 1805–1810 (2002).
Duret, L., Semon, M., Piganeau, G., Mouchiroud, D. & Galtier, N. Vanishing GC-rich isochores in mammalian genomes. Genetics 162, 1837–1847 (2002).
Vinogradov, A. E. Bendable genes of warm-blooded vertebrates. Mol. Biol. Evol. 18, 2195–2200 (2001).
Vinogradov, A. E. Isochores and tissue-specificity. Nucleic Acids Res. 31, 5212–5220 (2003).
Galtier, N., Piganeau, G., Mouchiroud, D. & Duret, L. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159, 907–911 (2001).
Meunier, J. & Duret, L. Recombination drives the evolution of GC-content in the human genome. Mol. Biol. Evol. 21, 984–990 (2004).
Galtier, N. Gene conversion drives GC content evolution in mammalian histones. Trends Genet. 19, 65–68 (2003).
Iida, K. & Akashi, H. A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 261, 93–105 (2000). By comparing exons within the same gene, this paper provided strong evidence for selection at synonymous sites in humans, controlling for isochore effects, regional variation in rates of evolution and transcription-associated biases.
Xing, Y. & Lee, C. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc. Natl Acad. Sci. USA 102, 13526–13531 (2005).
Pond, S. K. & Muse, S. V. Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol. 22, 2375–2385 (2005). Using a new method, the authors found evidence that significant heterogeneity in the synonymous substitution rate within mammalian genes is common. Consequently, certain sites are being erroneously identified as being under positive selection.
Karlin, S. & Mrazek, J. What drives codon choices in human genes? J. Mol. Biol. 262, 459–472 (1996).
Urrutia, A. O. & Hurst, L. D. Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159, 1191–1199 (2001).
Urrutia, A. O. & Hurst, L. D. The signature of selection mediated by expression on human genes. Genome Res. 13, 2260–2264 (2003). The first report of a broad correlation between codon-usage bias (corrected for the isochore effect) and expression rate in human genes.
Hughes, A. L. & Yeager, M. Comparative evolutionary rates of introns and exons in murine rodents. J. Mol. Evol. 45, 125–130 (1997).
DeBry, R. W. & Marzluff, W. F. Selection on silent sites in the rodent H3 histone gene family. Genetics 138, 191–202 (1994).
Duret, L. & Hurst, L. D. The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution. Mol. Biol. Evol. 18, 757–762 (2001).
Vinogradov, A. E. Within-intron correlation with base composition of adjacent exons in different genomes. Gene 276, 143–151 (2001).
Miyata, T. & Hayashida, H. Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons. Proc. Natl Acad. Sci. USA 78, 5739–5743 (1981).
Bustamante, C. D., Nielsen, R. & Hartl, D. L. A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Mol. Biol. Evol. 19, 110–117 (2002). In mammals, the rate of nucleotide substitution at synonymous sites is 70% of that in the cognate pseudogenes.
Green, P. et al. Transcription-associated mutational asymmetry in mammalian evolution. Nature Genet. 33, 514–517 (2003).
Majewski, J. Dependence of mutational asymmetry on gene-expression levels in the human genome. Am. J. Hum. Genet. 73, 688–692 (2003).
Matassi, G., Sharp, P. M. & Gautier, C. Chromosomal location effects on gene sequence evolution in mammals. Curr. Biol. 9, 786–791 (1999).
Lercher, M. J., Chamary, J. V. & Hurst, L. D. Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res. 14, 1002–1013 (2004).
Casane, D., Boissinot, S., Chang, B. H., Shimmin, L. C. & Li, W. H. Mutation pattern variation among regions of the primate genome. J. Mol. Evol. 45, 216–226 (1997).
Nachman, M. W. & Crowell, S. L. Estimate of the mutation rate per nucleotide in humans. Genetics 156, 297–304 (2000).
Majewski, J. & Ott, J. Distribution and characterization of regulatory elements in the human genome. Genome Res. 12, 1827–1836 (2002).
Keightley, P. D. & Gaffney, D. J. Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc. Natl Acad. Sci. USA 100, 13402–13406 (2003).
Chamary, J. V. & Hurst, L. D. Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol. Biol. Evol. 21, 1014–1023 (2004). Using mouse–rat alignments, the rate and patterns of evolution were compared between introns and synonymous sites, two classes of supposedly neutral sequence. Relative to intronic sites, C residues were found to be abundant and relatively stable at synonymous sites.
Hellmann, I. et al. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13, 831–837 (2003). By comparing human–chimpanzee divergence at fourfold synonymous sites relative to the intergenic spacer, this study indicates that nearly 40% of (non-CpG) synonymous mutations have been eliminated by purifying selection.
