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A data-driven approach for analysis of evolutionary origin and diversification of meso- and bathypelagic fishes

Research Project

Project/Area Number 26291083
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Biodiversity/Systematics
Research InstitutionNatural History Museum and Institute, Chiba

Principal Investigator

Miya Masaki  千葉県立中央博物館, その他部局等, 研究員 (30250137)

Co-Investigator(Kenkyū-buntansha) 岩崎 渉  東京大学, 理学(系)研究科(研究院), 准教授 (50545019)
杢 雅利  東京大学, 大気海洋研究所, その他 (30416466)
Co-Investigator(Renkei-kenkyūsha) SATO Yukuto  琉球大学, 特任講師 (20566418)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥15,600,000 (Direct Cost: ¥12,000,000、Indirect Cost: ¥3,600,000)
Fiscal Year 2016: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2015: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2014: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Keywords次世代シーケンサ / メタバーコーディング / 系統 / 進化 / 集団構造 / 起源 / 深海 / ミトゲノム / 中・深層性魚類 / 進化的起源 / 大量データ / 解析パイプライン / ミトゲノム全長配列 / 次世代シークエンサ
Outline of Final Research Achievements

In this study, we attempted to develop a novel, data-driven approach for biodiversity research, where descriptive studies have still been dominated. Our approach is based on massive genetic data derived from metabarcoding (simultaneous multispecies detection system) and genomic sequencing. By metabarcoding DNA from 1,164 fishes taken from midwater trawls across the North and South Pacific, we discovered two new species of deep-sea barrel eyes. We also developed a new method for sequencing whole mitogenome sequences from nearly 100 fish species in a single experiment and those data will be subjected to phylogenetic analysis to elucidate evolutionary origin of those fishes.

Report

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

Research Products

(19 results)

All 2017 2016 2015 2014 Other

All Journal Article (6 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 6 results,  Open Access: 6 results,  Acknowledgement Compliant: 6 results) Presentation (9 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results) Book (1 results) Remarks (3 results)

  • [Journal Article] Evolutionary affinities of the unfathomable Parabrotulidae: molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes2017

    • Author(s)
      Campbell, M.A., Nielsen, J.G., Sado, T., Shinzato, C., Kanda, M., Satoh, T.P., & Miya, M.
    • Journal Title

      Molecular Phylogenetics and Evolution

      Volume: 109 Pages: 337-342

    • DOI

      10.1016/j.ympev.2017.02.004

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Preservation obscures pelagic deep-sea fish diversity: doubling the number of sole-bearing opisthoproctids and resurrection of the genus Monacoa (Opisthoproctidae, Argentiniformes)2016

    • Author(s)
      Poulsen, J.Y., Sado, T., Hahn, C., Byrkjedal, I., Moku, M. and Miya, M.
    • Journal Title

      PLOS ONE

      Volume: 11

    • DOI

      10.1371/journal.pone.0159762

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Structure and variation of the mitochondrial genome of fishes2016

    • Author(s)
      Satoh, T.P., Miya, M., Mabuchi, K. & Nishida, M.
    • Journal Title

      BMC Genomics

      Volume: 17 Pages: 719-719

    • DOI

      10.1186/s12864-016-3054-y

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Use of a filter cartridge for filtration of water samples and extraction of environmental DNA2016

    • Author(s)
      Miya, M., Minamoto, T., Yamanaka, H., Oka, S., Sato, K., Yamamoto, S., Sado, T. & Doi, H.
    • Journal Title

      Journal of Visualized Experiments

      Volume: 117

    • DOI

      10.3791/54741

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species2015

    • Author(s)
      Masaki Miya et al.
    • Journal Title

      Roy. Soc. Open Sci.

      Volume: 2 Pages: 150088-150088

    • DOI

      10.1098/rsos.150088

    • NAID

      120006220784

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect2015

    • Author(s)
      Miya, M. and Nishida, M.
    • Journal Title

      Ichthyological Research

      Volume: 62 Pages: 29-71

    • DOI

      10.1007/s10228-014-0440-9

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Environmental DNA metabarcoding from fishes (and other vertebrates) using universal primers MiFish: A data-driven approach for fish community research2016

    • Author(s)
      Miya, M.
    • Organizer
      2016 The North Pacific Marine Science Organization (PICES) Annual Meeting
    • Place of Presentation
      OMNI Hotel, San Diego
    • Year and Date
      2016-11-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Environmental DNA metabarcoding from fishes (and other vertebrates) using universal primers MiFish: A data-driven approach for fish community research2016

