The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis

Area of Science:

• Evolutionary biology
• Genomics
• Molecular evolution

Background:

• Genomic data reveals substitution rate variation across genomes and lineages.
• The pacemaker model suggests proportionality constants in evolutionary tree branch lengths due to lineage effects.
• Previous studies on the pacemaker hypothesis yielded contrasting results across different clades.

Purpose of the Study:

• To evaluate the pacemaker hypothesis for the first time in all great apes (hominids).
• To investigate whether evolutionary rates in hominids conform to a pacemaker model, considering gene tree/species tree discordance.

Main Methods:

• Substitution rates were estimated using a calibration-free approach, the relative rate framework.
• Pacemakers were inferred while accounting for gene tree/species tree discordance.
• Evolutionary rates were analyzed across genomic regions in great apes.

Main Results:

• A large pacemaker was identified in great apes, encompassing most hominid genomic regions, indicating a predominant evolutionary trend.
• The majority of genes exhibited evolutionary paces closely aligned with a strict molecular clock.
• Slight decreases in evolutionary rates were detected in internal branches leading to humans, supporting the hominoid slowdown hypothesis.

Conclusions:

• The study provides evidence for a predominant evolutionary pacemaker across most genomic regions in great apes.
• While most genes adhere to a molecular clock, a notable slowdown occurred in human lineages.
• Life history traits are suggested as the primary drivers of substitution rate variation across the great ape genome.