Population genomics of rapid adaptation by soft selective sweeps

• There is mounting evidence that rapid adaptation often produces soft rather than hard selective sweeps.
• However, population genetic models typically assume mutation-limited scenarios and hard selective sweeps.
• We argue that this discrepancy reflects the confusion of two different definitions of the effective population size.

Organisms can often adapt surprisingly quickly to evolutionary challenges, such as the application of pesticides or antibiotics, suggesting an abundant supply of adaptive genetic variation. In these situations, adaptation should commonly produce ‘soft’ selective sweeps, where multiple adaptive alleles sweep through the population at the same time, either because the alleles were already present as standing genetic variation or arose independently by recurrent de novo mutations. Most well-known examples of rapid molecular adaptation indeed show signatures of such soft selective sweeps. Here, we review the current understanding of the mechanisms that produce soft sweeps and the approaches used for their identification in population genomic data. We argue that soft sweeps might be the dominant mode of adaptation in many species.