Advancement of sensory ecology and genomics of primates by contrasting New and Old Worlds

2021 Fiscal Year Annual Research Report

• Project/Area Number: 18H04005
• Research Institution: The University of Tokyo
• Principal Investigator: 河村 正二 東京大学, 大学院新領域創成科学研究科, 教授 (40282727)
• Co-Investigator(Kenkyū-buntansha): 今井 啓雄 京都大学, 霊長類研究所, 教授 (60314176)
• Project Period (FY): 2018-04-01 – 2022-03-31
• Keywords: 感覚進化 / 霊長類 / 色覚 / 嗅覚 / 味覚

Outline of Annual Research Achievements

ヒトの嗅覚受容体遺伝子ファミリーの多くの遺伝子に新規の構造欠損多型と遺伝子重複・欠失多型を検出した。ヒト参照全ゲノムデータベースでintactである嗅覚受容体遺伝子にも構造欠損アリルが高頻度見られる場合があり、ヒト参照全ゲノムデータベースでnearly intact偽遺伝子である嗅覚受容体遺伝子では構造欠損アリルは低頻度でしか見られない場合があることを見出した。また、遺伝子重複・欠失多型が特定のゲノム領域に偏在する傾向を見出し、クロマチン構造との関連の可能性を示唆した。さらに嗅覚受容体遺伝子ファミリーと中立対照領域を、単塩基多型の主成分分析、塩基配列多型に基づく集団系統樹、塩基頻度スペクトルを評価するTajima’s D指標で比較し、両者の遺伝的多様性の集団分化の違いを評価した。中立対照領域を用いたことで、嗅覚受容体遺伝子ファミリーは集団分化度が高い一方で、多様性のパターンが平衡選択と呼ばれる自然選択により維持されている可能性を示した。オナガザル科と広鼻猿類のintactである嗅覚受容体遺伝子の数と色覚の容態との間に明確な関係性はないことを示した。オナガザル科はその共通祖先において、苦味受容体遺伝子を増加させたのに対し、広鼻猿は真猿類の共通祖先からほとんど変化していないことを示した。オナガザル科のうちコロブス亜科はその共通祖先において、多くの苦味受容体を欠失したのに対し、オナガザル亜科は様々な系統において独立に少しずつ苦味受容体を欠失しており、結果的にintactな苦味受容体遺伝子数は両亜科で類似しているが、構成は異なることを示した。テナガザルはその共通祖先において苦味受容体遺伝子の多くを染色体上のクラスターごと欠失していることを示した。

Research Progress Status

令和3年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和3年度が最終年度であるため、記入しない。

Research Products

• [Int'l Joint Research] University of Calgary(カナダ)
  • Country Name: CANADA
  • Counterpart Institution: University of Calgary
• [Int'l Joint Research] University of Idaho/University of Texas at Austin(米国)
  • Country Name: U.S.A.
  • Counterpart Institution: University of Idaho/University of Texas at Austin
• [Int'l Joint Research] 浙江大学(中国)
  • Country Name: CHINA
  • Counterpart Institution: 浙江大学
• [Int'l Joint Research] Hpa-An University(ミャンマー)
  • Country Name: MYANMAR
  • Counterpart Institution: Hpa-An University
• [Journal Article] Genetic variation of olfactory receptor gene family in a Japanese population (2022)
  • Author(s): Akhtar, M. S., Ashino, R., Oota, H., Ishida, H., Niimura, Y., Touhara, K., Melin, A. D. and Kawamura, S.
  • Journal Title: Anthropological Science Volume: unassigned Pages: Online
  • DOI: 10.1537/ase.211024
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Evolution of the primate glutamate taste sensor from a nucleotide sensor (2021)
  • Author(s): Toda, Y., Hayakawa, T., Itoigawa, A., Kurihara, Y., Nakagita, T., Hayashi, M., Ashino, R., Melin, A. D., Ishimaru, Y., Kawamura, S., Imai, H., and Misaka, T.
