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Adaptation of fishes in Lake Biwa, an ancient temperate lake in Japan, and its genetic basis

Research Project

Project/Area Number 26291079
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Biodiversity/Systematics
Research InstitutionKyoto University

Principal Investigator

Watanabe Katsutoshi  京都大学, 理学(系)研究科(研究院), 准教授 (00324955)

Co-Investigator(Kenkyū-buntansha) 馬渕 浩司  東京大学, 大気海洋研究所, 助教 (50401295)
小北 智之  福井県立大学, 公私立大学の部局等, 准教授 (60372835)
Co-Investigator(Renkei-kenkyūsha) TAKESHIMA Hirohiko  統合地球環境学研究所, 特任助教 (50573086)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥15,730,000 (Direct Cost: ¥12,100,000、Indirect Cost: ¥3,630,000)
Fiscal Year 2016: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2015: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2014: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Keywords古代湖 / 琵琶湖 / 固有種 / 適応進化 / 遺伝基盤 / 人口統計学 / 分子系統 / 次世代シーケンサー / 集団・種多様性 / 適応 / 淡水魚
Outline of Final Research Achievements

To clarify the origins and genetic basis of the adaptations of endemic species in the unique freshwater fish fauna of Lake Biwa, an ancient temperate lake, morphological comparisons and analyses of mitogenomes, gene expression, and genome-wide polymorphisms were conducted for several species groups. The study used four approaches to deepen our understanding of the adaptive evolution of the endemic fishes. (1) Phenotypes (morphology and gene expression) related to lake adaptation were clarified. (2) Robust phylogenetic relationships and demographic histories were estimated based on genetic variation in mitochondrial and nuclear genomes. (3) Screening for candidate genes for adaptation, the commonalities and diversity among species groups were clarified. (4) Genomic regions associated with adaptation were detected by quantitative trait locus analysis.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report

Research Products

(45 results)

All 2017 2016 2015 2014 Other

All Journal Article (11 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 10 results,  Acknowledgement Compliant: 10 results,  Open Access: 3 results) Presentation (30 results) (of which Int'l Joint Research: 1 results,  Invited: 6 results) Book (1 results) Remarks (3 results)

  • [Journal Article] Morphological features of an endangered Japanese strain of Cyprinus carpio: reconstruction based on seven SNP markers2017

    • Author(s)
      Atsumi K, H Y Song, H Senou, K Inoue and K Mabuchi
    • Journal Title

      Journal of Fish Biology

      Volume: 90 Pages: 936-953

    • DOI

      10.1111/jfb.13213

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Rapid and effective isolation of candidate sequences for development of microsatellite markers in 30 fish species by using kit-based target capture and multiplexed parallel sequencing2017

    • Author(s)
      Hirohiko Takeshima, Nozomu Muto, Yasuyuki Sakai, Naoya Ishiguro, Keiichiro Iguchi, Satoshi Ishikawa, Mutsumi Nishida
    • Journal Title

      Conservation Genetics Resources

      Volume: online first Pages: 1-12

    • DOI

      10.1007/s12686-017-0699-z

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Genetic population structure of the Japanese torrent catfish Liobagrus reinii (Amblycipitidae) inferred from mitochondrial cytochrome b variations2016

    • Author(s)
      Nakagawa H, S Seki, T Ishikawa and K Watanabe
    • Journal Title

      Ichthyological Research

      Volume: 63

    • DOI

      10.1007/s10228-015-0503-6

    • NAID

      40020886702

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan2016

    • Author(s)
      Tabata R, R Kakioka, K Tominaga, T Komiya and K Watanabe
    • Journal Title

      Ecology and Evolution

      Volume: 6 Pages: 2601-2623

    • DOI

      10.1002/ece3.2070

    • NAID

      120005973364

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Cryptic divergence and phylogeography of the pike gudgeon Pseudogobio esocinus (Teleostei: Cyprinidae): a comprehensive case of freshwater phylogeography in Japan2016

    • Author(s)
      Tominaga K, J Nakajima and K Watanabe
    • Journal Title

      Ichthyological Research

      Volume: 63 Pages: 79-93

    • DOI

      10.1007/s10228-015-0478-3

    • NAID

      40020707392

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] A method for PCR-based identification of fish eggs attached to vegetation in Lake Biwa, Japan2016

    • Author(s)
      Mabuchi K
    • Journal Title

      Conservation Genetics Resources

      Volume: 8

    • DOI

      10.1007/s12686-016-0536-9

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Complete mitochondrial genomes of five introduced strains of common carp Cyprinus carpio in Japan with 29 diagnostic SNPs distinguishable by restriction enzyme analysis2016

