Details of the Researcher

PHOTO

Tomoko Hamabata
Section
Advanced Institute for Marine Ecosystem Change
Job title
Associate Professor
Degree

  • 博士（理学）（京都大学）

  • 修士（理学）（九州大学）

Professional Memberships 2

  • SOCIETY OF EVOLUTIONARY STUDIES, JAPAN

  • THE ECOLOGICAL SOCIETY OF JAPAN

Research Areas 3

  • Environmental science/Agricultural science / Biological resource conservation /

  • Life sciences / Ecology and environmental science /

  • Life sciences / Marine/Aquatic life sciences /

Papers 23

  1. Genetic characteristics of loggerhead turtles in the coastal corridor of the North West Pacific, around the Cape Muroto, Japan Peer-reviewed

    Takashi Ishihara, Naoki Kamezaki, Saya Hirai, Yoshimasa Matsuzawa, Tomoko Hamabata, Asuka Ishizaki, Peter H. Dutton

    Frontiers in Marine Science　11　2024/07/05

    Publisher: Frontiers Media SA

    DOI： 10.3389/fmars.2024.1303553 　

    eISSN： 2296-7745

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    Genetic characteristics of North Pacific loggerhead turtles captured as bycatch in pound nets operating in Muroto, Kochi, Japan were sampled to identify and estimate stock structure of coastal foraging aggregations. Tissue samples were obtained from juvenile, subadult and adult turtles from 2005–2006 and 2008–2010. For each of the years, 100 samples were processed and approximately 820 bp of mitochondrial DNA control region were sequenced. Straight carapace length of the turtles ranged from 56.3– 99.1 cm and their life stages were identified based on previous estimates of the size at puberty (66.0cm) and maturity (82.1cm). A total of 487 out of the 500 samples yielded sequences of sufficient quality to identify five different haplotypes. We conducted mixed stock analysis (MSA) using Bayesian approaches to estimate the contributions of three potential source nesting Management Units (MU) to the Muroto foraging aggregation. There were no significant differences between haplotype frequencies among the different size classes and life stages, nor among the different years, thus the haplotype frequencies were combined for the MSA. The MSA was run with and without consideration of MU size and distance, which resulted in similar MSA estimates. A >50% contribution was estimated from the Yakushima MU, and 40% from the Mainland MU, with only minor contribution from the Ryukyu MU. The estimated contribution from Mainland MU and Yakushima MU were disproportionately larger than the relative abundance of nesting at these MUs compared with Ryukyu MU, demonstrating that closer MUs had a greater contribution than those from further away. The lack of differences found in haplotype frequency among life stages, suggests that both juvenile and mature loggerhead turtles that remigrate to Japanese waters have the tendency to utilize foraging grounds and migration routes near their natal waters.

  2. Latest and comprehensive mitochondrial DNA haplotype data on green and hawksbill turtles collected in their habitats in Japan Peer-reviewed

    Tomoko Hamabata, Kazunari Kameda, Ryota Hayashi, Junichi Okuyama, Isao Kawazu, Hideaki Nishizawa

    Frontiers in Marine Science　11　2024/03/28

    Publisher: Frontiers Media SA

    DOI： 10.3389/fmars.2024.1328101 　

    eISSN： 2296-7745

  3. Overview of the population genetics and connectivity of sea turtles in the East Asia Region and their conservation implications Peer-reviewed

    Connie Ka Yan Ng, Takashi Ishihara, Tomoko Hamabata, Hideaki Nishizawa, Min Liu, Jia-hao Song, Tsung Hsien Li, Chia-Ling Fong, Dae Yeon Moon, Il Hun Kim

