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Development of eDNA methods for estimating intra-genetic variation of salmonid and migratory fish species

Research Project

Project/Area Number 20H03005
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 39060:Conservation of biological resources-related
Research InstitutionHokkaido University

Principal Investigator

Araki Hitoshi  北海道大学, 農学研究院, 教授 (20707129)

Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000)
Fiscal Year 2022: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2021: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2020: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Keywords環境DNA / 種内多型 / 魚類 / 回遊性魚類 / 純淡水魚 / マイクロサテライト
Outline of Research at the Start

本研究では、近年発展目覚ましい「環境DNA技術」を種内多型解析ツールとして発展させ、サケ科魚類に代表される地域特異性の高い回遊魚の生物分布と遺伝的多様性を同時に評価する手法を開発する。回遊魚は日本人にとって資源・文化両面から極めて重要な存在だが、分布域における季節性や個体群の遺伝的特性に関する情報はしばしば著しく制限されている。本研究では、捕獲に依らず、河川・沿岸で採取した環境水から抽出したDNAを解析する環境DNA技術を用いて回遊魚の移住特性と遺伝的背景の関係を明らかにすると共に、本技術を用いた効果的な水圏野生動物の遺伝的背景の解析技術を確立する。

Outline of Final Research Achievements

Salmonid fishes are highly valuable as fishery resources and play an important ecological role in linking forests, rivers, and oceans through the food chain. However, it is very difficult to comprehensively understand their ecology as they move over a wide area throughout their life history. In this study, we applied environmental DNA technology, which can efficiently estimate the distribution of organisms over a wide area, and developed it into a technology that can analyze intraspecific variation, thereby realizing the estimation of the distribution of aquatic organisms and their genetic diversity at the same time. As a result, we were able to quantitatively evaluate the distribution of Sakhalin taimen and the impact of non-native rainbow trout from DNA contained in river water. In addition, we were able to clearly distinguish the phylogenetic relationship of chum salmon in northern Japan.

Academic Significance and Societal Importance of the Research Achievements

サケなどの回遊性魚類は重要な水産資源であると同時に、食物連鎖を介して陸と海を繋ぐ重要な生態的役割を担っている。しかし、広範囲に移動する彼らの生態を網羅的に把握するのは非常に困難で、生物保全・管理上の障壁となってきた。そこで本研究では環境DNA技術を応用し、周辺水圏生物の在不在や分布のみならず、種内多型に関する情報の推定を試みた。その結果、希少種イトウの分布制限要因となるニジマスの影響を定量評価したほか、サケの個体群の遺伝的構成を環境水から再現することに成功した。これらの結果は水産有用種のみならず希少種・外来種管理に広く応用可能で、今後の生物モニタリングに広く適用されることが期待される。

Report

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

    (27 results)

All 2023 2022 2021 2020

All Journal Article (7 results) (of which Peer Reviewed: 7 results,  Open Access: 6 results) Presentation (18 results) (of which Int'l Joint Research: 6 results,  Invited: 4 results) Book (1 results) Funded Workshop (1 results)

  • [Journal Article] edna2021: The fourth annual meeting of The eDNA Society “Species distributions, and beyond”2022

    • Author(s)
      Araki Hitoshi、Kanbe Takashi、Yamanaka Hiroki、Minegishi Yuki、Koizumi Noriyuki
    • Journal Title

      Environmental DNA

      Volume: 00 Issue: 3 Pages: 1-5

    • DOI

      10.1002/edn3.278

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effectiveness of check-dam improvement on freshwater fishes: assessment based on long-term monitoring and environmental DNA applicability.2021

    • Author(s)
      HAYAMIZU Masato、ISHIYAMA Nobuo、MIZUMOTO Hiroki、KANBE Takashi、SHIMODA Kazutaka、MISAKA Naoyuki、URABE Hirokazu、NAGASAKA Akiko、NAGASAKA Yu、ONO Satoru、ARAKI Hitoshi、NAKAJIMA Nobuyoshi、FUKUSHIMA Michio
    • Journal Title

      Ecology and Civil Engineering

      Volume: 24 Issue: 1 Pages: 61-73

    • DOI

      10.3825/ece.20-00043

    • NAID

      130008095704

    • ISSN
      1344-3755, 1882-5974
    • Year and Date
      2021-07-28
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Utilizing environmental DNA for wide-range distributions of reproductive area of an invasive terrestrial toad in Ishikari river basin in Japan2021

    • Author(s)
      Mizumoto Hiroki、Kishida Osamu、Takai Kotaro、Matsuura Naru、Araki Hitoshi
    • Journal Title

      Biological Invasions

      Volume: 24 Issue: 4 Pages: 1199-1211

    • DOI

      10.1007/s10530-021-02709-y

    • Related Report
      2021 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
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An Environmental DNA Survey on Distribution of an Endangered Salmonid Species, Parahucho perryi, in Hokkaido, Japan2020

    • Author(s)
      Mizumoto Hiroki、Mitsuzuka Takashi、Araki Hitoshi
    • Journal Title

      Frontiers in Ecology and Evolution

      Volume: 8 Pages: 569425-569425

    • DOI

      10.3389/fevo.2020.569425

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Understanding seasonal migration of Shishamo smelt in coastal regions using environmental DNA2020

