DNA Sequence Evolution: The Sounds of Silence

Silent sites (positions that can undergo synonymous substitutions) in protein-coding genes can illuminate two evolutionary processes. First, despite being silent, they may be subject to natural selection. Among eukaryotes this is exemplified by yeast, where synonymous codon usage patterns are shaped...

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Published inPhilosophical transactions of the Royal Society of London. Series B. Biological sciences Vol. 349; no. 1329; pp. 241 - 247
Main Authors Sharp, Paul M., Averof, Michalis, Lloyd, Andrew T., Matassi, Giorgio, Peden, John F.
Format Journal Article
LanguageEnglish
Published London The Royal Society 29.09.1995
Subjects
Animals
Base Sequence
Chromosomes
Codon
Codons
DNA
Drosophila
Drosophila - genetics
Evolution
Evolution, Molecular
Genes
Genetic mutation
Genetic Variation
Genome
Genomes
Humans
Mammals - genetics
Models, Genetic
Molecular Sequence Data
Mutation
Natural selection
Nucleotide sequences
Saccharomyces cerevisiae - genetics
Selection, Genetic
Yeasts
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Summary:Silent sites (positions that can undergo synonymous substitutions) in protein-coding genes can illuminate two evolutionary processes. First, despite being silent, they may be subject to natural selection. Among eukaryotes this is exemplified by yeast, where synonymous codon usage patterns are shaped by selection for particular codons that are more efficiently and/or accurately translated by the most abundant tRNAs; codon usage across the genome, and the abundance of different tRNA species, are highly co-adapted. Second, in the absence of selection, silent sites reveal underlying mutational patterns. Codon usage varies enormously among human genes, and yet silent sites do not appear to be influenced by natural selection, suggesting that mutation patterns vary among regions of the genome. As first, the yeast and human genomes were thought to reflect a dichotomy between unicellular and multicellular organisms. However, it now appears that natural selection shapes codon usage in some multicellular species (e.g. Drosophila and Caenorhabditis), and that regional variations in mutation biases occur in yeast. Silent sites (in serine codons) also provide evidence for mutational events changing adjacent nucleotides simultaneously.
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ISSN:0962-8436
1471-2970
DOI:10.1098/rstb.1995.0108