  • Journal Title: Current Biology Volume: 31 Pages: 4641-4649.e5
  • DOI: 10.1016/j.cub.2021.08.002
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Color vision and niche partitioning in a diverse neotropical primate community in lowland Amazonian Ecuador (2021)
  • Author(s): Veilleux, C. C., Kawamura, S., Montague, M. J., Hiwatashi, T., Matsushita, Y., Fernandez-Duque, E., Link, A., Di Fiore, A., D. and Max Snodderly, M.
  • Journal Title: Ecology and Evolution Volume: 11 Pages: 5742-5758
  • DOI: 10.1002/ece3.7479
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Crumbs proteins stabilize the cone mosaics of photoreceptors and improve vision in zebrafish (2021)
  • Author(s): Hao, Q., Zheng, M., Weng, K., Hao, Y., Zhou, Y., Lin, Y., Gao, F., Kou, Z., Kawamura, S., Yao, K., Xu, P., Chen, J., Zou, J.
  • Journal Title: Journal of Genetics and Genomics Volume: 48 Pages: 52-62
  • DOI: 10.1016/j.jgg.2020.12.002
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] 色覚多様性の意味について (2021)
  • Author(s): 河村正二
  • Journal Title: FBNews放射線安全管理総合情報誌, 株式会社千代田テクノル Volume: 536 Pages: 1ー6
  • Peer Reviewed
• [Journal Article] 第18章-1 視覚にかかわるオプシン遺伝子群 (2021)
  • Author(s): 河村正二
  • Journal Title: ヒトゲノム事典 (井ノ上逸朗・今西 規・河村正二・斎藤成也・颯田葉子・田嶋 敦 編), 一色出版 Volume: 該当せず Pages: 256-259
  • Peer Reviewed
• [Journal Article] Interleukin-4 Promotes Tuft Cell Differentiation and Acetylcholine Production in Intestinal Organoids of Non-Human Primate (2021)
  • Author(s): Inaba Akihiko、Arinaga Ayane、Tanaka Keisuke、Endo Takaho、Hayatsu Norihito、Okazaki Yasushi、Yamane Takumi、Oishi Yuichi、Imai Hiroo、Iwatsuki Ken
  • Journal Title: International Journal of Molecular Sciences Volume: 22 Pages: 7921～7921
  • DOI: 10.3390/ijms22157921
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Lowered sensitivity of bitter taste receptors to β-glucosides in bamboo lemurs: an instance of parallel and adaptive functional decline in TAS2R16? (2021)
  • Author(s): Itoigawa Akihiro、Fierro Fabrizio、Chaney Morgan E.、Lauterbur M. Elise、Hayakawa Takashi、Tosi Anthony J.、Niv Masha Y.、Imai Hiroo
  • Journal Title: Proceedings of the Royal Society B: Biological Sciences Volume: 288 Pages: 20210346
  • DOI: 10.1098/rspb.2021.0346
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 味覚の個人差と味覚受容体の遺伝子進化 (2021)
  • Author(s): 沼部令奈, 今井啓雄
  • Journal Title: アグリバイオ味覚・食嗜好性研究の最前線、北隆館 Volume: unassigned Pages: 23-27
  • Peer Reviewed
• [Presentation] ヒトを含む霊長類における色覚、嗅覚、味覚センサー遺伝子群の進化多様性 (2022)
  • Author(s): 河村正二
  • Organizer: 霊長類人類学研究会「サルとヒトをそれぞれ対象とする多くの研究者が共同で取り組める研究課題を抽出する」、ホテル メルパルク松山、愛媛県松山市、3月28-29日
  • Invited
• [Presentation] 霊長類の嗅覚受容体および苦味受容体多重遺伝子族の進化多様性 (2022)
  • Author(s): 河村正二、侯旻、 孫樹、 新村芳人、 早川卓志、Amanda D. Melin、今井啓雄
  • Organizer: 京都大学霊長類研究所 共同利用研究会・第50回ホミニゼーション研究会 「人類進化と遺伝子」、京都大学霊長類研究所、犬山市/ Online ハイブリッド、3月22-23日
  • Invited
• [Presentation] 霊長類における旨味受容体のヌクレオチド感受性と食性の関わり (2022)
  • Author(s): 戸田安香、早川卓志、糸井川壮大、栗原洋介、中北智哉、Amanda D. Melin、河村正二、今井啓雄、石丸喜朗、三坂巧
  • Organizer: 日本農芸化学会2022年度大会、オンライン（主催者所属：京都大学農学研究科、京都市）、3月15-18日
• [Presentation] Molecular genetics of visual adaptation in monotremes (2022)
  • Author(s): Sakamoto, S., Matsushita, Y., Kawamura, S. and Hayakawa, T.
