Hybrid Drosophila genomes rapidly purge minority ancestry but repeatedly retain selected regions
Hybridization is increasingly recognized as a widespread evolutionary process across animals, plants, and fungi, and plays a key role in driving speciation, shaping genetic diversity, and facilitating adaptation. Initial hybrid genomes are rarely observed empirically, making it challenging to observe in real time how competing forces like purifying selection and adaptive introgression interact to shape post-hybridization genomes. Here, we use replicated experimental hybrid populations between Drosophila simulans and D. sechellia to track directly genome-wide evolutionary dynamics across approximately 45 generations post-hybridization. We show that hybrid populations with primarily D. simulans ancestry rapidly recover wild-type levels of fertility and fecundity, whereas populations carrying predominantly D. sechellia ancestry experience persistent fitness reductions and frequent extinction. Genome-wide ancestry trajectories show pervasive purifying selection against minority-ancestry alleles, leading to rapid regression toward majority ancestry across the genome, with stronger purging on the X chromosome than autosomes. Following the initial purging, neutral minority ancestry stabilized at low frequencies across the genome. In striking contrast, we observe repeated increases in D. sechellia ancestry on chromosome 4 and multiple regions on chromosome 3R within D. simulans-majority populations, providing evidence for adaptive introgression. High-density sequencing revealed that these regions were repeatedly retained across independently evolving populations despite near-complete genome-wide purging. Simulations support a model in which recombination rapidly uncouples beneficial introgressed alleles from linked incompatibility-associated alleles during the initial generations, allowing positive selection to act. Our temporal allele-frequency analyses suggest that hybrid genome stabilization of the introgressed regions is highly repeatable but not identical, yielding parallel outcomes across replicate populations. We establish a tractable experimental framework to directly observe how hybrid genomes reorganize in real time, and demonstrate how purifying selection, positive selection, recombination, and stochastic processes interact to restructure hybrid genomes shortly after admixture.