Subramanian, S. & Kumar, S. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 13, 838–844 (2003).
Chen, F. C. & Li, W. H. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68, 444–456 (2001).
Chen, F. C., Vallender, E. J., Wang, H., Tzeng, C. S. & Li, W. H. Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J. Hered. 92, 481–489 (2001).
Smith, N. G. C. & Hurst, L. D. Sensitivity of patterns of molecular evolution to alterations in methodology: a critique of Hughes and Yeager. J. Mol. Evol. 47, 493–500 (1998).
Mikkelsen, T. S. et al. Initial sequence of the chimpanzee genome and comparison with the human genome. 437, 69–87 (2005).
Lu, J. & Wu, C. I. Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc. Natl Acad. Sci. USA 102, 4063–4067 (2005). Using human–chimpanzee alignments, the authors compared rates of evolution between autosomes and the X chromosome to measure the strength of selection at synonymous sites. They found that more than 90% of synonymous mutations are under weak selection, but suggest that, for the most part, selection seems to be too weak to influence substitution rates.
Lavner, Y. & Kotlar, D. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345, 127–138 (2005).
Bulmer, M. Coevolution of codon usage and transfer RNA abundance. Nature 325, 728–730 (1987).
Sharp, P. M., Bailes, E., Grocock, R. J., Peden, J. F. & Sockett, R. E. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33, 1141–1153 (2005).
Comeron, J. M. Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 167, 1293–1304 (2004). References 63 and 66 provide evidence that human tRNA gene-copy numbers match a proposed set of preferred codons and correlate with expression-weighted frequencies of optimal codons.
Kaufmann, D., Kenner, O., Nurnberg, P., Vogel, W. & Bartelt, B. In NF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons. Eur. J. Hum. Genet. 12, 139–149 (2004).
Kanaya, S., Yamada, Y., Kinouchi, M., Kudo, Y. & Ikemura, T. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J. Mol. Evol. 53, 290–298 (2001). Unlike yeast, flies and worms, codon usage in the genes that encode ribosomal proteins and histones is not significantly biased in humans, which indicates that the primary factor influencing codon-usage diversity in these species is not translation efficiency.
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
dos Reis, M., Savva, R. & Wernisch, L. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32, 5036–5044 (2004). By measuring the extent to which tRNA copy-number and codon usage are co-adapted across genomes, the authors find no evidence for translational selection in humans.
Carlini, D. B. & Stephan, W. In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein. Genetics 163, 239–243 (2003).
Levy, J. P., Muldoon, R. R., Zolotukhin, S. & Link, C. J. Jr. Retroviral transfer and expression of a humanized, red-shifted green fluorescent protein gene into human tumor cells. Nature Biotechnol. 14, 610–614 (1996).
Zolotukhin, S., Potter, M., Hauswirth, W. W., Guy, J. & Muzyczka, N. A 'humanized' green fluorescent protein cDNA adapted for high-level expression in mammalian cells. J. Virol. 70, 4646–4654 (1996).
Kim, C. H., Oh, Y. & Lee, T. H. Codon optimization for high-level expression of human erythropoietin (EPO) in mammalian cells. Gene 199, 293–301 (1997).
Lercher, M. J., Urrutia, A. O., Pavlicek, A. & Hurst, L. D. A unification of mosaic structures in the human genome. Hum. Mol. Genet. 12, 2411–2415 (2003).
Semon, M., Mouchiroud, D. & Duret, L. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum. Mol. Genet. 14, 421–427 (2005).
Vinogradov, A. E. Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth. Trends Genet. 21, 639–643 (2005)
Chamary, J. V. & Hurst, L. D. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol. 6, R75 (2005). Provides evidence that the preference for C at synonymous sites (as shown in reference 55) could be explained by selection that favours thermodynamically stable mRNA secondary structures. Moreover, had synonymous substitutions occurred at locations other than those that were observed in the mouse lineage, the mRNA would have been less stable.
Buratti, E. & Baralle, F. E. Influence of RNA secondary structure on the pre-mRNA splicing process. Mol. Cell. Biol. 24, 10505–10514 (2004).
Shen, L. X., Basilion, J. P. & Stanton, V. P. Jr. Single-nucleotide polymorphisms can cause different structural folds of mRNA. Proc. Natl Acad. Sci. USA 96, 7871–7876 (1999).
Duan, J. et al. Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum. Mol. Genet. 12, 205–216 (2003). A well-worked example of how a synonymous mutation can affect mRNA stability. Of six naturally occurring synonymous SNPs in the DRD2 gene, only the mutation that decreases mRNA half-life and induced a conspicuous change in predicted secondary structure was linked to disease.