  • Organizer: The 17th International Symposium on Primatology and Wildlife Science, Kyoto University and online, March 7-8
  • Int'l Joint Research
• [Presentation] Genetic variation of olfactory receptor multigene family in humans evaluated by targeted capture (2022)
  • Author(s): Kawamura, S., Akhtar, M. S., Niimura, Y. and Melin, A. D.
  • Organizer: 国立遺伝学研究所集団遺伝研究室 斎藤成也教授 退職記念シンポジウム、国立遺伝学研究所、三島市／オンライン、3月5-6日
  • Invited
• [Presentation] Ancient origin of catarrhine L and M opsin genes in anthropoid common ancestor (2022)
  • Author(s): Kawamura, S., Matsushita, Y., Takezaki, N. and Melin, A. D.
  • Organizer: Joint Meeting of the International Primatological Society and the Latin American Society of Primatology (IPS-SLAPrim 2022), Quito, Ecuador and online, January 9-15
  • Int'l Joint Research
• [Presentation] Differentiation of bitter taste receptor family composition in cercopithecids (2022)
  • Author(s): Hou, M., Ashino, R., Melin, A. D. and Kawamura, S.
  • Organizer: Joint Meeting of the International Primatological Society and the Latin American Society of Primatology (IPS-SLAPrim 2022), Quito, Ecuador and online, January 9-15
  • Int'l Joint Research
• [Presentation] The heritability of red-green cone ratios in a population of free-ranging rhesus macaques (Macaca mulatta) (2022)
  • Author(s): Munds, R. A., Janiak, M. C., Montague, M. J., Martinez, M., Kawamura, S., Melin, A. D., and Higham, J. P.
  • Organizer: Joint Meeting of the International Primatological Society and the Latin American Society of Primatology (IPS-SLAPrim 2022), Quito, Ecuador and online, January 9-15
  • Int'l Joint Research
• [Presentation] Variation of Bitter Taste Receptor TAS2R38 of Macaca maura (2022)
  • Author(s): Kanthi Arum Widayati, Yan Xiaochan, Nami Suzuki-Hashido, Akihiro Itoigawa, Fahri Fahri, Yohey Terai, Bambang Suryobroto, Hiroo Imai
  • Organizer: 第50回ホミニぜーション研究会
• [Presentation] Low sensitivity of bitter taste receptor TAS2R16 to β-glucosides may contribute to feeding on cyanogenic bamboo in bamboo lemurs. (2022)
  • Author(s): Itoigawa A, Fierro F, Chaney ME, Lauterbur ME, Hayakawa T, Tosi AJ, Niv MY, Imai H
  • Organizer: Joint Meeting of the International Primatological Society and the Latin American Society of Primatology (IPS-SLAPrim 2022),
  • Int'l Joint Research
• [Presentation] Difference in the sensitivity to bitter compounds in coffee based on TAS2R gene polymorphism (2022)
  • Author(s): Rena Numabe, Akihiro Itoigawa, Hiroo Imai.
  • Organizer: The 17th International Symposium on Primatology & Wildlife Science
  • Int'l Joint Research
• [Presentation] マーモセットのgum食におけるCaSRの役割 (2022)
  • Author(s): 今井啓雄、伯川美穂、林 美紗、糸井川壮大、Leonardo Melo、Valdir da Silva、Maria Aderia
  • Organizer: 第11回日本マーモセット研究会大会
  • Int'l Joint Research
• [Presentation] Genetic variation of olfactory receptor (OR) gene family in Japanese population (2021)
  • Author(s): Akhtar, M. S., Ashino, R., Oota, H., Ishida, H., Niimura, Y. Touhara, K., Melin, A. D., and Kawamura, S.
