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Yamahira K, Kobayashi H, Kakioka R, Montenegro J, Masengi KWA, Okuda N, Nagano AJ, Tanaka R, Naruse K, Tatsumoto S, Go Y, Ansai S, Kusumi J. Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake. J Evol Biol 2023; 36:1484-1493. [PMID: 37737547 DOI: 10.1111/jeb.14223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/06/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023]
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.
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Affiliation(s)
- Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | | | - Noboru Okuda
- Research Center for Inland Seas, Kobe University, Kobe, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Japan
| | - Shoji Tatsumoto
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- Department of System Neuroscience, Division of Behavioral Development, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Japan
| | - Satoshi Ansai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
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2
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Flury JM, Meusemann K, Martin S, Hilgers L, Spanke T, Böhne A, Herder F, Mokodongan DF, Altmüller J, Wowor D, Misof B, Nolte AW, Schwarzer J. Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes. Genome Biol Evol 2023; 15:evad138. [PMID: 37493080 PMCID: PMC10465105 DOI: 10.1093/gbe/evad138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023] Open
Abstract
Transitions from no parental care to extensive care are costly and involve major changes in life history, behavior, and morphology. Nevertheless, in Sulawesi ricefishes, pelvic brooding evolved from transfer brooding in two distantly related lineages within the genera Adrianichthys and Oryzias, respectively. Females of pelvic brooding species carry their eggs attached to their belly until the fry hatches. Despite their phylogenetic distance, both pelvic brooding lineages share a set of external morphological traits. A recent study found no direct gene flow between pelvic brooding lineages, suggesting independent evolution of the derived reproductive strategy. Convergent evolution can, however, also rely on repeated sorting of preexisting variation of an admixed ancestral population, especially when subjected to similar external selection pressures. We thus used a multispecies coalescent model and D-statistics to identify gene-tree-species-tree incongruencies, to evaluate the evolution of pelvic brooding with respect to interspecific gene flow not only between pelvic brooding lineages but also between pelvic brooding lineages and other Sulawesi ricefish lineages. We found a general network-like evolution in Sulawesi ricefishes, and as previously reported, we detected no gene flow between the pelvic brooding lineages. Instead, we found hybridization between the ancestor of pelvic brooding Oryzias and the common ancestor of the Oryzias species from the Lake Poso area. We further detected signs of introgression within the confidence interval of a quantitative trait locus associated with pelvic brooding in O. eversi. Our results hint toward a contribution of ancient standing genetic variation to the evolution of pelvic brooding in Oryzias.
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Affiliation(s)
- Jana M Flury
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Karen Meusemann
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Sebastian Martin
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Leon Hilgers
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Tobias Spanke
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Astrid Böhne
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Fabian Herder
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Daniel F Mokodongan
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Cologne University, Cologne, Germany
| | - Daisy Wowor
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Bernhard Misof
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Arne W Nolte
- Department of Ecological Genomics, Carl von Ossietzky Universität, Oldenburg, Germany
| | - Julia Schwarzer
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
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3
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Mandagi IF, K A Sumarto B, Nuryadi H, Mokodongan DF, Lawelle SA, W A Masengi K, Nagano AJ, Kakioka R, Kitano J, Ansai S, Kusumi J, Yamahira K. Multiple colonizations and hybridization of a freshwater fish group on a satellite island of Sulawesi. Mol Phylogenet Evol 2023; 184:107804. [PMID: 37120113 DOI: 10.1016/j.ympev.2023.107804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Repeated colonizations and resultant hybridization may increase lineage diversity on an island if introgression occurs only in a portion of the indigenous island lineage. Therefore, to precisely understand how island biodiversity was shaped, it is essential to reconstruct the history of secondary colonization and resultant hybridization both in time and space. In this study, we reconstructed the history of multiple colonizations of the Oryzias woworae species group, a freshwater fish group of the family Adrianichthyidae, from Sulawesi Island to its southeast satellite island, Muna Island. Phylogenetic and species tree analyses using genome-wide single-nucleotide polymorphisms revealed that all local populations on Muna Island were monophyletic, but that there were several genetically distinct lineages within the island. Population structure and phylogenetic network analyses demonstrated that colonization of this island occurred more than once, and that secondary colonization and resultant introgressive hybridization occurred only in one local population on the island. The spatially heterogeneous introgression induced by the multiple colonizations were also supported by differential admixture analyses. In addition, the differential admixture analyses detected reverse colonization from Muna Island to the Sulawesi mainland. Coalescence-based demographic inference estimated that these mutual colonizations occurred during the middle to late Quaternary period, during which sea level repeatedly declined; this indicates that the colonizations occurred via land bridges. We conclude that these mutual colonizations between Muna Island and the Sulawesi mainland, and the resultant spatially heterogeneous introgression shaped the current biodiversity of this species group in this area.
