Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria.

Area of Science:

• Evolutionary Biology
• Genomics
• Molecular Biology

Background:

• Synonymous codon substitutions are traditionally assumed to be selectively neutral.
• However, codon usage patterns suggest some synonymous substitutions are under selection.
• Previous analyses often overlook the complexity of selection acting on synonymous sites.

Purpose of the Study:

• To develop a new model for estimating substitution rates that accounts for multiple classes of synonymous substitutions.
• To re-evaluate the impact of selection on codon usage bias in bacterial genomes.
• To investigate the strength of selection required to explain observed codon bias patterns.

Main Methods:

• Analysis of codon usage in 13 bacterial genomes from the Enterobacterales order.
• Development of a flexible multiclass synonymous substitution (MSS) model.
• Comparison of substitution rates estimated by the MSS model versus the standard codon model.

Main Results:

• The MSS model, which distinguishes between neutral and selected synonymous substitutions, yielded lower estimates of omega (ω) compared to the standard model.
• On average, omega (ω) values were 80% lower under the MSS model.
• Observed reductions in synonymous substitution rates can be explained by very weak selection (low Ne*s).

Conclusions:

• Conventional omega (ω) analyses may overestimate positive diversifying selection and underestimate purifying selection.
• Codon usage bias is influenced by weak selection, not solely by mutation bias or neutral processes.
• The findings necessitate a refinement of evolutionary models to accurately assess selection pressures on synonymous sites.