  • Organizer: 第75回日本人類学会大会、オンライン東京大学柏キャンパス、10月9-11日
• [Presentation] Evolutionary differentiation of bitter taste receptor gene repertoire between African/Asian and American monkeys (2021)
  • Author(s): Hou, H., Hayashi, M., Ashino, R., Melin, A. D. and Kawamura, S.
  • Organizer: 第23回日本進化学会大会、オンライン東京都立大学、8月18-21日
• [Presentation] 錐体視物質から辿る単孔類の進化 (2021)
  • Author(s): 阪本詩乃、松下裕香、Zhou, Y.、Zhang, G.、Grutzner, F.、河村正二, 早川卓志
  • Organizer: 第23回日本進化学会大会、オンライン東京都立大学、8月18-21日
• [Presentation] Cone ratio variation and heritability in free-ranging Rhesus macaques (Macaca mulatta) (2021)
  • Author(s): Melin, A. D., Munds, R. A., Cooper, E., Janiak, M. C., Lam, L. G., DeCasien, A., Bauman, S., Montague, M., Martinez, M., Kawamura, S. and Higham, J. P.
  • Organizer: The 2nd AsiaEvo Conference: Symposium “New approaches in evolutionary anthropology”, Online, August 16-19. (Symposium organized by Nakayama, K. and Kawamura, S.)
  • Int'l Joint Research / Invited
• [Presentation] Cone ratio variation in free-ranging Rhesus macaques (Macaca mulatta) (2021)
  • Author(s): Melin, A. D., Munds, R. A., Cooper, E., Janiak, M. C., Lam, L. G., DeCasien, A., Bauman, S., Montague, M., Martinez, M., Kawamura, S. and Higham, J. P.
  • Organizer: The 2021 Annual Meeting of the Society for Molecular Biology & Evolution (SMBE 2021): Symposium “Evolutionary and Functional Genomics of Primates”, Online, July 4-8.
  • Int'l Joint Research / Invited
• [Presentation] Allelic origin of human L and M opsin genes predating catarrhine-platyrrhine split (2021)
  • Author(s): Matsushita, Y., Takezaki, N., Melin, A. D., and Kawamura, S.
  • Organizer: The 2021 Annual Meeting of the Society for Molecular Biology & Evolution (SMBE 2021), Online, July 4-8
  • Int'l Joint Research
• [Presentation] Genetic variation of olfactory receptor repertoire across human populations (2021)
  • Author(s): Akhtar, M. S., Ashino, R., Niimura, Y. Touhara, K., Melin, A. D., and Kawamura, S.
  • Organizer: The 2021 Annual Meeting of the Society for Molecular Biology & Evolution (SMBE 2021), Online, July 4-8
  • Int'l Joint Research
• [Presentation] Evolutionary diversity of bitter taste receptor gene repertoire compared among cercopithecid and platyrrhine monkeys (2021)
  • Author(s): Hou, M., Hayashi, M., Ashino, R., Melin, A. D., and Kawamura, S.
  • Organizer: The 2021 Annual Meeting of the Society for Molecular Biology & Evolution (SMBE 2021), Online, July 4-8
  • Int'l Joint Research
• [Presentation] 進化の視点から見たヒトの色覚多様性について (2021)
  • Author(s): 河村正二
  • Organizer: 日本色彩学会第52回全国大会、オンライン、6月26-27日
  • Invited
• [Presentation] Sex and age variation and heritability of cone ratios in a free-ranging population of Rhesus macaques (Macaca mulatta) (2021)
  • Author(s): Munds, R. A., Cooper, E., Janiak, M. C., Lam, L. G., DeCasien, A., Bauman, S., Montague, M., Martinez, M., Kawamura, S., Higham, J. P. and Melin, A. D.