    • Author(s)
      Miya, M.
    • Organizer
      2016 Annual Meeting of the Asian Society of Ichthyologists
    • Place of Presentation
      Taipei Nangang Exhibition Center
    • Year and Date
      2016-05-19
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 魚類の環境DNAメタバーコーディング:データ主導型・発見探索型アプローチがもたらす新たな展開2016

    • Author(s)
      宮 正樹
    • Organizer
      日本生態学会第63回全国大会
    • Place of Presentation
      仙台国際センター
    • Year and Date
      2016-03-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 環境DNAを用いた魚類のメタバーコーディング:ビッグデータで魚類群集をモニタリングする2015

    • Author(s)
      宮 正樹
    • Organizer
      2015年度日本魚類学会年会
    • Place of Presentation
      近畿大学
    • Year and Date
      2015-09-06
    • Related Report
      2015 Annual Research Report
  • [Presentation] 北の海に未知なる生命と生物多様性を探る2015

    • Author(s)
      荒木仁志・宮 正樹・池田 実・矢部 衞・永野優季・神戸崇・鎌田頌子・佐土哲也・峰岸有紀・佐藤行人・佐藤俊平・Maslenikov, K.
    • Organizer
      日本進化学会第17回大会
    • Place of Presentation
      中央大学
    • Year and Date
      2015-08-22
    • Related Report
      2015 Annual Research Report
  • [Presentation] 環境DNAメタバーコーディング解析のためのパイプライン開発2015

    • Author(s)
      佐藤行人・荒木仁志・宮 正樹・佐土哲也・峰岸有紀・岩崎渉
    • Organizer
      日本進化学会第17回大会
    • Place of Presentation
      中央大学
    • Year and Date
      2015-08-22
    • Related Report
      2015 Annual Research Report
  • [Presentation] Miya, M., Y. Sato, T, Fukunaga, T. Sado, J. Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh and W. Iwasaki2015

    • Author(s)
      Miya, M., Y. Sato, T, Fukunaga, T. Sado, J. Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh and W. Iwasaki
    • Organizer
      6th International Barcode of Life Conference
    • Place of Presentation
      University of Guelph
    • Year and Date
      2015-08-19
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 魚類環境DNA 用ユニバーサルプライマーの開発と次世代シーケンサを用いた環境水分析法の確立:美ら海水族館の環境水から検出に成功した板鰓類2014

    • Author(s)
      宮 正樹・佐藤行人・福永津嵩・佐土哲也・佐藤圭一・源 利文・山中裕樹・荒木仁志・岩崎 渉
    • Organizer
      板鰓類シンポジウム2014「サメ・エイ類研究の最前線~現状と将来展望」
    • Place of Presentation
      東京大学農学部弥生講堂・一条ホール
    • Year and Date
      2014-12-04
    • Related Report
      2014 Annual Research Report
  • [Presentation] 魚類環境DNA 用ユニバーサルプライマーの開発と次世代シーケンサを用いた環境水分析法の確立2014

    • Author(s)
      宮 正樹・佐藤行人・福永津嵩・佐土哲也・佐藤圭一・源 利文・山中裕樹・荒木仁志・岩崎 渉
    • Organizer
      日本魚類学会年会
    • Place of Presentation
      神奈川県立・生命の星・地球博物館
    • Year and Date
      2014-11-16
    • Related Report
      2014 Annual Research Report
  • [Book] 新たな魚類大系統 ー 遺伝子で解き明かす魚類3万種の由来と現在2016

    • Author(s)
      宮 正樹
    • Total Pages
      218
    • Publisher
      慶應義塾大学出版会
    • Related Report
      2016 Annual Research Report
  • [Remarks] Masaki Miya Lab Home Page

    • URL

      https://sites.google.com/site/masakimiyalab/home

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report 2014 Annual Research Report
  • [Remarks] Google Scholar My Citations

    • URL

      https://scholar.google.com/citations?user=aTG4wPQAAAAJ&hl=en

    • Related Report
      2016 Annual Research Report
  • [Remarks] Research Gate

    • URL

      https://www.researchgate.net/profile/Masaki_Miya

    • Related Report
      2016 Annual Research Report

URL: 

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

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