Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhabditis remanei

Area of Science:

• Evolutionary biology
• Genomics
• Molecular evolution

Background:

• Codon usage bias reflects selection for translational efficiency and mutational biases.
• Synonymous codons can confer fitness advantages, indicating natural selection.
• Understanding codon usage is crucial for interpreting genomic data.

Purpose of the Study:

• To quantify the magnitude of selection on synonymous codons in Caenorhabditis remanei.
• To investigate the correlation between ongoing selection and long-term codon usage bias.
• To determine if biased gene conversion influences codon usage patterns.

Main Methods:

• Fitting mutation-selection-drift equilibrium models to empirical codon frequency distributions.
• Analyzing nucleotide polymorphism data in genes and introns.
• Estimating selection intensity (N(e)s) on synonymous codons.

Main Results:

• Estimated selection intensity on synonymous codons in highly biased genes as N(e)s = 0.17.
• Demonstrated a strong correlation between ongoing selection and long-term codon usage bias.
• Ruled out biased gene conversion as a driver of observed patterns.

Conclusions:

• Coincident patterns of current and ancient selection shape biased codon usage in C. remanei.
• Adaptive codon usage is a subtle yet significant evolutionary force.
• Findings provide insights into the mechanisms of molecular evolution.