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Affiliation(s)
- Ixchel F Mandagi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado 95115, Indonesia.
| | - Bayu K A Sumarto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Handung Nuryadi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Daniel F Mokodongan
- Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency, Cibinong 16911, Indonesia.
| | - Sjamsu A Lawelle
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia.
| | - Kawilarang W A Masengi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado 95115, Indonesia.
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan.
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka 819-0395, Japan.
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
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Yao Z, Long S, Wang C, Huang C, Zhang H, Jian L, Huang J, Guo Y, Dong Z, Wang Z. Population genetic characteristics of Hainan medaka with whole-genome resequencing. Front Genet 2022; 13:946006. [PMID: 36313474 PMCID: PMC9597887 DOI: 10.3389/fgene.2022.946006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022] Open
Abstract
The DMY gene is deleted in all males of the Sanya population (SY-medaka) of the Hainan medaka, Oryzias curvinotus, as recently reported by us. However, due to limited knowledge regarding their population genetic background, it is difficult to explore the possible evolutionary pathway. Herein, we resequenced the whole genome of four populations, including SY-medaka. A total of 56 mitogenomes and 32,826,105 SNPs were identified. We found that the genetic differentiation is highest between SY-medaka and the other populations. The results of the population history of the O. curvinotus suggest that the SY-medaka has been in a bottleneck period recently. Further analysis shows that SY-medaka are the most strongly affected by environmental selection. Moreover, we screened some potential genomic regions, and the genes contained in these regions may explain the potential mechanism of the selection process of the SY-medaka. In conclusion, our study can provide new clues for the adaptation process of medaka in the new environment of Sanya.
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Affiliation(s)
- Zebin Yao
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Shuisheng Long
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Chun Wang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Chengqin Huang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Hairui Zhang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Liao Jian
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jingru Huang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yusong Guo
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongdian Dong
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- *Correspondence: Zhongduo Wang,
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5
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Ansai S, Montenegro J, Masengi KWA, Nagano AJ, Yamahira K, Kitano J. Diversity of sex chromosomes in Sulawesian medaka fishes. J Evol Biol 2022; 35:1751-1764. [DOI: 10.1111/jeb.14076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/30/2022] [Accepted: 07/14/2022] [Indexed: 12/16/2022]
Affiliation(s)
- Satoshi Ansai
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
| | | | - Atsushi J. Nagano
- Faculty of Agriculture Ryukoku University Otsu Japan
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
| | - Jun Kitano
- Ecological Genetics Laboratory National Institute of Genetics Shizuoka Japan
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6
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Nofrianto AB, Lawelle SA, Mokodongan DF, Masengi KWA, Inomata N, Hashiguchi Y, Kitano J, Sumarto BKA, Kakioka R, Yamahira K. Ancient Admixture in Freshwater Halfbeaks of the Genus Nomorhamphus in Southeast Sulawesi. Zoolog Sci 2022; 39:453-458. [DOI: 10.2108/zs220023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Andy B. Nofrianto
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | - Sjamsu A. Lawelle
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | - Daniel F. Mokodongan
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | | | - Nobuyuki Inomata
- Department of Environmental Science, Fukuoka Women's University, Fukuoka 813-8529, Japan
| | - Yasuyuki Hashiguchi
- Department of Biology, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Bayu K. A. Sumarto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
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7
