Data from: Widespread hybridisation and bi-directional introgression in sympatric species of coral reef fish

Coral reefs are highly diverse ecosystems, where numerous closely related species often co-exist. How new species arise and are maintained in these high gene flow environments have been long-standing conundrums. Hybridisation and patterns of introgression between sympatric species provides a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridisation between two closely related species of coral reef fish: the common coral trout (Plectropomus leopardus) and the bar-cheek coral trout (Plectropomus maculatus). Using a complementary set of 25 microsatellite loci, we distinguish pure genotype classes from first- and later-generation hybrids. We provide the first evidence of extensive hybridisation between two co-occurring coral reef species within their common geographic range, identifying 124 interspecific hybrids from a collection of almost three thousand coral trout sampled in the southern Great Barrier Reef. Hybrid individuals were ubiquitous among reefs, fertile and spanned multiple generations. To explore the extent of genomic introgression, we constructed a ddRAD library of pure and hybrid classes, which recovered 2,271 SNP loci. An analysis of genomic clines indicates that genome-wide introgression has occurred with selection favouring both pure and hybrid genotypes. Our results show that hybridisation can occur among closely related species with common geographic ranges, and not just at biogeographic boundaries. We suggest that both evolutionary and ecological processes may act to maintain species barriers despite on-going introgression.