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

Contrary to the neutral theory, silent mutations can be under natural selection. This is often seen in organisms from large populations, but the authors present evidence that it also occurs in mammals, because synonymous mutations affect mRNA stability and splicing. Key Points Synonymous mutations i...

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Published inNature reviews. Genetics Vol. 7; no. 2; pp. 98 - 108
Main Authors Chamary, J. V., Parmley, Joanna L., Hurst, Laurence D.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.02.2006
Nature Publishing Group
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Abstract Contrary to the neutral theory, silent mutations can be under natural selection. This is often seen in organisms from large populations, but the authors present evidence that it also occurs in mammals, because synonymous mutations affect mRNA stability and splicing. 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 K a / K s 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. 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.
AbstractList 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.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.
Contrary to the neutral theory, silent mutations can be under natural selection. This is often seen in organisms from large populations, but the authors present evidence that it also occurs in mammals, because synonymous mutations affect mRNA stability and splicing. 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 K a / K s 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. 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.
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.
Audience Academic
Author Hurst, Laurence D.
Chamary, J. V.
Parmley, Joanna L.
Author_xml – sequence: 1
  givenname: J. V.
  surname: Chamary
  fullname: Chamary, J. V.
  email: j.v.chamary@unil.ch
  organization: Center for Integrative Genomics, University of Lausanne, Génopode building
– sequence: 2
  givenname: Joanna L.
  surname: Parmley
  fullname: Parmley, Joanna L.
  organization: Department of Biology and Biochemistry, University of Bath
– sequence: 3
  givenname: Laurence D.
  surname: Hurst
  fullname: Hurst, Laurence D.
  email: l.d.hurst@bath.ac.uk
  organization: Department of Biology and Biochemistry, University of Bath
BackLink http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17671634$$DView record in Pascal Francis
https://www.ncbi.nlm.nih.gov/pubmed/16418745$$D View this record in MEDLINE/PubMed
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Snippet Contrary to the neutral theory, silent mutations can be under natural selection. This is often seen in organisms from large populations, but the authors...
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...
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...
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SubjectTerms Agriculture
Animal Genetics and Genomics
Animals
Biological and medical sciences
Biomedical and Life Sciences
Biomedicine
Cancer Research
Evolution, Molecular
Fundamental and applied biological sciences. Psychology
Gene Function
Gene Silencing
Genetics of eukaryotes. Biological and molecular evolution
Human Genetics
Humans
Mammals - genetics
Mutation
review-article
Selection, Genetic
Title Hearing silence: non-neutral evolution at synonymous sites in mammals
URI https://link.springer.com/article/10.1038/nrg1770
https://www.ncbi.nlm.nih.gov/pubmed/16418745
https://www.proquest.com/docview/223750238
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https://www.proquest.com/docview/70686678
Volume 7
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