Unlock the biodiversity and functioning in food-webs using metabarcoding and metagenomics

• Project/Area Number: 16F16092
• Research Category: Grant-in-Aid for JSPS Fellows
• Allocation Type: Single-year Grants
• Section: 外国
• Research Field: Biodiversity/Systematics
• Research Institution: Kyoto University
• Principal Investigator: 本川 雅治 京都大学, 総合博物館, 教授 (30293939)
• Co-Investigator(Kenkyū-buntansha): HE KAI 京都大学, 総合博物館, 外国人特別研究員
• Project Period (FY): 2016-10-07 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥2,300,000 (Direct Cost: ¥2,300,000); Fiscal Year 2018: ¥500,000 (Direct Cost: ¥500,000); Fiscal Year 2017: ¥1,000,000 (Direct Cost: ¥1,000,000); Fiscal Year 2016: ¥800,000 (Direct Cost: ¥800,000)
• Keywords: メタバーコーディング / 哺乳類 / 生物多様性 / 種分化 / 真無盲腸類 / 同所的分布 / 垂直分布 / ＤＮＡバーコーディング

Outline of Annual Research Achievements

本研究ではメタバーコーディングとメタゲノミクスの手法を用い，同所的に分布する真無盲腸類（食虫類）の食性と腸内微生物相の多様性解明を目指した．前年度までに収集したサンプルについて，その食性を明らかにするためのメタバーコーディングと同位体解析を行った．胃内容物から動物性および植物性のＤＮＡを新たに抽出し，春，夏，秋の季節変化および標高（低，中，高）による違いを考慮した解析を行った．Illuminaプラットフォームを用いて，無脊椎動物についてはＣＯI，植物質についてはchloroplast trnl遺伝子をＤＮＡバーコーディング領域とした．得られた配列データはスーパーコンピュータを用いて，既存のＤＮＡバーコードデータとの比較を行い，真無盲腸類が食物として利用している無脊椎動物および植物質を明らかにした．腸内微生物相についてはメタゲノミクスにより腸内微生物相やその多様性を明らかにし，さらに真無盲腸類の種間，季節，標高による違いを解明した．研究では，真無盲腸類と同所的に分布するが生態学的・系統学的に異なるネズミ類との比較も行った．同位体分析は乾燥させた体毛を用い，種間，季節，標高を考慮して，Ｃ１３とＮ１５の同位体比をもとに食物連鎖において，同所的に分布する真無盲腸類がその生態学的位置を時系列で変化させていることを明らかにした．また，無脊椎動物への食物としての依存についても検証し，メタバーコーディングにより得られた結果との比較を進めている．一連の研究で得られた成果について現在投稿論文としての作成を進めている．