Capon, F. et al. A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. Hum. Mol. Genet. 13, 2361–2368 (2004).
Smith, N. G. & Hurst, L. D. The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. Genetics 153, 1395–1402 (1999).
Seffens, W. & Digby, D. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res. 27, 1578–1584 (1999).
Cohen, B. & Skiena, S. Natural selection and algorithmic design of mRNA. J. Comp. Biol. 10, 419–432 (2003).
Schroeder, R., Barta, A. & Semrad, K. Strategies for RNA folding and assembly. Nature Rev. Mol. Cell Biol. 5, 908–919 (2004).
Huynen, M. A., Konings, D. A. & Hogeweg, P. Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure. J. Mol. Evol. 34, 280–291 (1992).
Duan, J. & Antezana, M. A. Mammalian mutation pressure, synonymous codon choice, and mRNA degradation. J. Mol. Evol. 57, 694–701 (2003).
Cartegni, L., Chew, S. L. & Krainer, A. R. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nature Rev. Genet. 3, 285–298 (2002).
Pagani, F. & Baralle, F. E. Genomic variants in exons and introns: identifying the splicing spoilers. Nature Rev. Genet. 5, 389–396 (2004). References 89 and 90 are excellent reviews of how exonic mutations can disrupt the pre-mRNA splicing process.
Eskesen, S. T., Eskesen, F. N. & Ruvinsky, A. Natural selection affects frequencies of AG and GT dinucleotides at the 5′ and 3′ ends of exons. Genetics 167, 543–550 (2004).
Fairbrother, W. G., Yeh, R. F., Sharp, P. A. & Burge, C. B. Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007–1013 (2002).
Wang, Z. et al. Systematic identification and analysis of exonic splicing silencers. Cell 119, 831–845 (2004).
Blencowe, B. J. Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25, 106–110 (2000).
Willie, E. & Majewski, J. Evidence for codon bias selection at the pre-mRNA level in eukaryotes. Trends Genet. 20, 534–538 (2004). The first demonstration that codons associated with splicing are increasingly preferred near intron–exon junctions.
Chamary, J. V. & Hurst, L. D. Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? Trends Genet. 21, 256–259 (2005).
Parmley, J. L., Chamary, J. V. & Hurst, L. D. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol. 12 October 2005 (10.1093/molbev/msj035).
Hurst, L. D. & Pal, C. Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet. 17, 62–65 (2001). The first evidence from mammals that a K a/K s > 1 peak is due to a dip in the synonymous substitution rate, which reference 99 later revealed to coincide with the location of an ESE.
Orban, T. I. & Olah, E. Purifying selection on silent sites — a constraint from splicing regulation? Trends Genet. 17, 252–253 (2001).
Pagani, F., Raponi, M. & Baralle, F. E. Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc. Natl Acad. Sci. USA 102, 6368–6372 (2005). About 30% of synonymous mutations in exon 12 of CFTR are associated with splicing disruption.
Fairbrother, W. G., Holste, D., Burge, C. B. & Sharp, P. A. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol. 2, e268 (2004). As one approaches intron–exon junctions in humans, predicted ESE density increases while SNP density decreases. Additionally, the authors suggest that one-fifth of mutations that might potentially disrupt ESEs have been eliminated by purifying selection.
Carlini, D. B. & Genut, J. E. Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J. Mol. Evol. 30 November 2005 (10.1007/s00239-005-0055-x).
Cusack, B. P. & Wolfe, K. H. Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons. Mol. Biol. Evol. 22, 2198–2208 (2005).
Purvis, I. J. et al. The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. J. Mol. Biol. 193, 413–417 (1987).
Cortazzo, P. et al. Silent mutations affect in vivo protein folding in Escherichia coli. Biochem. Biophys. Res. Comm. 293, 537–541 (2002).
Thanaraj, T. A. & Argos, P. Ribosome-mediated translational pause and protein domain organization. Protein Sci. 5, 1594–1612 (1996).
Oresic, M. & Shalloway, D. Specific correlations between relative synonymous codon usage and protein secondary structure. J. Mol. Biol. 281, 31–48 (1998).
Netzer, W. J. & Hartl, F. U. Recombination of protein domains facilitated by co-translational folding in eukaryotes. Nature 388, 343–349 (1997).
Plotkin, J. B., Robins, H. & Levine, A. J. Tissue-specific codon usage and the expression of human genes. Proc. Natl Acad. Sci. USA 101, 12588–12591 (2004).
Hurst, L. D. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18, 486 (2002).
Carlini, D. B., Chen, Y. & Stephan, W. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr. Genetics 159, 623–633 (2001).
Carlini, D. B. Context-dependent codon bias and mRNA longevity in the yeast transcriptome. Mol. Biol. Evol. 22, 1403–1411 (2005).
