Genetic introgression is a catalyst for diversification in an Old World fruit bat radiation

Genetic introgression, the exchange of genes between closely related species, was once thought to be rare and counterproductive to species differentiation until more recent evidence showed that introgression is pervasive in nature and may even facilitate the transfer of important functional traits among species. However, evidence for the role of introgression in facilitating speciation in natural systems is rare. In this study, we investigated the role of introgression in accelerating trait sharing and speciation in a poorly understood group of South and Southeast Asian fruit bats of the genus Cynopterus using genome-wide DNA from 93 individuals, including both fresh and historic museum specimens. We uncovered substantial new species level diversity within the genus and retrieved multiple strong signatures of complex genetic introgression, including two putative events of hybrid speciation within this radiation. In the genomic areas implicated in most of these introgression events, we identified a locus potentially linked to sperm integrity and fusion of egg and sperm. Further, we observed high between-species divergence in an area of the genome linked to skull development. The Cynopterus radiation augments a small but growing list of examples showing that genetic introgression - rather than forming an impediment against differentiation - is likely to boost and reinforce diversification processes, for example through the transfer of functional loci that may facilitate innovations. Our study also highlights the importance of museum collections in understanding cryptic diversity and speciation in complex biogeographic settings.