    • Author(s)
      Mabuchi K
    • Journal Title

      Mitochondrial DNA Part B: Resources

      Volume: online

    • DOI

      10.1080/23802359.2016.1159931

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Phylogeny, hybridization, and life history evolution of Rhinogobius gobies in Japan, inferred from multiple nuclear gene sequences2015

    • Author(s)
      Yamasaki YY, M Nishida, T Suzuki, T Mukai and K Watanabe
    • Journal Title

      Molecular Phylogenetics and Evolution

      Volume: 90 Pages: 20-33

    • DOI

      10.1016/j.ympev.2015.04.012

    • NAID

      120005611374

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Population structure and cryptic replacement of local populations in the endangered bitterling Acheilognathus cyanostigma2015

    • Author(s)
      Kitajima J, M Matsuda, S Mori, T Kokita and K Watanabe
    • Journal Title

      Ichthyological Research

      Volume: 62 Pages: 122-130

    • DOI

      10.1007/s10228-014-0412-0

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes2015

    • Author(s)
      Kakioka, R., T. Kokita, H. Kumada, K. Watanabe and N. Okuda
    • Journal Title

      Molecular Ecology

      Volume: 24 Pages: 4159-4174

    • DOI

      10.1111/mec.13309

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] 2014 年度日本魚類学会シンポジウム「魚類における適応と種分化の進化遺伝機構 :研究最前線と今後の展望」の開催報告2015

    • Author(s)
      小北智之・渡辺勝敏
    • Journal Title

      魚類学雑誌

      Volume: 62 Pages: 93-96

    • Related Report
      2014 Annual Research Report
  • [Presentation] フナ属魚類における無性型頻度の地理的パターン:有性と無性の共存機構との関連性2017

    • Author(s)
      三品達平・渡辺勝敏
    • Organizer
      第64回日本生態学会大会
    • Place of Presentation
      早稲田大学(東京都新宿区)
    • Year and Date
      2017-03-15
    • Related Report
      2016 Annual Research Report
  • [Presentation] RNA-seqに基づく琵琶湖固有魚種の分岐年代と適応進化2017

    • Author(s)
      伊藤僚祐・三品達平・田畑諒一・小北智之・武島弘彦・橋口康之・渡辺勝敏
    • Organizer
      第64回日本生態学会大会
    • Place of Presentation
      早稲田大学(東京都新宿区)
    • Year and Date
      2017-03-15
    • Related Report
      2016 Annual Research Report
  • [Presentation] 琵琶湖の魚類の生い立ち―分子データからのアプローチ2016

    • Author(s)
      渡辺勝敏
    • Organizer
      化石研究会第146回例会
    • Place of Presentation
      滋賀県立琵琶湖博物館(滋賀県草津市)
    • Year and Date
      2016-11-20
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 琵琶湖の成り立ちと固有魚類の進化2016

    • Author(s)
      渡辺勝敏
    • Organizer
      琵琶湖博物館開館20週年国際シンポジウム:古代湖の魅力~琵琶湖と世界の古代湖
    • Place of Presentation
      滋賀県立琵琶湖博物館(滋賀県草津市)
    • Year and Date
      2016-10-22
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] ミトコンドリア全ゲノム情報に基づく琵琶湖産魚類の高精度な人口学的歴史の推定2016

    • Author(s)
      田畑諒一・武島弘彦・平瀬祥太朗・西田 睦・渡辺勝敏
    • Organizer
      第49回日本魚類学会年会
    • Place of Presentation
      岐阜大学(岐阜県岐阜市)
    • Year and Date
      2016-09-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 琵琶湖産ヒガイ類の色彩変異に関する形質遺伝学的解析2016

    • Author(s)
      上野浩太郎・木下直樹・松田征也・渡辺勝敏・小北智之
    • Organizer
      第49回日本魚類学会年会
    • Place of Presentation
      岐阜大学(岐阜県岐阜市)
    • Year and Date
      2016-09-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 日本産タモロコ属魚類におけるゲノムワイドな遺伝的変異2016

    • Author(s)
      柿岡 諒・近藤剛毅・永野 惇・手塚あゆみ・奥田 昇・小北智之
    • Organizer
      第49回日本魚類学会年会
    • Place of Presentation
      岐阜大学(岐阜県岐阜市)
    • Year and Date
      2016-09-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] ミトコンドリアDNA分析に基づく日本産ナマズ属3種の系統地理2016

    • Author(s)
      佐久間啓・松崎慎一郎・金尾滋史・舟尾俊範・鹿野雄一・武島弘彦
    • Organizer
      第49回日本魚類学会年会
    • Place of Presentation
      岐阜大学(岐阜県岐阜市)
    • Year and Date
      2016-09-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 大規模な地点サンプリングの戦略により明らかとなったアユの遺伝的集団構造2016