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Montenegro J, Fujimoto S, Ansai S, Nagano AJ, Sato M, Maeda Y, Tanaka R, Masengi KWA, Kimura R, Kitano J, Yamahira K. Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish. Mol Ecol 2022; 31:3798-3811. [PMID: 35638236 DOI: 10.1111/mec.16555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called "pelvic-fin brooding," wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved at least twice in two distant clades of the Adrianichthyidae. We investigated the genetic architecture of the evolution of this unique mode of reproduction. Morphological analyses and laboratory observations revealed that females of pelvic-fin brooders have longer pelvic fins and a deeper abdominal concavity, and that they can carry an egg clutch for longer than non-brooding adrianichthyids, suggesting that these traits play important roles in this reproductive mode. Quantitative trait locus mapping using a cross between a pelvic-fin brooder Oryzias eversi and a non-brooding O. dopingdopingensis reveals different traits involved in pelvic-fin brooding to be controlled by different loci on different chromosomes. Genomic analyses of admixture detected no signatures of introgression between two lineages with pelvic-fin brooders, indicating that introgression is unlikely to be responsible for repeated evolution of pelvic-fin brooding. These findings suggest that multiple independent mutations may have contributed to the convergent evolution of this novel mode of reproduction.
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Affiliation(s)
- Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Shingo Fujimoto
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.,Present address: Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masahiro Sato
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Yusuke Maeda
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | | | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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8
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Deeply divergent freshwater fish species within a single river system in central Sulawesi. Mol Phylogenet Evol 2022; 173:107519. [DOI: 10.1016/j.ympev.2022.107519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023]
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9
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Portinha B, Avril A, Bernasconi C, Helanterä H, Monaghan J, Seifert B, Sousa VC, Kulmuni J, Nouhaud P. Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges. Mol Ecol 2022; 31:3416-3431. [PMID: 35460311 PMCID: PMC9320829 DOI: 10.1111/mec.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole‐genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent‐based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (c. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration became negligible (2–19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.
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Affiliation(s)
- Beatriz Portinha
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,cE3c, Centre for Ecology, Evolution and Environmental changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, 1749-016, Lisboa, Portugal
| | - Amaury Avril
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | | | - Heikki Helanterä
- Ecology and Genetics research unit, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | | | | | - Vitor C Sousa
- cE3c, Centre for Ecology, Evolution and Environmental changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2, 1749-016, Lisboa, Portugal
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Pierre Nouhaud
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
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10
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Mandagi IF, Kakioka R, Montenegro J, Kobayashi H, Masengi KWA, Inomata N, Nagano AJ, Toyoda A, Ansai S, Matsunami M, Kimura R, Kitano J, Kusumi J, Yamahira K. Species divergence and repeated ancient hybridization in a Sulawesian lake system. J Evol Biol 2021; 34:1767-1780. [PMID: 34532915 DOI: 10.1111/jeb.13932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/09/2021] [Indexed: 01/02/2023]
Abstract
An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes; of these, one lake is inhabited by two species. Morphological and population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that these two sympatric species are phylogenetically sister to but substantially reproductively isolated from each other. Analyses of admixture and comparison of demographic models revealed that the two sympatric species experienced several substantial introgressions from outgroup populations that probably occurred soon after they had secondary contact with each other in the lake. However, the ratio of migrants from the outgroups was estimated to be different between the two species, which is consistent with the hypothesis that these introgressions aided their divergence or prevented them from forming a hybrid swarm. Repeated lake fragmentations and fusions may have promoted diversification of this freshwater fish species complex that is endemic to this ancient lake system.
