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

• Project/Area Number: 26291083
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Biodiversity/Systematics
• Research Institution: Natural 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: ¥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.

Research Products

• [Journal Article] Evolutionary affinities of the unfathomable Parabrotulidae: molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes (2017)
  • 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
  • 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 Issue: 8 Pages: e0159762-e0159762
  • DOI: 10.1371/journal.pone.0159762
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structure and variation of the mitochondrial genome of fishes (2016)
  • Author(s): Satoh, T.P., Miya, M., Mabuchi, K. & Nishida, M.
  • Journal Title: BMC Genomics Volume: 17 Issue: 1 Pages: 719-719
  • DOI: 10.1186/s12864-016-3054-y
  • 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 DNA (2016)
  • 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 Issue: 117
  • DOI: 10.3791/54741
  • 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 species (2015)
  • Author(s): Masaki Miya et al.
  • Journal Title: Royal Society open science Volume: 2 Issue: 7 Pages: 150088-150088
  • DOI: 10.1098/rsos.150088
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect (2015)
  • Author(s): Miya, M. and Nishida, M.
  • Journal Title: Ichthyological Research Volume: 62 Issue: 1 Pages: 29-71
  • DOI: 10.1007/s10228-014-0440-9
  • 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 research (2016)
  • 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
  • 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 research (2016)
  • 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
  • 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
  • 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
• [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
• [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
• [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. Iwasaki (2015)
  • 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
  • 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
• [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
• [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
• [Remarks] Masaki Miya Lab Home Page
  • URL: https://sites.google.com/site/masakimiyalab/home
• [Remarks] Google Scholar My Citations
  • URL: https://scholar.google.com/citations?user=aTG4wPQAAAAJ&hl=en
• [Remarks] Research Gate
  • URL: https://www.researchgate.net/profile/Masaki_Miya