    • Author(s)
      Yatsuyanagi Tetsu、Araki Hitoshi
    • Journal Title

      PLOS ONE

      Volume: 15 Issue: 10 Pages: e0239912-e0239912

    • DOI

      10.1371/journal.pone.0239912

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Environmental DNA monitoring for short‐term reproductive migration of endemic anadromous species, Shishamo smelt ( Spirinchus lanceolatus )2020

    • Author(s)
      Yatsuyanagi Tetsu、Ishida Ryotaro、Sakata Masayuki K.、Kanbe Takashi、Mizumoto Hiroki、Kobayashi Yumi、Kamada Shoko、Namba Satoko、Nii Hisaya、Minamoto Toshifumi、Araki Hitoshi
    • Journal Title

      Environmental DNA

      Volume: 2 Issue: 2 Pages: 130-139

    • DOI

      10.1002/edn3.50

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] eDNA applications to rare and invasive species in northern biosphere of Hokkaido, Japan2023

    • Author(s)
      Hitoshi Araki
    • Organizer
      1st Australian & New Zealand Environmental DNA Conference
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 河川・湖沼の環境DNAアプリケーション2022

    • Author(s)
      荒木仁志
    • Organizer
      信州大学・東京大学・北海道大学・水産技術研究所 合同研究セミナー
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Downstream migration of released salmon juveniles estimated with environmental DNA2022

    • Author(s)
      Fujii, Kanbe, Inoue, Araki
    • Organizer
      IYS 2022 Pan-Pacific Expedition Hybrid Preliminary Results Meeting
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] サケに触れずにサケを知る ~環境DNAの挑戦2022

    • Author(s)
      荒木仁志
    • Organizer
      第15 回 サケ学研究会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 環境DNAハプロタイピングにもとづくオショロコマの遺伝子浸透率推定2022

    • Author(s)
      小澤、神戸、荒木
    • Organizer
      環境DNA学会ワークショップ
    • Related Report
      2022 Annual Research Report
  • [Presentation] 環境DNAを透して見る北方水圏生態系の生き物たち2021

    • Author(s)
      荒木仁志
    • Organizer
      日本動物学会北海道支部・公開シンポジウム
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 環境DNAを用いた生物相モニタリングとその活用2021

    • Author(s)
      荒木仁志
    • Organizer
      全国湖沼河川養殖研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Anadromous fish monitoring using environmental DNA2021

    • Author(s)
      Hitoshi Araki, Hiroki Mizumoto, Tetsu Yatsuyanagi, Takashi Kanbe
    • Organizer
      NPAFC-IYS workshop
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 絶滅危惧種イトウの分布解明2021

    • Author(s)
      水本寛基、三塚多佳志、荒木仁志
    • Organizer
      野生生物と社会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Seasonally differentiated distributions of the two smelt species in Hokkaido2021

    • Author(s)
      Takahito Ikeda, Takashi Kanbe, Hitoshi Araki
    • Organizer
      環境DNA学会
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] eDNA survey on distribution of domestic alien freshwater shrimp, Paratya compressa, in Hokkaido2021

    • Author(s)
      Yuki Kato, Takashi Kanbe, Hitoshi Araki
    • Organizer
      環境DNA学会
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] An eDNA survey on toxic invasive toad in Hokkaido2021

    • Author(s)
      Hiroki MIZUMOTO, Osamu KISHIDA, Kotaro TAKAI, Naru MATSUURA, Hitoshi ARAKI
    • Organizer
      日本生態学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Environmental DNA for identifying “red zone” of endangered/invasive species2020

    • Author(s)
      Hitoshi Araki, Hiroki Yamanaka, Kimiko Uchii, Michinobu Kuwae, Hideyuki Doi
    • Organizer
      PICES
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development and Application of Environmental DNA Techniques for Evaluating Distribution and Population Status of Rare/Invasive Species2020

    • Author(s)
      Hitoshi Araki, Hiroki Yamanaka, Kimiko Uchii, Michinobu Kuwae, Hideyuki Doi
    • Organizer
      環境DNA学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 環境DNAを用いたナガレモンイワナのハプロタイプ解析2020

    • Author(s)
      水本 寛基、亀甲 武志、荒木 仁志
    • Organizer
      日本魚類学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 環境DNAにより推定された、純淡水魚フクドジョウの分布傾向と系統地理2020

    • Author(s)
      八柳哲、神戸崇、水本寛基、福島路生、中嶋信美、荒木仁志
    • Organizer
      日本進化学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Applicability of an eDNA technique for haplotype analysis on nagaremon-charr2020

    • Author(s)
      Hiroki MIZUMOTO, Takeshi KIKKO, Takashi KANBE, Jun-ichi TSUBOI, Kentaro MORITA, Hitoshi ARAKI
    • Organizer
      日本生態学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Phylogeographic analysis on Siberian stone loach based on environmental DNA2020

    • Author(s)
      Tetsu Yatsuyanagi, Takashi Kanbe, Hiroki Mizumoto, Nobuyoshi Nakajima, Michio Fukushima, Hitoshi Araki
    • Organizer
      日本生態学会
    • Related Report
      2020 Annual Research Report
  • [Book] 環境DNA2021

    • Author(s)
      一般社団法人 環境DNA学会、土居 秀幸、近藤 倫生
    • Total Pages
      300
    • Publisher
      共立出版
    • ISBN
      432005816X
    • Related Report
      2020 Annual Research Report
  • [Funded Workshop] edna2021:The 4th annual meeting of The eDNA Society2021

    • Related Report
      2021 Annual Research Report

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Published: 2020-04-28   Modified: 2024-01-30  

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