Is genetic diversity needed for species survival? Genomic analysis of a "long-lived heavy smoker"

• Project/Area Number: 17H03629
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Conservation of biological resources
• Research Institution: Fisheries Research and Education Agency
• Principal Investigator: Takahashi Hiroshi 国立研究開発法人水産研究・教育機構, 水産大学校, 准教授 (90399650)
• Co-Investigator(Kenkyū-buntansha): 中山 耕至 京都大学, 農学研究科, 助教 (50324661) ; 竹下 直彦 国立研究開発法人水産研究・教育機構, 水産大学校, 教授 (50399664) ; 武島 弘彦 総合地球環境学研究所, 研究部, 外来研究員 (50573086) ; 橋口 康之 大阪医科大学, 医学部, 講師 (70436517) ; 田上 英明 国立研究開発法人水産研究・教育機構, 水産大学校, 助教 (40601084)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000); Fiscal Year 2019: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2018: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000); Fiscal Year 2017: ¥7,930,000 (Direct Cost: ¥6,100,000、Indirect Cost: ¥1,830,000)
• Keywords: 保全生物 / 遺伝的多様性 / 保全遺伝学 / ゲノム分析

Outline of Final Research Achievements

Genetic diversity within a species is considered essential for species survival. In this study, we performed a genome analysis of a teleost fish (Lates japonicus) that has survived for a long period of time, despite having the lowest level of genetic diversity. Although genomic data showed that the genetic diversity of this species is the lowest among the vertebrates whose whole genome sequences are available at present, it became clear that some genome regions show high heterozygosity. The presence of such regions we examined suggests that it has been maintained by natural selection.

Academic Significance and Societal Importance of the Research Achievements

本研究では，アカメのゲノム全体の遺伝的多様性は現在ゲノムが解読されている脊椎動物種中最も低いこと，その一方で一部のゲノム領域において選択圧により遺伝的多様性が維持されていることが示され，遺伝的多様性が低いにもかかわらず長期間存続できたメカニズムの一端が解明された。遺伝的多様性は種の存続に必要か？という進化生物学や保全遺伝学の本質的問いに対して，中立的遺伝マーカーで捉えられるゲノム全体の遺伝的多様性がほぼ失われた種の詳細な全ゲノム分析から一定の答えを導き出した。

