Localised admixture triggers parallel adaptation in a coral species trio on the Great Barrier Reef

Abstract Hybridisation can shape evolutionary trajectories and fuel rapid adaptation. Yet, whether adaptive introgression repeatedly reconfigures genomes in predictable ways remains largely unknown. Here, we show that three-way admixture drives repeatable parallel differentiation in reef-building corals in the Acropora hyacinthus species complex. Adaptive introgression is confined to the southern Great Barrier Reef, where admixture timing coincides with a recent breakdown in species barriers despite limited historical gene flow. Genome-wide introgression is characterised by numerous shared minor-parent ancestry peaks that are enriched for stress-response genes and under positive selection for parallel adaptive admixture. Our results demonstrate that introgressive hybridisation can be geographically restricted between sympatric marine species and can promote repeated rapid adaptation that transcends species boundaries.