Adkins, R. M., Gelke, E. L., Rowe, D. & Honeycutt, R. L. Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol. Biol. Evol. 18, 777–791 (2001).
Grantham, R., Gautier, C. & Gouy, M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 8, 1893–1912 (1980).
Akashi, H. Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144, 1297–1307 (1996).
Kryukov, G. V., Schmidt, S. & Sunyaev, S. Small fitness effect of mutations in highly conserved non-coding regions. Hum. Mol. Genet. 14, 2221–2229 (2005).
Piganeau, G., Mouchiroud, D., Duret, L. & Gautier, C. Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores. J. Mol. Evol. 54, 129–133 (2002).
Denecke, J., Kranz, C., Kemming, D., Koch, H. G. & Marquardt, T. An activated 5′ cryptic splice site in the human ALG3 gene generates a premature termination codon insensitive to nonsense-mediated mRNA decay in a new case of congenital disorder of glycosylation type Id (CDG-Id). Hum. Mut. 23, 477–486 (2004).
Aretz, S. et al. Familial adenomatous polyposis: aberrant splicing due to missense or silent mutations in the APC gene. Hum. Mut. 24, 370–380 (2004).
O'Driscoll, M., Ruiz-Perez, V. L., Woods, C. G., Jeggo, P. A. & Goodship, J. A. A splicing mutation affecting expression of ataxia-telangiectasia and Rad3-related protein (ATR) results in Seckel syndrome. Nature Genet. 33, 497–501 (2003).
Ishibashi, F. et al. Improved superoxide-generating ability by interferon γ due to splicing pattern change of transcripts in neutrophils from patients with a splice site mutation in CYBB gene. Blood 98, 436–441 (2001).
Flusser, H. et al. Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation. Neurology 64, 1426–1430 (2005).
Harteveld, C. L. et al. An α-thalassemia phenotype in a Dutch Hindustani, caused by a new point mutation that creates an alternative splice, donor site in the first exon of the α2-globin gene. Hemoglobin 28, 255–259 (2004).
Wicklow, B. A. et al. Severe subacute GM2 gangliosidosis caused by an apparently silent HEXA mutation (V324V) that results in aberrant splicing and reduced HEXA mRNA. Am. J. Med. Genet. Part A 127A, 158–166 (2004).
Xie, J. L., Pabon, D., Jayo, A., Butta, N. & Gonzalez-Manchon, C. Type I Glanzmann thrombasthenia caused by an apparently silent β3 mutation that results in aberrant splicing and reduced β3 mRNA. Thromb. Haemost. 93, 897–903 (2005).
Buchroithner, B. et al. Analysis of the LAMB3 gene in a junctional epidermolysis bullosa patient reveals exonic splicing and allele-specific nonsense-mediated mRNA decay. Lab. Invest. 84, 1279–1288 (2004).
Du, Y. Z., Dickerson, C., Aylsworth, A. S. & Schwartz, C. E. A silent mutation, C924T (G308G), in the L1CAM gene results in X linked hydrocephalus (HSAS). J. Med. Genet. 35, 456–462 (1998).
Amati-Bonneau, P. et al. Sporadic optic atrophy due to synonymous codon change altering mRNA splicing of OPA1. Clin. Genet. 67, 102–103 (2005).
Fernandez-Cadenas, I. et al. Splicing mosaic of the myophosphorylase gene due to a silent mutation in McArdle disease. Neurology 61, 1432–1434 (2003).
Mizuguchi, T. et al. Heterozygous TGFBR2 mutations in Marfan syndrome. Nature Genet. 36, 855–860 (2004).
Hoopengardner, B., Bhalla, T., Staber, C. & Reenan, R. Nervous system targets of RNA editing identified by comparative genomics. Science 301, 832–836 (2003).
Sémon, M., Lobry, J. R. & Duret, L. No evidence for tissue-specific adaption of synonymous codon usage in human. Mol. Biol. Evol. 9 November 2005 (10.1093/molbev/msj053).
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.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Related links
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.
Rights and permissions
About this article
Cite this article
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
Issue Date:
DOI: https://doi.org/10.1038/nrg1770
This article is cited by
-
Hemizygosity can reveal variant pathogenicity on the X-chromosome
Human Genetics (2023)
-
Adaption of tobacco rattle virus to its solanaceous hosts is related to the codon usage bias of the hosts and that of the viral 16 K gene
European Journal of Plant Pathology (2023)
-
Genomic insights into positive selection during barley domestication
BMC Plant Biology (2022)
-
Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae
Communications Biology (2022)
-
Synonymous mutations in representative yeast genes are mostly strongly non-neutral
Nature (2022)