Research Products

• [Journal Article] Ecosystem size predicts the probability of speciation in migratory freshwater fish (2020)
  • Author(s): Yamasaki Yo Y.、Takeshima Hirohiko、Kano Yuichi、Oseko Naoharu、Suzuki Toshiyuki、Nishida Mutsumi、Watanabe Katsutoshi
  • Journal Title: Molecular Ecology Volume: － Issue: 16 Pages: 3071-3083
  • DOI: 10.1111/mec.15415
  • NAID: 120006843524
  • Peer Reviewed
• [Journal Article] A key metabolic gene for recurrent freshwater colonization and radiation in fishes (2019)
  • Author(s): Ishikawa Asano, Kabeya Naoki, Ikeya Koki, Kakioka Ryo, Cech Jennifer N., Osada Naoki, Leal Miguel C., Inoue Jun, Kume Manabu, Toyoda Atsushi, Tezuka Ayumi, Nagano Atsushi J., Yamasaki Yo Y., Suzuki Yuto, Kokita Tomoyuki, Takahashi Hiroshi et al.
  • Journal Title: Science Volume: 364 Issue: 6443 Pages: 886-889
  • DOI: 10.1126/science.aau5656
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Host selection and ovipositor length in eight sympatric species of sculpins that deposit their eggs into tunicates or sponges (2019)
  • Author(s): Awata Satoshi, Sasaki Haruka, Goto Tomohito, Koya Yasunori, Takeshima Hirohiko, Yamazaki Aya, Munehara Hiroyuki
  • Journal Title: Marine Biology Volume: 166 Issue: 5 Pages: 59-59
  • DOI: 10.1007/s00227-019-3506-4
  • NAID: 120006847758
  • Peer Reviewed / Open Access
• [Journal Article] Trace of outbreeding between Biwa salmon (Oncorhynchus masou subsp.) and amago (O. m. ishikawae) detected from the upper reaches of inlet streams within Lake Biwa water system, Japan (2018)
  • Author(s): Kuwahara Masayuki、Takahashi Hiroshi、Kikko Takeshi、Kurumi Seiji、Iguchi Kei’ichiro
  • Journal Title: Ichthyological Research Volume: 66 Issue: 1 Pages: 67-78
  • DOI: 10.1007/s10228-018-0650-7
  • NAID: 40021806350
  • Peer Reviewed
• [Journal Article] Tetrodotoxin distribution in natural hybrids between the pufferfish species Takifugu rubripes and Takifugu porphyreus (2018)
  • Author(s): Tatsuno Ryohei、Miyata Yumi、Yoshikawa Hiroyuki、Ino Yasuko、Fukuda Tsubasa、Furushita Manabu、Takahashi Hiroshi
  • Journal Title: Fisheries Science Volume: 85 Issue: 1 Pages: 237-245
  • DOI: 10.1007/s12562-018-1265-7
  • NAID: 40021782131
  • Peer Reviewed
• [Journal Article] Extra-pair paternity in socially monogamous Streaked Shearwaters: forced copulation or female solicitation? (2018)
  • Author(s): Sakao Miho、Takeshima Hirohiko、Inoue Koji、Sato Katsufumi
  • Journal Title: Journal of Ornithology Volume: 160 Issue: 1 Pages: 137-144
  • DOI: 10.1007/s10336-018-1587-3
  • Peer Reviewed
• [Journal Article] Next-generation sequencing analysis of multiplex families with atypical psychosis. (2018)
  • Author(s): Okayama T, Hashiguchi Y, Kikuyama H, Yoneda H, Kanazawa T.
  • Journal Title: Translational Psychiatry Volume: Oct 15;8(1):221 Issue: 1
  • DOI: 10.1038/s41398-018-0272-x
  • Peer Reviewed / Open Access
• [Journal Article] Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group (Teleostei: Adrianichthyidae) (2018)
  • Author(s): Mokodongan DF, Montenegro J, Mochida K, Fujimoto S, Ishikawa A, Kakioka R, Yong L, Mulis, Hadiaty RK, Mandagi IF, Masengi WA, Wachi N, Hashiguchi Y, Kitano J, Yamahira K
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 118 Pages: 194-203
  • DOI: 10.1016/j.ympev.2017.10.005
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Cryptic genetic divergence in Scolopsis taenioptera (Perciformes: Nemipteridae) in the western Pacific Ocean. (2018)
  • Author(s): Kakioka, R, N. Muto, H. Takeshima, AC. Gaje, RS. Cruz, UB. Alama, AMT. Guzman, RFM. Traifalgar, RP. Babaran, O. Muda, WM. Arshaad, S. Arnupapboon, K. Phuttharaksa, QV. Nguyen, TT. Pham, H. Motomura, F. Muto, S. Ishikawa.
  • Journal Title: Ichthyological Research Volume: 65 Issue: 1 Pages: 92-100
  • DOI: 10.1007/s10228-017-0596-1
  • NAID: 40021440756
