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 by selection for particular codons that are more efficiently and/or accurately translated by the most abundant tRNAs; c odon usage across the genome, and the abundance of different tRNA spec ies, are highly co-adapted. Second, in the absence of selection, silen t sites reveal underlying mutational patterns. Codon usage varies enor mously among human genes, and yet silent sites do not appear to be inf luenced by natural selection, suggesting that mutation patterns vary a mong regions of the genome. At 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 Caenorhabdit is), and that regional variations in mutation biases occur in yeast. S ilent sites (in serine codons) also provide evidence for mutational ev ents changing adjacent nucleotides simultaneously.