    Frontiers in Marine Science　11　2024/03/08

    Publisher: Frontiers Media SA

    DOI： 10.3389/fmars.2024.1325849 　

    eISSN： 2296-7745

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    Understanding the current status and recent development of the population genetics and connectivity of sea turtles is crucial for effective conservation management of the species. Five sea turtle species, green turtle (Chelonia mydas), loggerhead turtle (Caretta caretta), hawksbill turtle (Eretmochelys imbricata), olive ridley turtle (Lepidochelys olivacea) and leatherback turtle (Dermochelys coriacea), are recorded in the East Asia Region situated in the western side of the North Pacific Ocean. We compiled information from 35 published genetic studies on the five sea turtle species, with a focus on green turtle and loggerhead turtle, which are the most studied species (in 30 studies) in view of their commonness and occurrence of nesting populations. We provided an overview of the key methods and findings of these previous studies, addressing two main objectives on genetic structure of the rookeries and their differences compared to other populations, and connectivity of the rookeries and foraging aggregations. By identifying information gaps and conservation needs, we discussed future developments for sea turtle genetic studies and conservation implications in the region.

  4. Twenty-year changes in the composition of a mixed stock of foraging green turtles in the Yaeyama Islands of Japan Peer-reviewed

    Tomoko Hamabata, Masakado Kawata, Satomi Kondo, Ayumi Matsuo, Yoshihisa Suyama, Kazuyuki Suzuki, Kazunari Kameda

    Marine Ecology Progress Series　716　93-105　2023/08

    DOI： 10.3354/meps14367 　

  5. Absence of Genetic Structure among Streaked Shearwaters Calonectris leucomelas Breeding in Japan, Despite Limited Dispersal Events Peer-reviewed

    Miho Sakao, Tomoko Hamabata, Katsufumi Sato, Shinichi Watanabe, Ken Yoda, Kozue Shiomi

    Ornithological Science　22　(2)　111-121　2023/07/26

    Publisher: Ornithological Society of Japan

    DOI： 10.2326/osj.22.111 　

    ISSN： 1347-0558

  6. Natal Origin Identification of Green Turtles in the North Pacific by Genome-Wide Population Analysis With Limited DNA Samples Peer-reviewed

    Tomoko Hamabata, Ayumi Matsuo, Mitsuhiko P. Sato, Satomi Kondo, Kazunari Kameda, Isao Kawazu, Takuya Fukuoka, Katsufumi Sato, Yoshihisa Suyama, Masakado Kawata

    Frontiers in Marine Science　7　2020/08/07

    Publisher: Frontiers Media SA

    DOI： 10.3389/fmars.2020.00658 　

    eISSN： 2296-7745

  7. Significant loss of genetic diversity and accumulation of deleterious genetic variation in a critically endangered azalea species, Rhododendron boninense, growing on the Bonin Islands Peer-reviewed

    Yuji Isagi, Takashi Makino, Tomoko Hamabata, Ping-Lin Cao, Satoshi Narita, Yoshiteru Komaki, Kazuki Ktuita, Akiyo Naiki, Yoshiaki Kameyama, Toshiaki Kondo, Mayu Shibabayashi

    PLANT SPECIES BIOLOGY　35　(3)　166-174　2020/07

    DOI： 10.1111/1442-1984.12270 　

    ISSN： 0913-557X

    eISSN： 1442-1984

  8. Inferred adult foraging grounds of two marine turtle species nesting at Amami-Oshima, Japan Peer-reviewed

    Katsuki Oki, Tomoko Hamabata, Toshimitsu Arata, Denise M. Parker, Connie Ka, Yan Ng, George H. Balazs

    Chelonian Conservation and Biology　18　(1)　91-97　2019/06

    DOI： 10.2744/CCB-1337.1 　

  9. The evolutionary history and global phylogeography of the green turtle (Chelonia mydas) Peer-reviewed

    Jensen Michael, Fitzsimmons Nancy N, Bourjea Jerome, Hamabata Tomoko, Reece Joshua, Dutton Peter H

    Journal of Biogeography　2019　(46)　860-870　2019/05

    DOI： 10.1111/jbi.13483 　

  10. Endangered island endemic plants have vulnerable genomes. International-journal Peer-reviewed

    Tomoko Hamabata, Gohta Kinoshita, Kazuki Kurita, Ping-Lin Cao, Motomi Ito, Jin Murata, Yoshiteru Komaki, Yuji Isagi, Takashi Makino

