Data from: Ancient and recent hybridization in the Oreochromis cichlid fishes

Cichlid fishes of the genus Oreochromis (tilapia) are among the most
important fish for inland capture fisheries and global aquaculture.
Deliberate introductions of non-native species for fisheries improvement
and accidental escapees from farms have resulted in admixture with
indigenous species. Such hybridization may be detrimental to native
biodiversity, potentially leading to genomic homogenization of populations
and the loss of important genetic material associated with local
adaptation. By contrast, introgression may fuel diversification when
combined with ecological opportunity, by supplying novel genetic
combinations. To date, the role of introgression in the evolutionary
history of tilapia has not been explored. Here we studied both ancient and
recent hybridization in tilapia, using whole genome resequencing of 575
individuals from 23 species. We focused on Tanzania, a natural hotspot of
tilapia diversity, and a country where hybridization between exotic and
native species in the natural environment has been previously reported. We
reconstruct the first genome-scale phylogeny of the genus and reveal
prevalent ancient gene flow across the Oreochromis phylogeny. This has
likely resulted in hybrid speciation of one species, O. chungruruensis. We
identify multiple cases of recent hybridization between native and
introduced species in the wild, linked to the use of non-native species in
both capture fisheries improvement and aquaculture. This has potential
implications for both conservation of wild populations and the development
of the global tilapia aquaculture industry.