A simple method for estimating the intensity of purifying selection in protein-coding genes

Area of Science:

• Evolutionary Biology
• Molecular Evolution
• Genetics

Background:

• Estimating the intensity of purifying selection is crucial for understanding molecular evolution.
• Previous methods often struggle to disentangle the effects of mutation rate from selective pressures.
• Processed pseudogenes offer a unique window into neutral mutation accumulation.

Purpose of the Study:

• To propose and validate a novel method for quantifying purifying selection intensity.
• To compare purifying selection across different codon positions and between species (humans and murids).
• To investigate the role of purifying selection in driving evolutionary rate differences.

Main Methods:

• Utilized three aligned homologous sequences: a processed pseudogene (psi), a functional paralog (g), and a functional ortholog (o).
• Calculated nucleotide substitution rates (K psi and K(g)) along pseudogene and functional gene branches.
• Derived the fraction of neutral mutations (fg) as K(g)/K psi, with 1-fg representing purifying selection intensity.

Main Results:

• The K(g)/K psi ratio effectively estimates purifying selection intensity, separating it from mutation rate effects.
• Purifying selection is strongest at the second codon position and weakest at the third.
• A substantial fraction of third codon positions (synonymous sites) are under selective constraint (41-42% neutral).
• Significant variation in selection intensity was observed between orthologous genes in humans and murids.
• No statistically significant overall difference in purifying selection intensity was found between humans and murids.

Conclusions:

• The proposed method accurately estimates purifying selection intensity.
• Synonymous mutations are under considerable selective constraint, challenging the notion of complete neutrality.
• Purifying selection does not appear to be a major driver of evolutionary rate differences between humans and murids.