Research Progress Status

平成30年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

平成30年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Systematics and macroevolution of extant and fossil scalopine moles (Mammalia, Talpidae) (2019)
  • Author(s): Schwermann Achim H.、He Kai、Peters Benjamin J.、Plogschties Thorsten、Sansalone Gabriele
  • Journal Title: Palaeontology Volume: - Issue: 4 Pages: 661-676
  • DOI: 10.1111/pala.12422
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A new genus of Asiatic short-tailed shrew (Soricidae, Eulipotyphla) based on molecular and morphological comparisons (2018)
  • Author(s): Kai He, Xing Chen, Peng Chen, Shui-Wang He, Feng Cheng, Xue-Long Jiang, Kevin Campbell
  • Journal Title: Zoological Research Volume: 39 Issue: 5 Pages: 321-334
  • DOI: 10.24272/j.issn.2095-8137.2018.058
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Taxonomic revision of the genus Mesechinus (Mammalia: Erinaceidae) with description of a new species (2018)
  • Author(s): Huai-Sen Ai*, Kai He*,#, Zhong-Zheng Chen*, Jia-Qi Li, Tao Wan, Quan Li, Wen-Hui Nie, Jin-Huan Wang, Wei-Ting Su, Xue-Long Jiang
  • Journal Title: Zoological Research Volume: 39 Issue: 5 Pages: 335-347
  • DOI: 10.24272/j.issn.2095-8137.2018.034
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Species identification of crested gibbons (Nomascus) in captivity in China using karyotyping- and PCR-based approaches (2018)
  • Author(s): Wenhui Nie#, Jinhuan Wang, Wei-Ting Su, Yi Hu, Shuiwang He, Xuelong Jiang#, Kai He
  • Journal Title: Zoological Research Volume: 39 Issue: 5 Pages: 356-363
  • DOI: 10.24272/j.issn.2095-8137.2018.036
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses (2018)
  • Author(s): Shao-Ying Liu, Kai He, Shun-De Chen, Wei Jin, Robert W. Murphy, Ming-Kun Tang, Rui Liao, Feng-Jun Li
  • Journal Title: Zoological Research Volume: 39 Issue: 5 Pages: 309-320
  • DOI: 10.24272/j.issn.2095-8137.2018.053
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Fossil gibbons (Mammalia, Hylobatidae) from the Pleistocene of Chongzuo, Guangxi Zhuang Autonomous (2018)
  • Author(s): Ying-Qi Zhang, Chang-Zhu Jin, Yuan Wang, Alejandra Ortiz, Kai He, Terry Harrison
  • Journal Title: Vertebrata PalAsiatica Volume: 56 Pages: 248-263
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Dispersal and female philopatry in a long-term, stable, polygynous gibbon population: Evidence from 16 years field observation and genetics (2018)
  • Author(s): Hu Naiqing、Guan Zhenhua、Huang Bei、Ning Wenhe、He Kai、Fan Pengfei、Jiang Xuelong
  • Journal Title: American Journal of Primatology Volume: 80 Issue: 9
  • DOI: 10.1002/ajp.22922
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Climate niche conservatism and complex topography illuminate the cryptic diversification of Asian shrew-like moles (2018)
  • Author(s): Wan Tao、He Kai、Jin Wei、Liu Shao-Ying、Chen Zhong-Zheng、Zhang Bin、Murphy Robert W.、Jiang Xue-Long
  • Journal Title: Journal of Biogeography Volume: 45 Issue: 10 Pages: 2400-2414
  • DOI: 10.1111/jbi.13401
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Molecular phylogeny and taxonomy of subgenus Eothenomys (Cricetidae: Arvicolinae: Eothenomys) with the description of four new species from Sichuan, China (2018)
  • Author(s): Liu Shao-Ying、Chen Shun-De、He Kai、Tang Mingkun、Liu Yang、Jin Wei、Li Song、Li Quan、Zeng Tao、Sun Zhi-Yu、Fu Jian-Rong、Liao Rui、Meng Yang、Wang Xin、Jiang Xue-Long、Murphy Robert W
  • Journal Title: Zoological Journal of the Linnean Society Volume: - Issue: 2 Pages: 569-598
  • DOI: 10.1093/zoolinnean/zly071
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Taxonomy based on science is necessary for global conservation (2018)
  • Author(s): Thomson, S.A.ほか182名（71/183）
  • Journal Title: PLoS Biology Volume: 16 Issue: 3 Pages: e2005075-e2005075
  • DOI: 10.1371/journal.pbio.2005075
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mitochondrial DNA analyses and ecological niche modeling reveal post-LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya (2018)
  • Author(s): Khanal Laxman、Chalise Mukesh K.、He Kai、Acharya Bipin K.、Kawamoto Yoshi、Jiang Xuelong
  • Journal Title: American Journal of Primatology Volume: 80 Issue: 3
  • DOI: 10.1002/ajp.22748
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Altered hemoglobin co-factor sensitivity does not underlie the evolution of derived fossorial specializations in the family Talpidae (2018)
  • Author(s): Campbell, K.L., Gaudry, M.J., He, K., Suzuki, H., Zhang, Y.-p., Jiang, X.-L., Weber, R.E.
  • Journal Title: Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology Volume: - Pages: 150-155
  • DOI: 10.1016/j.cbpb.2018.01.001
