Contrast and Genomic Characterisation of Ancient and Recent Interspecific Introgression Between Deeply Diverged Moustache Toads (Leptobrachium)

ABSTRACT Recent genomic analyses have provided new insights into the process of interspecific introgression and its consequences on species evolution. Most recent studies, however, focused on hybridization between recently radiated species, with few examining the genomic outcomes of ancient hybridization across deeply diverged species. Using whole genome data of moustache toads ( Leptobrachium ), we identified signals of three hybridization events among nine species that diverged at the Eocene. An ancient introgression from L. leishanense to the ancestral branch (C1) of L. liui introduced adaptive variants. The highly introgressed regions include genes with important functions in odorant detection and immune responses. These genes are preserved in all three descendent populations of L. liui _C1, and these regions likely have been positively selected over a long filtering process. A recent introgression occurred from L. huashen to L. tengchongense , with the introgressed regions being mostly neutral. Furthermore, one F1 hybrid individual was detected between sympatric L. ailaonicum and L. promustache . The signals of introgression largely disappeared after removing the hybrid individual, indicating an occasional hybridization but minimal introgression. Further examination of highly divergent but low introgressed genomic regions revealed both pre‐mating isolation and genetic incompatibility as potential mechanisms of resisting introgression and maintaining species boundaries. Additionally, no large X‐effect was found in these introgression events. Hybridization between deeply diverged amphibian species may be common, but detectable introgressions are likely less so, with recent introgression being mostly neutral and the rare ancient one potentially adaptive. Our findings complement recent genomic work, and together they provide a better understanding of the genomic characteristics of interspecific introgression and its significance in species adaptation and evolution.