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Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake

Yamahira, Kazunori1; Kobayashi, Hirozumi1; Kakioka, Ryo1; Montenegro, Javier1; Masengi, Kawilarang2; Okuda, Noboru3; Nagano, Atsushi4; Tanaka, Rieko5; Naruse, Kiyoshi6; Tatsumoto, Shoji7; Go, Yasuhiro7; Ansai, Satoshi8; Kusumi, Junko9

Published Aug 23, 2023; Updated Sep 05, 2023 on Dryad. https://doi.org/10.5061/dryad.qbzkh18pb

Data files

Aug 23, 2023 version files 308.18 MB
Sep 05, 2023 version files 308.20 MB

Abstract

Because speciation might have been promoted by ancient introgression from an extinct lineage, it is important to detect the existence of “ghost introgression” in focal taxa and examine its contribution to their diversification. In this study, we examined possible ghost introgression and its contributions to the diversification of ricefishes of the genus Adrianichthysin Lake Poso, an ancient lake on Sulawesi Island, in which some extinctions are known to have occurred. Population genomic analysis revealed that two extant Adrianichthys species, A. oophorus and A. poptae, are reproductively isolated from each other. Comparisons of demographic models demonstrated that introgression from a ghost population, which diverged from the common ancestor of A. oophorus and A. poptae, is essential for reconstructing the demographic history of Adrianichthys. The best model estimated that the divergence of the ghost population greatly predated the divergence between A. oophorus and A. poptae, and that the ghost population secondarily contacted the two extant species within Lake Poso more recently. Genome scans and simulations detected a greatly divergent locus, which cannot be explained without ghost introgression. This locus was also completely segregated between A. oophorus and A. poptae. These findings suggest that variants that came from a ghost population have contributed to the divergence between A. oophorusand A. poptae, but the large time-lag between their divergence and ghost introgression indicates that the contribution of introgression may be restricted.