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Affiliation(s)
- Ixchel F Mandagi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | | | - Nobuyuki Inomata
- Department of Environmental Science, Fukuoka Women's University, Fukuoka, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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11
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Kakioka R, Sutra N, Kobayashi H, Ansai S, Masengi KWA, Nagano AJ, Okuda N, Tanaka R, Sato M, Yamahira K. Resource partitioning is not coupled with assortative mating in sympatrically divergent ricefish in a Wallacean ancient lake. J Evol Biol 2021; 34:1133-1143. [PMID: 34077583 DOI: 10.1111/jeb.13874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 11/30/2022]
Abstract
Sympatric speciation is considered to be difficult without the coupling between ecological traits that allow resource partitioning and reproductive traits that allow assortative mating. Such "magic traits" are known to be involved in most of the compelling examples of sympatric speciation. In this study, we report a possible case of sympatric speciation without magic traits. Three species of ricefish (genus Oryzias) are suggested to have diverged sympatrically within Lake Poso, an ancient lake in Sulawesi. An analysis of genome-wide single-nucleotide polymorphisms showed that these three species are reproductively isolated from each other throughout the lake. Stable isotope analyses revealed that the three species use different food resources, which reflect differences in their feeding morphologies (gill rakers and digestive tracts) and feeding sites. Field and laboratory observations showed that O. nebulosus and O. orthognathus share a mating habitat of cobbles, where they scatter fertilized eggs, whereas this site is never used by O. nigrimas, indicating that assortative mating is partly achieved by spatial isolation. The small, less-adhesive eggs of O. nebulosus and O. orthognathus probably reflect their adaptation to spawning on cobble beaches. Laboratory mating experiments showed strong prezygotic isolation between O. nebulosus and O. orthognathus, which is achieved by strong species recognition presumably by both sexes based on species-specific mating dances and nuptial coloration. In summary, the assortative mating of O. nebulosus and O. orthognathus is probably not coupled to resource partitioning. We discussed how sympatric speciation among these species might have been achieved even without magic traits.
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Affiliation(s)
- Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Nobu Sutra
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | | | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Masahiro Sato
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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12
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Horoiwa M, Mandagi IF, Sutra N, Montenegro J, Tantu FY, Masengi KWA, Nagano AJ, Kusumi J, Yasuda N, Yamahira K. Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island. PLoS One 2021; 16:e0245316. [PMID: 34111145 PMCID: PMC8192020 DOI: 10.1371/journal.pone.0245316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals of Oryzias sarasinorum endemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes of O. eversi, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small fountain. In this study, we tested if this reflects ancient admixture of O. eversi and O. sarasinorum. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that O. eversi and O. sarasinorum are substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture from O. eversi to O. sarasinorum was more supported than the models assuming no admixture; this supported the idea that the O. eversi-like mitochondrial haplotype in O. sarasinorum was introgressed from O. eversi. This study is the first to demonstrate ancient admixture of lacustrine or pond organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.
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Affiliation(s)
- Mizuki Horoiwa
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ixchel F. Mandagi
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Nobu Sutra
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- Graduate School of Hasanuddin University, Makassar, Indonesia
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Fadly Y. Tantu
- Faculty of Animal Husbandry and Fisheries, Tadulako University, Palu, Indonesia
| | | | | | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Nina Yasuda
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail:
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13
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Ansai S, Mochida K, Fujimoto S, Mokodongan DF, Sumarto BKA, Masengi KWA, Hadiaty RK, Nagano AJ, Toyoda A, Naruse K, Yamahira K, Kitano J. Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes. Nat Commun 2021; 12:1350. [PMID: 33649298 PMCID: PMC7921647 DOI: 10.1038/s41467-021-21697-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Sexual selection drives rapid phenotypic diversification of mating traits. However, we know little about the causative genes underlying divergence in sexually selected traits. Here, we investigate the genetic basis of male mating trait diversification in the medaka fishes (genus Oryzias) from Sulawesi, Indonesia. Using linkage mapping, transcriptome analysis, and genome editing, we identify csf1 as a causative gene for red pectoral fins that are unique to male Oryzias woworae. A cis-regulatory mutation enables androgen-induced expression of csf1 in male fins. csf1-knockout males have reduced red coloration and require longer for mating, suggesting that coloration can contribute to male reproductive success. Contrary to expectations, non-red males are more attractive to a predatory fish than are red males. Our results demonstrate that integrating genomics with genome editing enables us to identify causative genes underlying sexually selected traits and provides a new avenue for testing theories of sexual selection.
