Polygenic adaptation after a sudden change in environment

Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Importantly, we describe the two phases of the allele dynamics: a rapid phase in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, which ultimately lead to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, our key results should hold in more general settings, and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.