Figure 3. A cartoon of allele dynamics.

We divide the allele dynamics into rapid and equilibration phases, based on the rate of phenotypic change, and consider the trajectories of alleles with opposing effects of the same magnitude, which start at the same initial minor frequency. During the rapid phase, alleles whose effects align with the shift slightly increase in frequency relative to those with opposing effects. During the equilibration phase, this frequency difference can increase further and eventually leads aligned alleles to fix with slightly greater probabilities than opposing ones.