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Establishing a novel method of molecular phylogenetic analysis based on comprehensive sequence data from a single gene to the whole genome

Research Project

Project/Area Number 24370033
Research Category

Grant-in-Aid for Scientific Research (B)

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

Principal Investigator

TODA Masanori  北海道大学, 総合博物館, 資料部研究員 (40113592)

Co-Investigator(Kenkyū-buntansha) WATADA Masayoshi  愛媛大学, 大学院理工学研究科, 教授 (00210881)
TAMURA Koichiro  首都大学東京, 大学院理工学研究科, 教授 (00254144)
KATOH Toru  北海道大学, 大学院理学研究院, 助教 (80374198)
Project Period (FY) 2012-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2014: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2013: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2012: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Keywords系統推定法 / ショウジョウバエ / トランスクリプトーム / ゲノム / 網羅的分子系統樹 / PCRプライマー / モデル生物 / 分類学 / 系統 / ショウジョウバエ科 / 100遺伝子 / 国際情報交換 / 中国:英国 / cDNA / 中国:米国 / 中国:米国
Outline of Final Research Achievements

We developed a novel method of molecular phylogenetic analysis that enables us to employ comprehensive data of DNA sequences of various genes in the skeleton framework of whole genome sequences, and applied it to the family Drosophilidae as a model group of organisms. The inferred phylogeny was highly resolved, corroborating the efficiency of the novel methodology. Especially, as to the largest genus Drosophila of which phylogeny has not fully been resolved, several important new findings have been brought, which will lead to fundamental changes in the framework of taxonomic and evolutionary studies on the Drosophilidae.

Report

(5 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (41 results)

All 2015 2014 2013 2012 Other

All Int'l Joint Research (2 results) Journal Article (12 results) (of which Peer Reviewed: 11 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (26 results) (of which Int'l Joint Research: 3 results,  Invited: 5 results) Remarks (1 results)

  • [Int'l Joint Research] 雲南大学(中国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] ケンブリッジ大学(英国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] ゲノム配列を利用した網羅的系統解析とこれからの分類学2015

    • Author(s)
      戸田正憲
    • Journal Title

      Panmixia

      Volume: 18 Pages: 18-24

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
  • [Journal Article] Phylogenetic placement of metagenomic reads using the minimum evolution principle.2015

    • Author(s)
      Filipski, A., Tamura, K., Billing-Ross, P., Murillo, O. & Kumar, S.
    • Journal Title

      BMC Genomics

      Volume: 16 Issue: S1

    • DOI

      10.1186/1471-2164-16-s1-s13

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Taxonomy of the Colocasiomyia gigantea species group (Diptera, Drosophilidae), with descriptions of four new species from Yunnan, China.2014

    • Author(s)
      Li, N.-n., Toda, M. J., Fu, Z., Chen, J.-m., Li, S.-h. & Gao, J.-j.
    • Journal Title

      ZooKeys

      Volume: 406 Pages: 41-64

    • DOI

      10.3897/zookeys.406.7176

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] MEGA-MD: Molecular Evolutionary Genetics Analysis software with mutational diagnosis of amino acid variation.2014

    • Author(s)
      Stecher, G., Liu, L., Sanderford, M., Peterson, P., Tamura, K. & Kumar S.
    • Journal Title

      Bioinformatics

      Volume: 30 Issue: 9 Pages: 1305-1307

    • DOI

      10.1093/bioinformatics/btu018

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Prospects for building large timetrees using molecular data with incomplete gene coverage among species.2014

    • Author(s)
      Filipski, A., Murillo, O., Freydenzon, A., Tamura, K. & Kumar, S.
    • Journal Title

      Molecular Biology and Evolution

      Volume: 31 Issue: 9 Pages: 2542-2550

    • DOI

      10.1093/molbev/msu200

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Colocasiomyia (Diptera: Drosophilidae) revised phylogenetically, with a new species group having peculiar life cycles on monsteroid (Araceae) host plants.2013

    • Author(s)
      Fartyal, R. S., Gao, J.-j., Toda, M. J., Hu, Y.-g., Takenaka Takano, K., Suwito, A., Katoh, T., Takigahira, T. & Yin, J.-t.
    • Journal Title

      Systematic Entomology

      Volume: 38 Issue: 4 Pages: 763-782

    • DOI

      10.1111/syen.12027

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Revision of Asian species of the Drosophila melanica species group (Diptera: Drosophilidae), with a description of a new species from Vietnam2013

    • Author(s)
      Suwito, A., Toda, M., Takamori, H., Harada, K. and Watabe, H.
    • Journal Title

      Entomological Science

      Volume: 16 Issue: 1 Pages: 75-85

    • DOI

      10.1111/ens.12028

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.2013

    • Author(s)
      Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S.
    • Journal Title

      Molecular Biology and Evolution

      Volume: 30 Issue: 12 Pages: 2725-2729

    • DOI

      10.1093/molbev/mst197

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Courtship patterns in the Drosophila montium species subgroup: repeated loss of precopulatory courtship?2013

