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Unraveling variation patterns and the formation/maintenance mechanisms of fish community structures through multi-site, high-frequency environmental DNA sampling

Research Project

Project/Area Number 19H03291
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 45030:Biodiversity and systematics-related
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(移行) (30250137)

Co-Investigator(Kenkyū-buntansha) 潮 雅之  京都大学, 白眉センター, 特定准教授 (40722814)
Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥16,900,000 (Direct Cost: ¥13,000,000、Indirect Cost: ¥3,900,000)
Fiscal Year 2021: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2020: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2019: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Keywords環境DNA / メタバーコーディング / MiFish法 / 時系列解析 / 魚類群集 / 種間関係 / モニタリング / 生物多様性 / 環境DNAメタバーコーディング / 時空間分析 / 房総半島 / 黒潮 / 多様性分析 / 時空間動態 / 多地点高頻度調査 / ビッグデータ / 時空間分布 / 多地点・高頻度観測 / 変動様式 / 地理的構造 / 魚類 / 群集
Outline of Research at the Start

本研究は,多地点・高頻度環境DNA観測を行い,さまざまな時空間スケールにおける魚類群集構造の変動様式をMiFish法によって明らかにすることを第一の目的とする。また,MiFish法で得られたデータを最新の手法で定量化することにより,先の調査で明らかになった魚類群集構造の形成・維持機構を解き明かすことを第二の目的とする。これら二つの目的を達成するため,房総半島南部の岩礁海岸に11測点を設け,MiFish法による魚類群集モニタリングをさまざまな時空間スケールで行う。さらに,魚類群集の動態予測や制御につながるデータ駆動型・仮説発見型の新たな分野を創出することを第三の目的とする。

Outline of Final Research Achievements

To explore spatio-temporal patterns and the mechanisms forming and maintaining fish communities, we collected 550 environmental DNA samples from 11 sites along the southern coast of the Boso Peninsula, central Japan, over a two-year period. MiFish metabarcoding was performed on all 550 samples, followed by a time-series analysis using a newly-developed method. In total, we identified 856 fish species across 33 orders, 167 families, and 466 genera. The observed occurrence patterns of these species exhibited spatio-temporal variations, likely influenced by ocean currents and the contrasting environments between the open ocean and inner bay areas. Furthermore, our analysis of the interspecific interaction strengths among the 50 most frequently detected species revealed diverse temperature-dependent patterns. These findings provide substantial implications for future research on fish community stability in the face of climate change.

Academic Significance and Societal Importance of the Research Achievements

本研究は,近年発展が著しい環境DNA分析に最先端の時系列解析法を適用することによって,生物間の関係性に新たに焦点を当てることに成功した。すなわち,これまでの環境DNA研究で得られる情報は「何がどこにいるか」だけだったのが,本研究の手法を使えば「何と何がどれくらいの強さで関係しているか」まで推定できるようになったことを意味する。さらに,魚類群集における種間関係強度の温度依存性の存在を実証できたことは,全世界的に大きな問題となっている地球温暖化が,魚類群集のような複雑系に何らかの影響を与えることをも示唆している。環境DNAを用いた生物多様性モニタリングを継続していく意義を高めたと言ってもよい。

Report

(4 results)
  • 2022 Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (16 results)

All 2022 2021 2020 2019 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 5 results) Presentation (4 results) (of which Int'l Joint Research: 4 results,  Invited: 4 results) Remarks (1 results)

  • [Journal Article] Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities2022

    • Author(s)
      Masaki Miya
    • Journal Title

      Annual Review of Marine Science

      Volume: 14 Issue: 1 Pages: 161-185

    • DOI

      10.1146/annurev-marine-041421-082251

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Optimization of environmental DNA extraction and amplification methods for metabarcoding of deep-sea fish2021

    • Author(s)
      Masaru Kawato,Takao Yoshida,Masaki Miya,Shinji Tsuchida,Yuriko Nagano,Michiyasu Nomura,Akinori Yabuki,Yoshihiro Fujiwara,Katsunori Fujikura
    • Journal Title

      MethodsX

      Volume: 8 Pages: 101238-101238

    • DOI

      10.1016/j.mex.2021.101238

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation2020

    • Author(s)
      Oka Shin‐ichiro、Doi Hideyuki、Miyamoto Kei、Hanahara Nozomi、Sado Tetsuya、Miya Masaki
    • Journal Title