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] First records of Indochinese Arboreal Niviventer (Chiromyscus langbianis) in Yunnan Province, China (2018)
  • Author(s): Feng Cheng, Zhongzheng Chen, Bin Zhang, Kai He, Xuelong Jiang
  • Journal Title: Acta Theriologica Sinica Volume: 38 Pages: 217-220
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Capture Hybridization of Long-Range DNA Fragments for High-Throughput Sequencing (2018)
  • Author(s): Chen, X., Ni, G., He, K., Ding, Z.-l., Li, G.-m., Adeola, A.C., Murphy, R.W., Wang, W.-z., Zhang, Y.-P.
  • Journal Title: Huang T, editor. Computational Systems Biology: Methods and Protocols. Springer New York. Volume: - Pages: 29-44
  • DOI: 10.1007/978-1-4939-7717-8_3
  • ISBN: 9781493977161, 9781493977178
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] First records of Taiwanese Gray Shrew (Crocidura tanakae) in Yunnan Province, China (2017)
  • Author(s): CHENG Feng, WAN Tao, CHEN Zhong-Zheng, Narayan Prasad Koju, HE Kai, JIANG Xue-Long
  • Journal Title: Chinese Journal of Zoology Volume: 52 Pages: 865-869
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Phylogeny and systematic revision of the genus Typhlomys (Rodentia, Platacanthomyidae): with description of new species. (2017)
  • Author(s): Feng Cheng,Kai He, Zhong-Zheng Chen, Bin Zhang, Tao Wan, Bao-Wei Zhang, Xue-Long Jiang.
  • Journal Title: Journal of Mammalogy Volume: - Issue: 3 Pages: 731-743
  • DOI: 10.1093/jmammal/gyx016
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Description of a new species of Hoolock gibbon (Primates: Hylobatidae) based on integrative taxonomy (2017)
  • Author(s): Fan, Peng-Fei, He, Kai, Chen, Xing, Ortiz, Alejandra, Zhang, Bin, Zhao, Chao, Li, Yun-Qiao, Zhang, Hai-Bo, Kimock, Clare, Wang, Wen-Zhi, Groves, Colin, Turvey, Samuel T., Roos, Christian, Helgen, Kristofer M. and Jiang, Xue-Long
  • Journal Title: American Journal of Primatology Volume: 79 Issue: 5
  • DOI: 10.1002/ajp.22631
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Talpid mole phylogeny unites shrew moles and illuminates overlooked cryptic species diversity (2017)
  • Author(s): He, Kai, Shinohara, Akio, Helgen, Kristofer M., Springer, Mark S., Jiang, Xue-Long and Campbell, Kevin L.
  • Journal Title: Molecular Biology and Evolution Volume: 34 Issue: 1 Pages: 78-87
  • DOI: 10.1093/molbev/msw221
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China (2017)
  • Author(s): Koju, Narayan Prasad, He, Kai, Chalise, Mukesh Kumar, Ray, Chris, Chen, Zhongzheng, Zhang, Bin, Wan, Tao, Chen, Shunde and Jiang, Xuelong.
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 107 Pages: 237-245
  • DOI: 10.1016/j.ympev.2016.11.005
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China. (2016)
  • Author(s): Zhang, Bin, He, Kai, Wan, Tao, Chen, Peng, Sun, Guozheng, Liu, Shaoying, Nguyen, Truong Son, Lin, Liangkong and Jiang, Xuelong
  • Journal Title: BMC Evolutionary Biology Volume: 16 Issue: 1
  • DOI: 10.1186/s12862-016-0832-8
  • NAID: 120006338060
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] Niche partitioning and Gut microbiome of small mammals shaped by environmental habitats and seasonal change (2018)
  • Author(s): He Kai, 斉藤浩明, 本川雅治
  • Organizer: The 2018 Annual Meeting of the Mammal Society of Japan
• [Presentation] Uncover small mammal diversity using integrative approaches with implication on the mammal fauna in northern Myanmar (2017)
  • Author(s): Kai HE, Jin-Wen SHI, Masaharu MOTOKAWA
  • Organizer: Kyoto University and University of Yangon International Symposium/ AVIS2017
  • Int'l Joint Research / Invited
• [Presentation] Seasonality of small mammal communities in Mt. Nishikoma (Nagano), and its potential toward the understanding of ecological network (preliminary data) (2017)
  • Author(s): Kai HE, 斉藤浩明, 本川雅治
  • Organizer: The 2017 Annual Meeting of the Mammal Society of Japan
• [Presentation] Cryptic diversity in an enigmatic mammal species from the sky islands of southwestern China (2016)
  • Author(s): Kai He, Tao Wan, Klaus-Peter Koepfli, Xue-Long Jiang
  • Organizer: The 22nd International Congress of Zoology
  • Place of Presentation: 沖縄科学技術大学院大学（沖縄県・恩納村）
  • Year and Date: 2016-11-16
  • Int'l Joint Research
• [Presentation] A new taxon of hoolock gibbon from Southwest China (2016)
  • Author(s): Fan, Peng-Fei, He, Kai, Chen, Xing, Ortiz, Alejandra, Zhang, Bin, Zhao, Chao, Li, Yun-Qiao, Zhang, Hai-Bo, Kimock, Clare, Wang, Wen-Zhi, Groves, Colin, Turvey, Samuel T., Roos, Christian, Helgen, Kristofer M. and Jiang, Xue-Long
  • Organizer: 日本哺乳類学会2016年大会
  • Place of Presentation: つくば大学（茨城県・つくば市）
  • Year and Date: 2016-09-23