    Communications biology　2　(1)　244-244　2019

    DOI： 10.1038/s42003-019-0490-7 　

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    Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk. However, there is little evidence for higher vulnerability and extinction risk in endangered species based on genomic differences between endangered and non-endangered species. This is true even in the case of functional loci, which are more likely to relate to the fitness of species than neutral loci. Here, we compared the genome-wide genetic diversity, proportion of duplicated genes (PD), and accumulation of deleterious variations of endangered island endemic (EIE) plants from four genera with those of their non-endangered (NE) widespread congeners. We focused on exhaustive sequences of expressed genes obtained by RNA sequencing. Most EIE species exhibited significantly lower genetic diversity and PD than NE species. Additionally, all endangered species accumulated deleterious variations. Our findings provide new insights into the genomic traits of EIE species.

  11. Stock composition of green turtles Chelonia mydas foraging in the Ryukyu Archipelago differs with size class Peer-reviewed

    Tomoko Hamabata, Hideaki Nishizawa, Isao Kawazu, Kazunari Kameda, Naoki Kamezaki, Tsutomu Hikida

    Marine Ecology Progress Series　600　151-163　2018/07

    DOI： 10.3354/meps12657 　

    ISSN： 0171-8630

  12. Mass-stranding suggests natal area and migration of loggerhead turtle hatchlings in the Sea of Japan Peer-reviewed

    Takashi Ishihar, Yoshimasa Matsuzawa, Naoki Kamezaki, Kei Okamoto, Tomoko Hamabata, Akira Aoyagi, Akihiro Aoyama, Kei Ichisawa, Shinichiro Ikeguchi, Kazuhiro Minowa, Katsumi Miyachi, Shogo Murakami, Yukihiro Nakamura, Yukimasa Nashiki, Takashi Nomura, Masayoshi Takeda, Toshiyuki Tanaka, Seiji Teraoka, Kenjiro Ui, Toshifumi Wada

    Japanese Journal of Ecology　67　(1)　3-12　2017

    Publisher: Tohoku University

    DOI： 10.18960/seitai.67.1_3 　

    ISSN： 0021-5007

  13. MtDNA Analysis Suggests Local Origin of Pelagic-Stage Juvenile Green Turtles Collected in Japanese Coastal Waters Peer-reviewed

    Tomoko Hamabata, Tsutomu Hikida, Takashi Ishihara, Isao Kawazu, Yukimasa Nashiki, Katsuki Oki, Toshiyuki Tanaka, Kenjiro Ui, Naoki Kamezaki

    Pacific Science　70　(1)　45-54　2016/01

    DOI： 10.2984/70.1.4 　

    ISSN： 0030-8870

    eISSN： 1534-6188

  14. Fine-scale genetic population structure of loggerhead turtles in the Northwest Pacific Peer-reviewed

    Y. Matsuzawa, N. Kamezaki, T. Ishihara, K. Omuta, H. Takeshita, K. Goto, T. Arata, H. Honda, K. Kameda, Y. Kashima, M. Kayo, I. Kawazu, J. Kodama, Y. Kumazawa, K. Kuroyanagi, K. Mizobuchi, K. Mizuno, K. Oki, K. K. Watanabe, A. Yamamoto, Y. Yamashita, T. Yamato, T. Hamabata, A. Ishizaki, P. H. Dutton

    Endangered Species Research　30　83-93　2016

    DOI： 10.3354/esr00724 　

    ISSN： 1863-5407

    eISSN： 1613-4796

  15. Ontogenetic habitat shifts of green turtles (Chelonia mydas) suggested by the size modality in foraging aggregations along the coasts of the western Japanese main islands Peer-reviewed

