Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales

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Abstract
Recent empirical studies of taxa including humans, fish, and birds have shown elevated rates of molecular evolution between species that diverged recently. Using the Moran model, we calculate expected divergence as a function of time. Our findings suggest that the observed phenomenon of elevated rates at short timescales is consistent with standard population genetics theory. The apparent acceleration of the molecular clock at short timescales can be explained by segregating polymorphisms present at the time of the ancestral population, both neutral and slightly deleterious, and not newly arising slightly deleterious mutations as has been previously hypothesized. Our work also suggests that the duration of the rate elevation depends on the effective population size, providing a method to correct time estimates of recent divergence events. Our model concords with estimates of divergence obtained from African cichlid fish and humans. As an additional application of our model, we calculate that Ka/Ks is elevated within a population before decaying slowly to its long-term value. Similar to the molecular clock, the duration and magnitude of Ka/Ks elevation depend on the effective population size. Unlike the molecular clock, however, Ka/Ks elevation is caused by newly arising slightly deleterious mutations. This elevation, although not as severe in magnitude as had been previously predicted in models neglecting ancestral polymorphism, persists slightly longer.