The evolution of codon preferences in Drosophila: a maximum-likelihood approach to parameter estimation and...

Area of Science:

• Evolutionary biology
• Population genetics
• Molecular evolution

Background:

• Synonymous codon usage varies across species due to mutation bias, selection efficiency, and codon preferences.
• Understanding these variations is key to deciphering evolutionary dynamics at the molecular level.

Purpose of the Study:

• To develop and apply a maximum-likelihood method using population genetic models to analyze the evolution of codon usage parameters.
• To investigate differences in codon usage selection between D. melanogaster and D. virilis.

Main Methods:

• Developed a maximum-likelihood method incorporating explicit population genetic models.
• Applied the method to analyze twofold degenerate amino acids in 50 orthologous genes from D. melanogaster and D. virilis.

Main Results:

• D. virilis exhibits significantly reduced selection on codon usage compared to D. melanogaster.
• Selection strength on codon usage differs across amino acids, with cysteine showing distinct patterns in both species.
• The data suggest shifts in codon preference, not just a uniform difference in selection strength (effective population size, Ne).

Conclusions:

• Codon usage evolution is shaped by complex interactions between mutation bias and varying selection pressures.
• Cysteine codons may experience dual selection pressures for translational efficiency and accuracy.
• While selection coefficients are correlated between orthologous genes, significant deviations indicate gene-specific evolutionary trajectories.