  • Organizer: The 2021 Joint Annual Meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN), Online, June 21-25
  • Int'l Joint Research
• [Presentation] ヒトの色覚の起源と多様性 (2021)
  • Author(s): 河村正二
  • Organizer: 大人が楽しむ科学教室、千葉市科学館、千葉市、5月8日
  • Invited
• [Presentation] オプシン分化とヒト色覚多様性の起源について (2021)
  • Author(s): 松下裕香、河村正二
  • Organizer: 東海大学BMIセミナー、オンライン、4月27日
  • Invited
• [Presentation] Flipping the opsin switch: Cis-regulatory elements required for thyroid hormone-mediated differential expression of the tandemly-replicated long wavelength-sensitive (lws) opsin genes of the zebrafish (2021)
  • Author(s): Stenkamp, D. L., Mackin, R. D., Ashino, R. and Kawamura, S.
  • Organizer: The 2021 Annual Meeting of Association for Research in Vision and Ophthalmology (ARVO 2021), Online, May 1-7
  • Int'l Joint Research
• [Presentation] Genetic basis of the speciation in Sulawesi macaques, Indonesia (2021)
  • Author(s): Yan Xiaochan, Kanthi Arum Widayati, Bajeber Fahri, Akihiro Itoigawa, Laurentia Purba, Bambang Suryobroto, Yohey Terai, Hiroo Imai
  • Organizer: he 16th International Symposium on Primatology and Wildlife Science
  • Int'l Joint Research
• [Presentation] Local adaptation may cause pseudogenization in the evolution of Sulawesi macaque species (2021)
  • Author(s): Nami Arakawa, Kanthi Arum Widayati, Laurentia Purba, Xiaochan Yan, Hiroo Imai, Bambang Suryobroto, Yohey Terai
  • Organizer: SMBE (Society of Molecular Biology and Evolution)
  • Int'l Joint Research
• [Presentation] 隣接した生息域を持つスラウェシマカクでの遺伝的分化とgene flow (2021)
  • Author(s): 荒川那海, Kanthi Arum Widayati, Laurentia Purba, Xiaochan Yan, 今井啓雄, Bambang Suryobroto, 寺井洋平
  • Organizer: 日本進化学会第23回東京大会
• [Presentation] Response profiles of bitter taste receptors in egg-laying mammals provide insight into foraging behavior and functional evolution of the receptors in mammals. (2021)
  • Author(s): Itoigawa A, Hayakawa T, Zhou Y, Manning AD, Zhang G, Grutzner F, Imai H
  • Organizer: The 2nd AsiaEvo Conference
  • Int'l Joint Research
• [Presentation] TAS2Rの遺伝子多型によるコーヒーに含まれる苦味物質への応答性の差異 (2021)
  • Author(s): 沼部令奈, 糸井川壮大, 今井啓雄
  • Organizer: 日本味と匂学会第55回大会
• [Presentation] Difference in the sensitivity to bitter compounds in coffee based on TAS2R gene polymorphism (2021)
  • Author(s): Rena Numabe, Akihiro Itoigawa, Hiroo Imai.
  • Organizer: The 16th International Symposium on Primatology & Wildlife Science
  • Int'l Joint Research
• [Presentation] 非ヒト霊長類モデルを用いた腸管Tuft細胞の分子発現解析 (2021)
  • Author(s): 稲葉明彦, 有永理峰, 田中啓介, 遠藤高帆, 早津徳人, 岡崎康司, 岩槻健, 今井啓雄
  • Organizer: 第44回日本分子生物学会
• [Book] ヒトゲノム事典 (2021)
  • Author(s): 井ノ上 逸朗, 今西 規, 河村 正二, 斎藤 成也, 颯田 葉子, 田嶋 敦 編
  • Total Pages: 448
  • Publisher: 一色出版
  • ISBN: 4910389121
• [Remarks] 河村正二研究室ホームページ
  • URL: http://www.jinrui.ib.k.u-tokyo.ac.jp/kawamura-home.html
• [Remarks] Shoji Kawamura Lab Home Page
  • URL: http://www.jinrui.ib.k.u-tokyo.ac.jp/kawamura-home-E.html
• [Funded Workshop] The 2nd AsiaEvo Conference, Symposium "New approaches in evolutionary anthropology" (2021)