MBE Advance Access originally published online on November 28, 2007
Molecular Biology and Evolution 2008 25(2):339-351; doi:10.1093/molbev/msm259
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Research Articles |
Codon Usage in Mitochondrial Genomes: Distinguishing Context-Dependent Mutation from Translational Selection
Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
E-mail: higgsp{at}mcmaster.ca.
Accepted for publication November 6, 2007.
We analyze the frequencies of synonymous codons in animal mitochondrial genomes, focusing particularly on mammals and fish. The frequencies of bases at 4-fold degenerate sites are found to be strongly influenced by context-dependent mutation, which causes correlations between pairs of neighboring bases. There is a pattern of excess of certain dinucleotides and deficit of others that is consistent across large numbers of species, despite the wide variation of single-nucleotide frequencies among species. In many bacteria, translational selection is an important influence on codon usage. In order to test whether translational selection also plays a role in mitochondria, we need to control for context-dependent mutation. Selection for translational accuracy can be detected by comparison of codon usage in conserved and variable sites in the same genes. We give a test of this type that works in the presence of context-dependent mutation. There is very little evidence for translational accuracy selection in the mitochondrial genes considered here. Selection for translational efficiency might lead to preference for codons that match the limited repertoire of anticodons on the mitochondrial tRNAs. This is difficult to detect because the effect would usually be in the same direction in comparable to codon families and so would not cause an observable difference in codon usage between families. Several lines of evidence suggest that this type of selection is weak in most cases. However, we found several cases where unusual bases occur at the wobble position of the tRNA, and in these cases, some evidence for selection on codon usage was found. We discuss the way that these unusual cases are associated with codon reassignments in the mitochondrial genetic code.
Key Words: mitochondrial genomes • codon usage • context-dependent mutation • translational selection • genetic code • codon reassignment
Jeffrey Thorne, Associate Editor
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  P. G. Higgs and W. Ran Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage Mol. Biol. Evol., November 1, 2008; 25(11): 2279 - 2291. [Abstract] [Full Text] [PDF]
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