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Affiliation(s)
- Satoshi Ansai
- grid.288127.60000 0004 0466 9350Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan ,grid.419396.00000 0004 0618 8593Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan ,grid.69566.3a0000 0001 2248 6943Present Address: Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi Japan
| | - Koji Mochida
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.26091.3c0000 0004 1936 9959Department of Biology, Keio University, Yokohama, Kanagawa, Japan
| | - Shingo Fujimoto
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.267625.20000 0001 0685 5104Present Address: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa Japan
| | - Daniel F. Mokodongan
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan ,grid.249566.a0000 0004 0644 6054Present Address: Museum Zoologicum Bogoriense (MZB), Zoology Division of Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Bayu Kreshna Adhitya Sumarto
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Kawilarang W. A. Masengi
- grid.412381.d0000 0001 0702 3254Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Renny K. Hadiaty
- grid.249566.a0000 0004 0644 6054Research Center for Biology, Indonesian Institute of Science (LIPI), Cibinong, Indonesia
| | - Atsushi J. Nagano
- grid.440926.d0000 0001 0744 5780Faculty of Agriculture, Ryukoku University, Ohtsu, Shiga, Japan
| | - Atsushi Toyoda
- grid.288127.60000 0004 0466 9350Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kiyoshi Naruse
- grid.419396.00000 0004 0618 8593Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kazunori Yamahira
- grid.267625.20000 0001 0685 5104Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Jun Kitano
- grid.288127.60000 0004 0466 9350Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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14
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Klotz W, von Rintelen T, Wowor D, Lukhaup C, von Rintelen K. Lake Poso's shrimp fauna revisited: the description of five new species of the genus Caridina (Crustacea, Decapoda, Atyidae) more than doubles the number of endemic lacustrine species. Zookeys 2021; 1009:81-122. [PMID: 33505196 PMCID: PMC7801368 DOI: 10.3897/zookeys.1009.54303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/20/2020] [Indexed: 11/12/2022] Open
Abstract
Lake Poso, an ancient lake system on the Indonesian island Sulawesi, harbours an endemic species flock of six, four lacustrine and two riverine species of the freshwater shrimp genus Caridina. In this study, five new lacustrine species are described, bringing the total to eleven species altogether. The number of lacustrine species is more than doubled to nine species compared to the last taxonomic revision in 2009. One of them, Caridina mayamareenae Klotz, Wowor & von Rintelen, sp. nov., even represents the first case of an atyid shrimp associated with freshwater snails which is morphologically adapted to living in shells. An integrative approach was used by providing a combination of morphological, ecological, and molecular data. Based on standard morphological characters, distribution, substrate preferences, and colouration of living specimens in the field, five distinct undescribed species could be distinguished. To support our species-hypothesis based on the mitochondrial genes 16S and COI, a molecular phylogeny was used for all eleven species from Lake Poso. All species form a well-supported monophyletic group, but only four morphospecies consistently correspond to mtDNA clades - a possible reason could be introgressive hybridisation, incomplete lineage sorting, or not yet fixed species boundaries. These results are discussed further in the context of adaptive radiation, which turned out to be more diverse than previously described. Finally, yet importantly, subjecting all new species to similar threats and to the same IUCN category and criterion than the previously described species from the lake is recommended.
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Affiliation(s)
- Werner Klotz
- Wiesenweg 1, A-6063 Rum, AustriaUnaffiliatedRumAustria
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, D-10115 Berlin, GermanyLeibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Daisy Wowor
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong 16911, IndonesiaResearch Center for Biology, Indonesian Institute of SciencesCibinongIndonesia
| | - Chris Lukhaup
- Waldstrasse 5a, D-66999 Hinterweidenthal, GermanyUnaffiliatedHinterweidenthalGermany
| | - Kristina von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, D-10115 Berlin, GermanyLeibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
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