The persistence and loss of hard selective sweeps amid ancient human admixture.

The extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift, and fluctuations in selection pressures remains unknown. Understanding which loci are particularly resilient to such forces may shed light on the traits that were important for humans throughout multiple time periods. Yet, detecting ancient selection events is challenging from modern and ancient DNA due to the data and/or signal being severely degraded. Here we use a domain-adaptive neural network (DANN) trained on simulated data and applied to ancient and modern DNA for sweep detection. We show that the DANN can account for simulation misspecification, or discrepancies between the simulations and real aDNA, thereby improving the ability to detect sweeps in real data. Application of the DANN to more than 800 ancient and modern human genomes spanning the last 7000 years recovered 16 known sweeps at loci including