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Asymmetric hybridization and introgression between sibling species of the pufferfish Takifugu that have undergone explosive speciation (2017)
  • Author(s): Takahashi Hiroshi、Toyoda Airi、Yamazaki Taku、Narita Shusaku、Mashiko Tsuyoshi、Yamazaki Yukio
  • Journal Title: Marine Biology Volume: 164 Issue: 4
  • DOI: 10.1007/s00227-017-3120-2
  • Peer Reviewed
• [Journal Article] Molecular phylogeny of obligate fish-parasites of the family Cymothoidae (Isopoda, Crustacea): Evolution of the attachment mode to host fish and the habitat shift from saline water to freshwater. (2017)
  • Author(s): Hata, H., Sogabe, A., Tada, S., Nishimoto, R., Nakano, R., Kohya, N., Takeshima, H., Kawanishi, R.
  • Journal Title: Marine Biology Volume: 164 Issue: 5 Pages: 105-105
  • DOI: 10.1007/s00227-017-3138-5
  • Peer Reviewed
• [Journal Article] Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing. (2017)
  • Author(s): Sun Y., Kurisaki M., Hashiguchi Y. and Kumazawa Y.
  • Journal Title: BMC Genomics Volume: 18 Issue: 1 Pages: 665-665
  • DOI: 10.1186/s12864-017-4080-0
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Genomic analysis of progress toward complete speciation in stickelbacks (2020)
  • Author(s): Yo Yamasaki, Ryo Kakioka, Hiroshi Takahashi, Atsushi Toyoda, Jun Kitano
  • Organizer: The 67th Annual Meeting of the Ecological Society of Japan (ESJ67)
• [Presentation] アマゴ・サツキマスにおける回遊多型の遺伝基盤の探索 (2020)
  • Author(s): 上田るい・ 田中達也・勝村啓史・橋口康之・武島弘彦・Michael R. MILLER・佐藤拓哉
  • Organizer: 第67回日本生態学会大会
• [Presentation] トゲウオ科魚類における形態の収斂進化の遺伝基盤 (2019)
  • Author(s): 柿岡 諒・北野 潤・石川麻乃・永野 惇・八杉公基・髙橋 洋
  • Organizer: 日本進化学会第21会大会
• [Presentation] マイクロサテライト DNA および SNP によるアカメの遺伝的集団構造分析 (2019)
  • Author(s): 内藤拓哉・中山耕至・武島弘彦・橋口康之・三品達平・竹下直彦・田上英明・髙橋 洋
  • Organizer: 2019年度日本魚類学会年会
• [Presentation] アカメ Lates japonicus における高い遺伝的多様性を示すゲノム領域の探索 (2019)
  • Author(s): 橋口康之・三品達平・武島弘彦・中山耕至・田上英明・竹下直彦・ 髙橋 洋
  • Organizer: 2019年度日本魚類学会年会
• [Presentation] フナ類における無性型３倍体の起源とゲノム多様性 (2019)
  • Author(s): 三品達平・井口恵一朗・武島弘彦・橋口康之・西田 睦・渡辺勝敏
  • Organizer: 2019年度日本魚類学会年会
• [Presentation] トラフグ属魚類人工交雑家系を用いた雑種判別手法の検証 (2019)
  • Author(s): 房尾奈生子・吉川廣幸・髙橋 洋
  • Organizer: 2019年度日本魚類学会年会
• [Presentation] Mass occurrence of hybrid pufferfish and its implications in food safety (2019)
  • Author(s): Hiroshi Takahashi
  • Organizer: The 34th Annual Meeting of the Korean Society of Food Hygiene and Safety
  • Int'l Joint Research / Invited
• [Presentation] 極めて低い遺伝的多様性をもつアカメLates japonicusの全ゲノム分析 (2018)
  • Author(s): 髙橋 洋・三品達平・橋口康之・武島弘彦・中山耕至・田上英明・竹下直彦
  • Organizer: 2018年度日本魚類学会年会
• [Presentation] 大野川水系神原川におけるイワメおよびアマゴ個体群の遺伝的構造 (2018)
  • Author(s): 北西 滋・近藤卓哉・髙橋 洋・竹下直彦・星野和夫・永田新悟・宮村栄一・岩永純二・大倉鉄也・江戸謙顕
  • Organizer: 2018年度日本魚類学会年会
• [Presentation] Tetrodotoxin distribution in natural hybrids between Takifugu rubripes and Takifugu porphyreus (2018)
  • Author(s): Yumi Miyata, Ryohei Tatsuno, Hiroshi Takahashi, Hiroyuki Yoshikawa, Yasuko Ino, Tsubasa Fukuda, Manabu Furushita
  • Organizer: 24th Joint International Symposium between National Fisheries University and Pukyong National University
  • Int'l Joint Research
• [Presentation] ゲノムワイドに探る種間交雑に伴う淡水カジカの適応進化 (2018)
  • Author(s): 伊藤僚祐・三品達平・武島弘彦・渡辺勝敏
  • Organizer: 第65回日本生態学会大会
• [Presentation] Acoustic tracking of the Japanese endemic fish (Lates japonicas) during the spawning season (2017)
  • Author(s): Gonzalvo Sara、Tanoue Hideaki、Komatsu Teruhisa
  • Organizer: 日仏海洋学会術研究発表会
  • Int'l Joint Research
• [Presentation] 山口県沿岸の日本海におけるヒラマサとブリの自然種間交雑現象 (2017)
  • Author(s): 髙橋洋・黒厚子大輝・下山諒
  • Organizer: 2017年度日本魚類学会年会
• [Presentation] “稀な性”と倍数性を超えた遺伝子流動がもたらす3倍体フナの進化と多様性 (2017)
  • Author(s): 三品達平・武島弘彦・高田未来美・井口恵一朗・川原玲香・橋口康之・田畑諒一・佐々木剛・西田睦・渡辺勝敏
  • Organizer: 2017年度日本魚類学会年会
• [Book] 魚類学の百科事典 (2018)
  • Author(s): 一般社団法人日本魚類学会
  • Total Pages: 756
  • Publisher: 丸善出版
  • ISBN: 9784621303177
• [Book] 小学館の図鑑Z 日本魚類館 (2018)
  • Author(s): 中坊 徹次、松沢 陽士
  • Total Pages: 544
  • Publisher: 小学館
  • ISBN: 4092083114