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Related Experiment Videos

DNA sequence evolution: the sounds of silence

P M Sharp1, M Averof, A T Lloyd

  • 1Department of Genetics, University of Nottingham, Queens Medical Centre, U.K.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|September 29, 1995
PubMed
Summary

Silent sites in genes reveal evolutionary processes. Natural selection shapes codon usage in some species, while mutation patterns vary across genomes, challenging previous assumptions.

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Molecular evolution

Background:

  • Silent sites in protein-coding genes can provide insights into evolutionary processes.
  • These sites, capable of synonymous substitutions, may be influenced by natural selection or reflect underlying mutational patterns.
  • Previous understanding suggested a dichotomy between unicellular (yeast) and multicellular (human) organisms regarding selection on codon usage.

Purpose of the Study:

  • To investigate the dual role of silent sites in revealing natural selection and mutational biases in gene evolution.
  • To re-evaluate the influence of natural selection on codon usage across different species, including multicellular organisms.
  • To explore regional variations in mutation patterns within genomes.

Main Methods:

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  • Analysis of synonymous codon usage patterns in protein-coding genes across various species (e.g., yeast, humans, Drosophila, Caenorhabditis).
  • Comparison of codon usage bias with tRNA abundance to infer selection pressures.
  • Examination of silent site variations to identify underlying mutational biases and potential regional differences.

    • Main Results:

    • In yeast, codon usage is shaped by selection for efficient translation, with co-adaptation between codon usage and tRNA abundance.
    • Human silent sites show significant codon usage variation but appear largely uninfluenced by natural selection, suggesting regional mutation bias.
    • Natural selection on codon usage is observed in some multicellular species (Drosophila, Caenorhabditis), and regional mutation biases are found in yeast.

    Conclusions:

    • Silent sites are valuable indicators of both natural selection and mutational processes in genome evolution.
    • The influence of natural selection on codon usage is more widespread than previously thought, extending to some multicellular organisms.
    • Genomes exhibit regional variations in mutation patterns, impacting silent site evolution.