    • Author(s)
      武島弘彦・井口恵一朗・橋口康之・西田 睦
    • Organizer
      第49回日本魚類学会年会
    • Place of Presentation
      岐阜大学(岐阜県岐阜市)
    • Year and Date
      2016-09-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 琵琶湖沖合における日本在来および導入コイの遊泳行動2016

    • Author(s)
      吉田 誠・馬渕浩司・井上広滋・佐藤克文
    • Organizer
      第49回日本魚類学会年会
    • Place of Presentation
      岐阜大学(岐阜県岐阜市)
    • Year and Date
      2016-09-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] 琵琶湖の固有魚類相の形成史に関する論考2016

    • Author(s)
      渡辺勝敏
    • Organizer
      総合研究「自然観」(前近代を中心とした琵琶湖周辺地域における自然および自然観の通時的変遷に関する研究)第7回研究会
    • Place of Presentation
      滋賀県立琵琶湖博物館(滋賀県草津市)
    • Year and Date
      2016-09-04
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] コイは外来種か? 最新のDNA研究から見えてきたこと2016

    • Author(s)
      馬渕浩司
    • Organizer
      日本魚類学会2016年度市民公開講座
    • Place of Presentation
      名城大学天白キャンパス(愛知県名古屋市)
    • Year and Date
      2016-08-27
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 定性トランスクリプトーム解析を用いた琵琶湖固有魚種の湖沼適応遺伝子の探索2016

    • Author(s)
      伊藤僚祐・三品達平・橋口康之・小北智之・武島弘彦・渡辺勝敏
    • Organizer
      日本進化学会第18回東京大会
    • Place of Presentation
      東京工業大学大岡山キャンパス(東京都目黒区)
    • Year and Date
      2016-08-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 交雑起源の無性生殖種のゲノムワイドなアリル発現パターン:遺伝的不和合の補償との関連性2016

    • Author(s)
      三品達平・橋口康之・武島弘彦・川原玲香・佐々木 剛・遠藤未来美・西田 睦・渡辺勝敏
    • Organizer
      日本進化学会第18回東京大会
    • Place of Presentation
      東京工業大学大岡山キャンパス(東京都目黒区)
    • Year and Date
      2016-08-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 琵琶湖内にみられるコイの体型の地域間変異2016

    • Author(s)
      渥美圭佑・馬渕浩司・瀬能 宏・井上広滋
    • Organizer
      日本生態学会第63回大会
    • Place of Presentation
      仙台市国際センター、仙台市情報・産業プラザ(宮城県仙台市)
    • Year and Date
      2016-03-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] 有性・無性の生殖サイクルを介した稀な遺伝子流動が促進するフナ類の多様化2015

    • Author(s)
      三品達平・武島弘彦・高田未来美・井口恵一朗・田畑諒一・西田 睦・渡辺勝敏
    • Organizer
      第48回日本魚類学会年会
    • Place of Presentation
      近畿大学奈良キャンパス(奈良県奈良市)
    • Year and Date
      2015-09-06
    • Related Report
      2015 Annual Research Report
  • [Presentation] ウキゴリ属魚類のロドプシン進化パターン2015

    • Author(s)
      伊藤僚祐・原田慈雄・田畑諒一・渡辺勝敏
    • Organizer
      第48回日本魚類学会年会
    • Place of Presentation
      近畿大学奈良キャンパス(奈良県奈良市)
    • Year and Date
      2015-09-06
    • Related Report
      2015 Annual Research Report
  • [Presentation] 琵琶湖水系における底生魚カマツカの形態的多様性と遺伝的集団構造2015

    • Author(s)
      遠藤千晴・富永浩史・三品達平・山﨑 曜・武島弘彦・渡辺勝敏
    • Organizer
      第48回日本魚類学会年会
    • Place of Presentation
      近畿大学奈良キャンパス(奈良県奈良市)
    • Year and Date
      2015-09-06
    • Related Report
      2015 Annual Research Report
  • [Presentation] 明治10年代の琵琶湖のコイ:パリ国立自然史博物館標本にもとづく考察2015

    • Author(s)
      渥美圭佑・馬渕浩司・瀬能 宏・井上広滋・滝川祐子
    • Organizer
      第48回日本魚類学会年会
    • Place of Presentation
      近畿大学奈良キャンパス(奈良県奈良市)
    • Year and Date
      2015-09-05
    • Related Report
      2015 Annual Research Report
  • [Presentation] 琵琶湖水系のタモロコ属ペア種におけるOXPHOS関連遺伝子群の共適応の可能性2015

    • Author(s)
      近藤剛毅・小北智之
    • Organizer
      第48回日本魚類学会年会
    • Place of Presentation
      近畿大学奈良キャンパス(奈良県奈良市)
    • Year and Date
      2015-09-05
    • Related Report
      2015 Annual Research Report
  • [Presentation] Comparative mitogenomics of endemic fishes in Lake Biwa: evidence of natural selection and adaptation to lake environments2015