    Tomoko Hamabata, Tsutomu Hikida, Kei Okamoto, Saya Watanabe, Naoki Kamezaki

    Journal of Experimental Marine Biology and Ecology　463　181-188　2015/02

    DOI： 10.1016/j.jembe.2014.12.007 　

    ISSN： 0022-0981

    eISSN： 1879-1697

  16. Genetic structure of green turtle (Chelonia mydas) peripheral populations nesting in the northwestern Pacific rookeries: evidence for northern refugia and postglacial colonization Peer-reviewed

    Tomoko Hamabata, Naoki Kamezaki, Tsutomu Hikida

    Marine Biology　161　(3)　495-507　2014/03

    DOI： 10.1007/s00227-013-2352-z 　

    ISSN： 0025-3162

    eISSN： 1432-1793

  17. Genetic composition of loggerhead turtle feeding aggregations: migration patterns in the North Pacific Peer-reviewed

    Hideaki Nishizawa, Tomoko Narazaki, Takuya Fukuoka, Katsufumi Sato, Tomoko Hamabata, Masato Kinoshita, Nobuaki Arai

    Endangered Species Research　24　(1)　85-93　2014

    DOI： 10.3354/esr00588 　

    ISSN： 1863-5407

    eISSN： 1613-4796

  18. Juvenile green turtles on the northern edge of their range: mtDNA evidence of long-distance westward dispersals in the northern Pacific Ocean Peer-reviewed

    Hideaki Nishizawa, Tomoko Narazaki, Takuya Fukuoka, Katsufumi Sato, Tomoko Hamabata, Masato Kinoshita, Nobuaki Arai

    Endangered Species Research　24　(2)　171-179　2014

    DOI： 10.3354/esr00592 　

    ISSN： 1863-5407

    eISSN： 1613-4796

  19. Differential expression of three types of gonadotropin-releasing hormone genes during the spawning season in grass puffer, Takifugu niphobles Peer-reviewed

    Md. Shahjahan, Tomoko Hamabata, Eiji Motohashi, Hiroyuki Doi, Hironori Ando

    General and Comparative Endocrinology　167　(1)　153-163　2010/05

    DOI： 10.1016/j.ygcen.2010.01.018 　

    ISSN： 0016-6480

  20. Genetic structure of populations of the green turtle (Chelonia mydas) in Japan using mtDNA control region sequences Peer-reviewed

    Hamabata Tomoko, Nishida Shin, Kamezaki Naoki, Koike Hiroko

    Bulletin of the Graduate School of Social and Cultural Studies, Kyushu University　15　35-50　2009

    Publisher: 九州大学大学院比較社会文化学府

    DOI： 10.15017/13994 　

    ISSN： 1341-1659

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    The green turtle Chelonia mydas is distributed throughout tropical and subtropical oceans worldwide. The Japanese population, the northernmost population of this species, is decreasing due to loss of spawning beaches, and peopling to the coastal area. To examine the genetic structure and genetic diversity of the Japanese population, a total of 294 individuals from seven foraging localities and 20 individuals from two nesting sites were analyzed using muscle and skin samples. The control region of mitochondrial DNA (mtDNA) was amplified with specific primers, and 32 haplotypes were detected from the Japanese population. Haplotype diversities (h) of the southern islands (0.89 at Yaeyama and 0.83 at Amami-Ohshima) were higher than those of the main islands (0.69, 0.63, and 0.67 at Nomaike, Muroto, and Owase, respectively). A median-joining tree using the 32 haplotypes showed three clades, and dominant haplotypes were situated in the middle of each clade. The exact test and F_ST for geographic heterogeneity in haplotype frequency distributions for the five foraging localities showed that significant differences were detected between Yaeyama and the main island localities, and between the Amami-Ohshima and Nomaike/Owase localities.

