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

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  • Yamahira, Kazunori
    Tropical Biosphere Research Center University of the Ryukyus
  • Kobayashi, Hirozumi
    Tropical Biosphere Research Center University of the Ryukyus
  • Kakioka, Ryo
    Tropical Biosphere Research Center University of the Ryukyus
  • Montenegro, Javier
    Tropical Biosphere Research Center University of the Ryukyus
  • Masengi, Kawilarang W. A.
    Faculty of Fisheries and Marine Science Sam Ratulangi University Manado
  • Okuda, Noboru
    Research Center for Inland Seas Kobe University
  • Nagano, Atsushi J.
    Institute for Advanced Biosciences Keio University Faculty of Agriculture Ryukoku University
  • Tanaka, Rieko
    World Medaka Aquarium Nagoya Higashiyama Zoo and Botanical Gardens
  • Naruse, Kiyoshi
    Laboratory of Bioresources National Institute for Basic Biology
  • Tatsumoto, Shoji
    Exploratory Research Center on Life and Living Systems (ExCELLS) National Institutes of Natural Sciences
  • Go, Yasuhiro
    Exploratory Research Center on Life and Living Systems (ExCELLS) National Institutes of Natural Sciences School of Life Science The Graduate University for Advanced Studies (SOKENDAI)
  • Ansai, Satoshi
    Graduate School of Agriculture Kyoto University
  • Kusumi, Junko
    Faculty of Social and Cultural Studies Kyushu University

Description

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.

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