Integrated model of the protein molecular clock across mammalian species

One of the foundational concepts in molecular evolution is the protein molecular clock [1-3], encapsulating the observation that proteins tend to accumulate amino acid substitutions at approximately constant and protein-specific rates over long evolutionary timescales. According to the neutral theory of molecular evolution, the majority of protein substitutions have neutral or nearly neutral effects on species fitness. The neutral theory suggests the existence of a strong generation time effect, positing that species with shorter generation times should accumulate protein substitutions faster per unit time compared to species with longer generation times. However, earlier studies failed to detect a significant generation time effect for amino acid substitutions in vertebrates, raising questions about core tenets of the neutral theory. In this study, we take advantage of the recently accumulated evolutionary and genomics data to investigate the scaling of substitution rates with generation time among many dozens of mammalian species and thousands of proteins. Our findings reveal a strong generation time effect both for synonymous and non-synonymous substitutions. We demonstrate that the empirically observed generation time effect is fully consistent with several mechanisms, such as functional and mutation rate selection. Building on these results, we develop an integrated model of protein evolution that incorporates changes in substitution rates due to variation in species generation times throughout their evolutionary history. Overall, our analysis shows that protein evolution is consistent with neutral or nearly neutral theories and explains time-like behavior of the protein molecular clock across deep phylogenetic lineages.