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Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake |
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| Authors: | Kazunori Yamahira Hirozumi Kobayashi Ryo Kakioka Javier Montenegro Kawilarang W A Masengi Noboru Okuda Atsushi J Nagano Rieko Tanaka Kiyoshi Naruse Shoji Tatsumoto Yasuhiro Go Satoshi Ansai Junko Kusumi |
| Institution: | 1. Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan;2. Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
Contribution: Conceptualization (supporting), Formal analysis (supporting), ?Investigation (equal);3. Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan Contribution: ?Investigation (equal);4. Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia Contribution: ?Investigation (equal), Project administration (equal);5. Research Center for Inland Seas, Kobe University, Kobe, Japan Contribution: ?Investigation (equal), Writing - original draft (supporting);6. Faculty of Agriculture, Ryukoku University, Otsu, Japan Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan Contribution: ?Investigation (equal);7. World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan Contribution: ?Investigation (equal);8. Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Japan Contribution: ?Investigation (equal);9. Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan Contribution: Formal analysis (equal);10. Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan;11. Graduate School of Agriculture, Kyoto University, Kyoto, Japan Contribution: Formal analysis (supporting), ?Investigation (equal), Writing - original draft (supporting);12. Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan |
| 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 Adrianichthys in 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. oophorus and A. poptae, but the large time-lag between their divergence and ghost introgression indicates that the contribution of introgression may be restricted. |
| Keywords: | demography extinct lineage introgressive hybridization reproductive isolation secondary contact Sulawesi |