Frequent lineage-specific substitution rate changes support an episodic model for protein evolution.

Area of Science:

• Evolutionary biology
• Genomics
• Molecular evolution

Background:

• The molecular clock model assumes constant evolutionary rates for protein families.
• Anomalies are known, but genome-wide tests of this null model are scarce.
• Divergence rate comparisons in closely related species are crucial for accurate analysis.

Purpose of the Study:

• To systematically test the null model of constant protein evolution rates across a genome.
• To identify instances of lineage-specific acceleration and deceleration in protein divergence.
• To investigate the history of substitution rate changes in closely related species.

Main Methods:

• Generated a high-confidence dataset of syntenic orthologs from four ape species, including humans.
• Performed divergence rate comparisons to identify changes in substitution rates.
• Analyzed specific genes with high percentages of branch-specific substitutions.

Main Results:

• Despite an overall clock-like pattern, hundreds of protein families show dynamic, lineage-specific rate changes.
• Each lineage exhibits unique sets of fast-diverging proteins.
• Identified specific genes like ADCYAP1, CALU, SLC39A14, RNF128, and S100Z with high branch-specific substitutions.
• Observed potential biased mutation processes in genes like ADCYAP1.

Conclusions:

• The assumption of constant evolutionary rates is problematic for many proteins.
• Protein evolution is more dynamic and episodic than often assumed, even in closely related lineages.
• Future evolutionary trajectory predictions should account for these dynamic rate changes.