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Analysis of a shift in codon usage in Drosophila
Jeffrey R Powell1, Erminia Sezzi, Etsuko N Moriyama
1Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA. jeffrey.powell@yale.edu
Journal of Molecular Evolution
|March 11, 2004
Summary
A shift in codon usage in the Drosophila willistoni lineage is ancient and stable, predating species diversification. This codon bias is likely due to changes in transfer RNA abundance, not mutation bias or selection pressures.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Evolution
Background:
- Codon usage bias is a known phenomenon in Drosophila melanogaster.
- Previous observations indicated a distinct codon usage pattern in Drosophila willistoni.
Purpose of the Study:
- To investigate the evolutionary history and underlying mechanisms of codon usage shift in the Drosophila willistoni lineage.
- To compare codon usage patterns across six species within the willistoni and saltans groups.
Main Methods:
- Analysis of seven genes from six species within the willistoni/saltans lineage.
- Sequencing of genes obtained from GenBank or newly generated.
- Examination of introns and G/C composition at four-fold degenerate sites.
Main Results:
- All studied species showed significant codon usage differences compared to D. melanogaster.
- Codon usage is homogeneous within the willistoni/saltans lineage, indicating an ancient shift.
- Little evidence for altered mutation bias or sufficiency of relaxed selection/reduced recombination.
Conclusions:
- The codon usage shift in the D. willistoni lineage is ancient (approx. 20 million years old) and stable.
- Changes in isoaccepting tRNA abundance are a plausible explanation for the observed codon bias.
- The pattern may represent a "frozen accident" rather than an adaptive evolutionary change.