  21. Structure of neurohypophysial hormone genes and changes in the levels of expression during spawning season in grass puffer (Takifugu niphobles) Peer-reviewed

    Eiji Mototiashi, Tomoko Hamabata, Hironorl Ando

    General and Comparative Endocrinology　155　(2)　456-463　2008/01

    DOI： 10.1016/j.ygcen.2007.07.009 　

    ISSN： 0016-6480

  22. Structures of neurohypophysial hormone genes and there expression patterns during spawning of Takifugu niphobles Peer-reviewed

    Eiji Motohashi, Tomoko Hamabata, Hironori Ando

    ZOOLOGICAL SCIENCE　23　(12)　1212-1212　2006/12

    ISSN： 0289-0003

  23. Structures of vasotocin precursor genes in three species of Tetraodontidae

    MOTOHASHI Eiji, FURUKUMA Shunji, HAMABATA Tomoko, ANDO Hironori

    Proceedings of the Japan Society for Comparative Endocrinology　(20)　80-80　2005/11/12

    ISSN： 0913-9036

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Misc. 5

  1. Foraging dynamics of green turtles around Japanese waters and distribution boundary observed between subtropical and temperate waters

    Hamabata T, Nishizawa H, Kawazu I, Kameda K, Kamezaki N, Hikida T

    38th International Sea Turtle Symposium　2018/02

  2. 南西諸島で産卵するアカウミガメの特性

    石原孝, 興克樹, 水野康次郎, 嘉陽宗幸, 山下芳也, 浜端朋子, 亀崎直樹

    は虫両棲類学会報　2014　(1)　45　2014/05/31

    ISSN： 1345-5826

  3. 日本産アオウミガメChelonia mydasの遺伝的構造

    浜端朋子, 亀崎直樹, 疋田努

    は虫両棲類学会報　2012　(1)　53　2012/03/31

    ISSN： 1345-5826

  4. 日本沿岸に回遊するアオウミガメchelonia mydasの分子生態

    浜端朋子, 小池裕子, 亀崎直樹, 石原孝, 武内有加, 島達也, 水野康次郎

    日本生態学会大会講演要旨集　55th　463　2008/03/14

  5. 日本沿岸で索餌するアオウミガメ(Chelonia mydas)の遺伝的構造の解析

    浜端朋子, 武内有加, 亀崎直樹, 黒柳賢治, 小池裕子

    日本ベントス学会・日本プランクトン学会合同大会講演要旨集　2007　112　2007/09/21

Presentations 7

  1. Genetic approaches to hidden life histories of marine megafauna

    Tomoko Hamabata

    The 11th Case Western Reserve X Tohoku Joint Symposium　2025/08/08

  2. Balancing marine life: towards managing green turtles and seagrass ecosystems in Okinawa, Japan

    Tomoko Hamabata, Hideaki Nishizawa, Kotaro Ichikawa, Nao Yoshida, Hiromori Shimabukuro, Kenji Sudo, Toshihide Kitakado, Masakazu Hori, Yoshiki Yamagata, Aoi Sugimoto, Junichi Okuyama

    The Xiamen Symposium on Marine Environmental Sciences (XMAS 2025)　2025/01/15

  3. Surviving the Northernmost waters: Genetic insights into green turtles' adaptation in Japan

    Tomoko Hamabata

    42nd International Sea Turtle Symposium　2024/03

  4. Exploring the Adaptation of Green Turtles: Genetic Signatures of the Northernmost Population

    Tomoko Hamabata

    3rd AsiaEvo International Conference　2023/12/16

  5. The level of bottleneck experienced by endangered green turtles

    Tomoko HAMABATA, Satomi KONDO, Kazunari KAMEDA, Takuya FUKUOKA, Katsufumi SATO, Makoto TERAUCHI, Hideki NOGUCHI, Masakado KAWATA

    2023/03

  6. Balancing marine life: towards managing green turtles and seagrass ecosystems in Okinawa, Japan Invited

    Tomoko Hamabata, Hideaki Nishizawa, Kotaro Ichikawa, Nao Yoshida, Hiromori Shimabukuro, Kenji Sudo, Toshihide Kitakado, Masakazu Hori, Yoshiki Yamagata, Aoi Sugimoto, Junichi Okuyama