      Environmental DNA

      Volume: 3 Issue: 1 Pages: 55-69

    • DOI

      10.1002/edn3.132

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols2020

    • Author(s)
      Minamoto Toshifumi、Miya Masaki、Sado Tetsuya、Seino Satoquo、Doi Hideyuki、Kondoh Michio、Nakamura Keigo、Takahara Teruhiko、Yamamoto Satoshi、Yamanaka Hiroki、Araki Hitoshi、Iwasaki Wataru、Kasai Akihide、Masuda Reiji、Uchii Kimiko
    • Journal Title

      Environmental DNA

      Volume: 3 Issue: 1 Pages: 8-13

    • DOI

      10.1002/edn3.121

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding2020

    • Author(s)
      H. Ahn, M. Kume, Y. Terashima, F. Ye, S. Kameyama, M. Miya, Y. Yamashita, A. Kasai
    • Journal Title

      PLOS ONE

      Volume: 15 Issue: 10 Pages: e0231127-e0231127

    • DOI

      10.1371/journal.pone.0231127

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples2020

    • Author(s)
      Masaki Miya, Ryo O. Gotoh, Tetsuya Sado
    • Journal Title

      Fisheries Science

      Volume: 86 Issue: 6 Pages: 939-970

    • DOI

      10.1007/s12562-020-01461-x

    • NAID

      40022414234

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA2020

    • Author(s)
      Sakata Masayuki K.、Yamamoto Satoshi、Gotoh Ryo O.、Miya Masaki、Yamanaka Hiroki、Minamoto Toshifumi
    • Journal Title

      Environmental DNA

      Volume: - Issue: 4 Pages: 505-518

    • DOI

      10.1002/edn3.75

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA2020

    • Author(s)
      Sakata, M.K. , Yamamoto, S. , Gotoh, R.O. , Miya, M. , Yamanaka, H. , Minamoto, M.
    • Journal Title

      Environmental DNA

      Volume: 3

    • NAID

      120006975750

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs2020

    • Author(s)
      HAYAMI Kana , SAKATA Masayuki K. , INAGAWA Takashi , OKITSU Jiro , KATANO Izumi , DOI Hideyuki , NAKAI Katsuki , ICHIYANAGI Hidetaka , GOTOH Ryo O. , MIYA Masaki , SATO Hirotoshi , YAMANAKA Hiroki , MINAMOTO Toshifumi
    • Journal Title

      Ecology and Evolution

      Volume: -

    • NAID

      120006872999

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ongoing localized extinctions of stream-dwelling white-spotted charr populations in small dammed-off habitats of Hokkaido Island, Japan2019

    • Author(s)
      Kentaro Morita, Genki Sahashi, Masaki Miya, Shouko Kamada, Takashi Kanbe, Hitoshi Araki
    • Journal Title

      Hydrobiologia

      Volume: 印刷中 Issue: 1 Pages: 1-7

    • DOI

      10.1007/s10750-019-3891-1

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water2019

    • Author(s)
      Tsuji S , Miya M , Ushio M , Satoh H , Minamoto T , Yamanaka H
    • Journal Title

      Environmental DNA

      Volume: 2 Pages: 42-52

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Presentation] Environmental DNA metabarcoding enables a data-driven approach for fish community research in large spatiotemporal scales2019

    • Author(s)
      Miya, M
    • Organizer
      Gordon Research Conference in Marine Molecular Ecology: Novel Insights into Marine Patterns and Processes
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Environmental DNA metabarcoding enables a data-driven approach for fish community research in large spatiotemporal scales2019

    • Author(s)
      Miya, M
    • Organizer
      FSBI symposium 2019: Advances in eDNA-based Approaches to Fish Ecology and Management
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Environmental DNA metabarcoding: a new biodiversity monitoring method that enables a data-driven approach for fish community research2019

    • Author(s)
      Miya, M
    • Organizer
      Marine Biotechnology Conference 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Environmental DNA metabarcoding: a new biodiversity monitoring method that enables a data-driven approach for fish community research2019

    • Author(s)
      Miya, M
    • Organizer
      The International Symposium of Hydrological Sciences and High-efficiency Water Resources Utilization under the Changing Environment
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Remarks] researchmap 宮 正樹

    • URL

      https://researchmap.jp/mum-usagi

    • Related Report
      2019 Annual Research Report

URL: 

Published: 2019-04-18   Modified: 2024-01-30  

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