    • Author(s)
      Chen, C.C., Watada, M., Miyake, H., Kotoh, T.K., Sun, Z., Li, Y.F., Ritchie, M.G. & Wen, S.Y.
    • Journal Title

      Zoological Science

      Volume: 30 Issue: 12 Pages: 1056-1062

    • DOI

      10.2108/zsj.30.1056

    • NAID

      40019900569

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Review of the Drosophila (Drosophila) quadrisetata species group (Diptera: Drosophilidae), with descriptions of three new species from the Oriental Regions2013

    • Author(s)
      Suwito, A., Watabe, H. and Toda, M. J.
    • Journal Title

      Entomological Science

      Volume: 16 Issue: 1 Pages: 66-82

    • DOI

      10.1111/j.1479-8298.2012.00530.x

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Estimating divergence times in large molecular phylogenies.2012

    • Author(s)
      Tamura, K.
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 109 Issue: 47 Pages: 19333-19338

    • DOI

      10.1073/pnas.1213199109

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MEGA-CC : Computing Core of Molecular Evolutionary Genetics Analysis program for automated and iterative data analysis.2012

    • Author(s)
      Kumar, S.
    • Journal Title

      Bioinformatics

      Volume: 28 Issue: 20 Pages: 2685-2686

    • DOI

      10.1093/bioinformatics/bts507

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] Molecular phylogenetic analyses using MEGA software.2015

    • Author(s)
      Tamura, K.
    • Organizer
      International Symposium on Evolutionary Genomics and Bioinformatics 2015
    • Place of Presentation
      Taipei (Taiwan)
    • Year and Date
      2015-11-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] MEGA7による分子系統解析2015

    • Author(s)
      田村浩一郎
    • Organizer
      第196回農林交流センターワークショップ
    • Place of Presentation
      農業環境技術研究所(茨城県・つくば市)
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Sophophora 亜属およびその関連分類群における50遺伝子を用いた分子系統学的研究2015

    • Author(s)
      加藤雄大,和多田正義
    • Organizer
      日本遺伝学会第87回大会
    • Place of Presentation
      東北大学(宮城県・仙台市)
    • Year and Date
      2015-09-25
    • Related Report
      2015 Annual Research Report
  • [Presentation] 進化パターンの変化による分子系統解析の歪みとデータフィルタリングによるその抑制(2)2015

    • Author(s)
      岩本栄介,田村浩一郎
    • Organizer
      日本遺伝学会第87回大会
    • Place of Presentation
      東北大学(宮城県・仙台市)
    • Year and Date
      2015-09-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] 次世代データの系統解析New Technology -プロローグ:次世代系統解析の問題と課題-2015

    • Author(s)
      田村浩一郎
    • Organizer
      日本進化学会第17回大会
    • Place of Presentation
      中央大学(東京都・文京区)
    • Year and Date
      2015-08-23
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 進化パターンの変化による分子系統解析の歪みとデータフィルタリングによるその抑制(2)2015

    • Author(s)
      岩本栄介,田村浩一郎
    • Organizer
      日本進化学会第17回大会
    • Place of Presentation
      中央大学(東京都・文京区)
    • Year and Date
      2015-08-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] 菌食性ショウジョウバエの系統関係と菌食性の起源の推定.2015

    • Author(s)
      福田洋之,戸田正憲,加藤徹
    • Organizer
      日本進化学会第17回大会
    • Place of Presentation
      中央大学(東京都・文京区)
    • Year and Date
      2015-08-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] Failure of phylogenetic tree reconstruction by heterogeneous substitution pattern among lineages and the method for its recovery.2015

    • Author(s)
      Iwamoto, E. & Tamura, K.
    • Organizer
      SMBE 2015
    • Place of Presentation
      Vienna (Austria)
    • Year and Date
      2015-07-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Evolution of the immigrans species group revealed by using big sequence data.2015

    • Author(s)
      Seto, Y., Toda, M. J. & Tamura, K.
    • Organizer
      SMBE 2015
    • Place of Presentation
      Vienna (Austria)
    • Year and Date
      2015-07-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 巨大配列データセットを用いたオオショウジョウバエ種群の分子系統解析2014

    • Author(s)
      瀬戸陽介,田村浩一郎
    • Organizer
      日本遺伝学会第86回大会
    • Place of Presentation
      長浜バイオ大学(長浜市)
    • Year and Date
      2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] 次世代シーケンス技術による多数遺伝子座を用いたショウジョウバエの分子系統解析2014

    • Author(s)
      岩崎祐磨,田村浩一郎
    • Organizer
      日本遺伝学会第86回大会
    • Place of Presentation
      長浜バイオ大学(長浜市)
    • Year and Date
      2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] 多数の遺伝子配列を用いたSophophora亜属の分子系統学的研究2014

