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Selection on codon usage in Drosophila americana
Xulio Maside1, Angela Weishan Lee, Brian Charlesworth
1Institute of Cell, Animal and Population Biology, University of Edinburgh, Kings Buildings, West Mains Road, EH9 3JT Edinburgh, UK. xulio.maside@ed.ac.uk
Current Biology : CB
|January 24, 2004
Summary
Synonymous codon usage bias in Drosophila is shaped by both natural selection and mutation. New estimates suggest selection intensity is compatible with observed codon bias levels, supporting evolutionary models.
Area of Science:
- Evolutionary biology
- Genomics
- Molecular evolution
Background:
- Synonymous codons are not randomly used, influencing genome base composition.
- The selection-mutation-drift model explains this bias via natural selection for preferred codons.
- Previous estimates of selection intensity in Drosophila were potentially inflated by demographic history.
Purpose of the Study:
- To investigate codon usage bias in three Drosophila virilis group species.
- To apply a novel method for estimating selection intensity on synonymous mutations.
- To reconcile observed codon bias with theoretical predictions.
Main Methods:
- Analysis of polymorphism and divergence patterns in 18 genes.
- Development and application of a new method to estimate selection intensity (N(e)s) using unpreferred mutation frequencies.
- Studying species less affected by confounding demographic effects.
Main Results:
- Estimated selection intensities (N(e)s) around 0.65, aligning with codon bias levels.
- Evidence supporting the combined roles of selection and mutational bias in codon usage.
- Indication of approximate equilibrium in codon usage and genome composition in the D. americana lineage.
Conclusions:
- The findings support the interplay of selection and mutation in driving codon usage bias.
- Codon usage patterns in the D. americana lineage appear to be in equilibrium.
- Biased gene conversion may also play a role in observed genomic patterns.