    • Author(s)
      Tabata, R., H. Takeshima, S. Hirase, M. Nishida and K. Watanabe
    • Organizer
      Speciation in Ancient Lakes 7
    • Place of Presentation
      Great Lakes Institute for Environmental Research(カナダ)
    • Year and Date
      2015-08-17
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 日本のコイ:DNAデータが語るその起源2015

    • Author(s)
      馬渕浩司
    • Organizer
      在来家畜研究会・日本動物遺伝育種学会合同シンポジウム
    • Place of Presentation
      宇都宮大学峰キャンパス,宇都宮
    • Year and Date
      2015-03-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 琵琶湖の淡水魚カマツカにおける形態の多様化およびその摂餌機能との関連性2015

    • Author(s)
      遠藤千晴・富永浩史・渡辺勝敏
    • Organizer
      第62回日本生態学会大会
    • Place of Presentation
      鹿児島大学,鹿児島市
    • Year and Date
      2015-03-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] 隠れた外来種問題:コイ日本在来系統と導入系統の形態比較2015

    • Author(s)
      渥美圭佑・馬渕浩司・瀬能 宏・井上広滋
    • Organizer
      第62回日本生態学会大会
    • Place of Presentation
      鹿児島大学,鹿児島市
    • Year and Date
      2015-03-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] Japanese native strain of common carp (Cyprinus carpio) and Lake Biwa as a refuge from biological invasion of introduced "Eurasian" strains2015

    • Author(s)
      Kohji Mabuchi
    • Organizer
      International Sancheoneo Symposium in Hwacheon
    • Place of Presentation
      Hwacheon, Korea
    • Year and Date
      2015-01-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 日本の古代湖「琵琶湖」における固有魚類群集の起源と適応2014

    • Author(s)
      渡辺勝敏
    • Organizer
      第47回日本魚類学会年会
    • Place of Presentation
      神奈川県立生命の星・地球館,小田原市
    • Year and Date
      2014-11-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] 日本列島のフナの集団構造2014

    • Author(s)
      三品達平・高田未来美・武島弘彦・井口恵一朗・西田 睦・渡辺勝敏
    • Organizer
      第47回日本魚類学会年会
    • Place of Presentation
      神奈川県立生命の星・地球館,小田原市
    • Year and Date
      2014-11-15 – 2014-11-16
    • Related Report
      2014 Annual Research Report
  • [Presentation] 琵琶湖における淡水魚カマツカの形態変異と遺伝的集団構造2014

    • Author(s)
      遠藤千晴・富永浩史・三品達平・山﨑 曜・武島弘彦・渡辺勝敏
    • Organizer
      第47回日本魚類学会年会
    • Place of Presentation
      神奈川県立生命の星・地球館,小田原市
    • Year and Date
      2014-11-15 – 2014-11-16
    • Related Report
      2014 Annual Research Report
  • [Presentation] 琵琶湖固有魚類の比較ミトゲノミクス:自然淘汰の痕跡と琵琶湖環境への適応2014

    • Author(s)
      田畑諒一・武島弘彦・平瀬祥太朗・西田 睦・渡辺勝敏
    • Organizer
      第47回日本魚類学会年会
    • Place of Presentation
      神奈川県立生命の星・地球館,小田原市
    • Year and Date
      2014-11-15 – 2014-11-16
    • Related Report
      2014 Annual Research Report
  • [Presentation] 御蔵島・御代が池のコイが語る外来系統の導入史2014

    • Author(s)
      馬渕浩司
    • Organizer
      生き物文化誌学会
    • Place of Presentation
      東京大学,東京
    • Year and Date
      2014-08-02 – 2014-08-03
    • Related Report
      2014 Annual Research Report
  • [Book] Chapter 7. Japanese freshwater fishes: biogeography and cryptic diversity. In: Species Diversity of Animals in Japan, Diversity and Commonality in Animals (M. Motokawa and H. Kajihara eds.)2016

    • Author(s)
      Watanabe, K., K. Tominaga, J. Nakajima, R. Kakioka and R. Tabata
    • Total Pages
      721
    • Publisher
      Springer
    • Related Report
      2016 Annual Research Report
  • [Remarks] 淡水魚遺伝的多様性データベースGEDIMAP

    • URL

      http://gedimap.zool.kyoto-u.ac.jp

    • Related Report
      2016 Annual Research Report
  • [Remarks] GEDIMAP: 淡水魚遺伝的多様性データベース

    • URL

      http://gedimap.zool.kyoto-u.ac.jp

    • Related Report
      2015 Annual Research Report
  • [Remarks] GEDIMAP:淡水魚遺伝的多様性データベース

    • URL

      http://gedimap.zool.kyoto-u.ac.jp

    • Related Report
      2014 Annual Research Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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