Variation in synonymous codon use and DNA polymorphism within the Drosophila genome

Area of Science:

• Evolutionary biology
• Genomics
• Molecular evolution

Background:

• A negative correlation exists between amino acid substitution rates and codon usage bias in Drosophila.
• This correlation is hypothesized to result from interference between positive selection on protein sequences and weak selection on codon usage.

Purpose of the Study:

• To investigate polymorphism and divergence at synonymous, nonsynonymous, and intronic sites in relation to codon bias.
• To determine the relative contributions of protein evolution and local interference (genetic draft) to codon bias variation.

Main Methods:

• Analysis of polymorphism and divergence data in Drosophila melanogaster and Drosophila simulans.
• Comparison of variation patterns across synonymous, nonsynonymous, and intronic sites.
• Assessment of correlation between genetic variation, recombination rates, and codon usage bias.

Main Results:

• Protein evolution significantly explains codon bias variation (r² ≈ 40%).
• Synonymous and intronic diversities did not significantly covary with codon bias or protein evolution.
• Polymorphism levels decreased in low recombination regions, but codon bias did not.
• Nonsynonymous diversities were correlated across species, but synonymous and intronic diversities were not.

Conclusions:

• Selective constraint on proteins is a stable factor in gene evolution, whereas local interference (genetic draft) is unstable.
• Genetic draft appears to be a minor determinant of codon bias variance.
• Selective constraints for optimal codon usage are likely correlated with selective constraints on the protein, both within and between genes.