    • Author(s)
      加藤雄大,和多田正義
    • Organizer
      日本遺伝学会第86回大会
    • Place of Presentation
      長浜バイオ大学(長浜市)
    • Year and Date
      2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] 進化パターンの変化による分子系統解析の歪みとデータフィルタリングによるその抑制2014

    • Author(s)
      岩本栄介,田村浩一郎
    • Organizer
      日本遺伝学会第86回大会
    • Place of Presentation
      長浜バイオ大学(長浜市)
    • Year and Date
      2014-09-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Scaptomyza属ショウジョウバエの系統進化2014

    • Author(s)
      加藤徹,山下伸志,福田洋之,Matthew H. Dick,和多田正義
    • Organizer
      日本昆虫学会第74回大会
    • Place of Presentation
      広島大学教育学部(東広島市)
    • Year and Date
      2014-09-15
    • Related Report
      2014 Annual Research Report
  • [Presentation] ハワイ産ショウジョウバエと大陸産Scaptomyza属の起源2014

    • Author(s)
      瀬戸陽介,田村浩一郎
    • Organizer
      日本進化学会第16回大会
    • Place of Presentation
      高槻現代劇場(高槻市)
    • Year and Date
      2014-08-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] 次世代シーケンス技術による多数遺伝子座を用いたショウジョウバエの分子系統解析2014

    • Author(s)
      岩崎祐磨,田村浩一郎
    • Organizer
      日本進化学会第16回大会
    • Place of Presentation
      高槻現代劇場(高槻市)
    • Year and Date
      2014-08-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] 進化パターンの変化による分子系統解析の歪みとデータフィルタリングによるその抑制2014

    • Author(s)
      岩本栄介,田村浩一郎
    • Organizer
      日本進化学会第16回大会
    • Place of Presentation
      高槻現代劇場(高槻市)
    • Year and Date
      2014-08-21
    • Related Report
      2014 Annual Research Report
  • [Presentation] Scaptomyza属ショウジョウバエの起源と系統関係2012

    • Author(s)
      加藤徹
    • Organizer
      日本遺伝学会第84回大会
    • Place of Presentation
      九州大学(福岡市)
    • Year and Date
      2012-09-24
    • Related Report
      2012 Annual Research Report
  • [Presentation] 全ゲノム配列による系統解析 -限界と課題-2012

    • Author(s)
      田村浩一郎
    • Organizer
      日本進化学会第14回大会
    • Place of Presentation
      首都大学東京(八王子市)(招待講演)
    • Year and Date
      2012-08-24
    • Related Report
      2012 Annual Research Report
  • [Presentation] 系統推定にとって有害なデータの除去による系統樹推定改良法の開発2012

    • Author(s)
      岩本栄介
    • Organizer
      日本進化学会第14回大会
    • Place of Presentation
      首都大学東京(八王子市)
    • Year and Date
      2012-08-22
    • Related Report
      2012 Annual Research Report
  • [Presentation] 次世代シーケンス技術によるアカショウジョウバエゲノムの遺伝的多様性解析2012

    • Author(s)
      橋本英明
    • Organizer
      日本進化学会第14回大会
    • Place of Presentation
      首都大学東京(八王子市)
    • Year and Date
      2012-08-22
    • Related Report
      2012 Annual Research Report
  • [Presentation] ショウジョウバエの分類と系統:古い問題と新しい挑戦2012

    • Author(s)
      戸田正憲
    • Organizer
      日本進化学会第14回大会
    • Place of Presentation
      首都大学東京(八王子市)(招待講演)
    • Year and Date
      2012-08-21
    • Related Report
      2012 Annual Research Report
  • [Presentation] ショウジョウバエの分子系統と共生細菌2012

    • Author(s)
      和多田正義
    • Organizer
      日本進化学会第14回大会
    • Place of Presentation
      首都大学東京(八王子市)(招待講演)
    • Year and Date
      2012-08-21
    • Related Report
      2012 Annual Research Report
  • [Presentation] Drosophila亜属の系統と進化-quinaria sectionのショウジョウバエを中心に-2012

    • Author(s)
      加藤徹
    • Organizer
      日本進化学会第14回大会
    • Place of Presentation
      首都大学東京(八王子市)(招待講演)
    • Year and Date
      2012-08-21
    • Related Report
      2012 Annual Research Report
  • [Presentation] ゲノム配列を利用した網羅的系統解析とこれからの分類学

    • Author(s)
      戸田正憲
    • Organizer
      日本昆虫学会第73回大会・シンポジウム「昆虫分類学若手懇談会シンポジウム:分類学の過去・現在・未来」
    • Place of Presentation
      北海道大学(札幌市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 分子進化遺伝学解析のバイオインフォマティクス

    • Author(s)
      田村浩一郎
    • Organizer
      京都賞記念ワークショップ
    • Place of Presentation
      国立京都国際会館(京都府)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Remarks] Toru Katoh

    • URL

      http://www.sci.hokudai.ac.jp/~tkatoh/

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report

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Published: 2012-04-24   Modified: 2022-01-31  

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