    4th Annual Hawaii Pacific University Sea Turtle Workshop　2024/10/04

  7. 島嶼生態系生物多様性ホットスポットの進化・保全ゲノミクス: 絶滅危惧植物における遺伝的多様性の低下と有害変異の蓄積

    浜端朋子, 牧野能士

    日本生態学会第64回大会　2017/03

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Research Projects 3

  1. Estimation the impact of genetic factors on sea turtle population recovery

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Tohoku University

    2024/04/01 - 2028/03/31

  2. ウミガメ類における過去の種間交雑と遺伝子浸透による新規環境適応の検証

    浜端 朋子

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 若手研究

    Institution: 東北大学

    2021/04 - 2025/03

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    日本には、アオウミガメの北太平洋の北限の産卵地と北太平洋唯一のアカウミガメ産卵地が分布する。これらの２種は、種分化してから長い時間が経過しているが、現在でも野生で稀に交雑することがわかっている。本研究では、北西部太平洋におけるアオウミガメとアカウミガメの歴史的な種間交雑と遺伝子浸透の可能性、北限環境においてアオウミガメが多様化した背景について調べる。 今年度は、アオウミガメの４個体の追加全ゲノムリシーケンスとアカウミガメ４個体の全ゲノムリシーケンスを新たに行った。アオウミガメのゲノム配列は、Vertebrate Genomes Projectで解読されたものが既に公開中であったが、7月に再度アセンブルし直されたものへと更新された。そこで、この新規のリファレンスゲノムに差し替えて変異取得のためのパイプラインの構築を進めた。予備的解析において、北太平洋のアオウミガメのうち、北限の小笠原集団のみで保有されている非同義変異を抽出してみたところ、70個以上の遺伝子で非同義変異が確認された。今後、種間交雑の検証していく解析とともに、アカウミガメについてもコード領域の配列取得を実施し、比較するためのデータを準備していく。 また今年度は、オンラインで月に１回開催されたAsia-Pacific Marine Turtle Genetic Working Groupのワークショプに参加し、これまでゲノム解析研究で行ってきたことと現在進行中の研究の計画について発表した。

  3. アオウミガメの個体数増加が藻場に与える生態学的インパクトの解明

    浜端 朋子

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特別研究員奨励費

    Institution: 東北大学

    2018/04 - 2021/03

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    昨年度までに取得し終えていたリシーケンスデータ及び、６個体の追加データ、さらに2013年ドラフトゲノム構築に使用された個体のリードデータもNCBIから取得して北太平洋全域から全25個体のゲノムデータを揃えた。最終年度となる本年度は、当初予定されていた時期よりも遅れたものの11月末にVertebrate Genome Projectの対象種として染色体レベルまでアセンブルされたアオウミガメのゲノムが新たに公開された。この新たなゲノムをリファレンスとして系統樹やPCA解析を元に集団構造を確認した。さらに以前のバージョンのドラフトゲノムではリソースの限界からできなかった、Multiple sequentially Markovian coalescent (MSMC)モデルを用いて複数個体のゲノムデータで実施する過去の有効集団サイズの変遷を推定した。また集団間の過去の遺伝子流動についても推定し、小集団による集団が維持される中で起こった近親交配についても推定した。 その結果、北太平洋は地域間で明瞭な集団構造が確認された。特に、北限の小笠原諸島の集団の有効集団サイズは、およそ100万年前から低緯度集団とは異なる挙動を示し、低緯度集団に比べて小さな有効集団サイズで推移したことがMSMCにより明らかになった。この結果は、昨年度まで行っていた１個体のゲノムを用いてPairwise sequentially Markovian coalescent (PSMC)モデルによって推定する手法では不明瞭であったが、今年度のデータにより確認することができた。地域集団間で過去に頻繁な遺伝子流動が起きた形跡についても確認されず、アオウミガメはメスの母浜回帰だけでなく、オスも生まれた地域へ戻って繁殖する性質が強く、その生態が集団構造の維持に働いたことが全ゲノム解析により示された。