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Less-invasive age estimation using hair based on DNA methylation in brown bears

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Abstract

Information on chronological age is essential for exploring the life history, conservation, and management of wildlife. Recently, DNA methylation-based methods using blood or skin have been established as alternatives to the traditional tooth-based method in bear species. However, the collection of these tissues is limited to captured or dead individuals. In the present study, we established the first hair-based age estimation model based on DNA methylation levels in brown bears, aiming for future application to less-invasively obtained hair of wild individuals. We performed bisulfite pyrosequencing and measured the methylation levels of hair root DNA. The methylation levels of cytosine-phosphate-guanine sites adjacent to the genes VGF, KCNK12, and ELOVL2 were found to be correlated with age. The best age estimation model used three cytosine-phosphate-guanine sites adjacent to two genes, VGF and KCNK12, with a mean absolute error of 3.2 years and median absolute error of 2.2 years after leave-one-out cross-validation. Our method is innovative because of the simplicity of sampling and the lack of requirement to capture bears. If this method can be widely applied to hair samples obtained in the field, the age structure of wild populations can be understood, contributing to ecological research, conservation, and management of bear species.

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Data availability

The data obtained from pyrosequencing analyses are available in Dryad at: https://doi.org/10.5061/dryad.h44j0zpzc.

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Acknowledgements

We would like to express our sincere thanks to all staff at Noboribetsu Bear Park for providing bear hair and sample information. We wish to thank Hatsusaburo Ose and all the members of the Shiretoko Fishery Productive Association for their kind support. We are deeply grateful to all the members of the Shiretoko Nature Foundation for their generous support. We also thank everyone involved in sample collection. We would like to express our sincere gratitude to Dr. Miho Inoue-Murayama from Wildlife Research Center, Kyoto University for her support and helpful advice. Finally, we thank Editage (www.editage.jp) for English language editing.

Funding

This study was supported by funding from the Japan Society for the Promotion of Science (JSPS) (https://www.jsps.go.jp/english/e-grants/index.html) KAKENHI grant numbers JP19K06833, JP23K05312, JP25H01002, JP24KJ0304, and JP22K14910, Grant for Basic Science Research Projects from The Sumitomo Foundation (grant no. 200561), a grants-in-aid of The Inui Memorial Trust for Research on Animal Science, Japan, JST SPRING (grant no. JPMJSP2119), and World-leading Innovative and Smart Education (WISE) Program from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (grant no. 1801).

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Authors and Affiliations

  1. Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Hokkaido, Japan

    Shiori Nakamura, Jumpei Yamazaki, Mina Jimbo, Yojiro Yanagawa, Toshio Tsubota & Michito Shimozuru

  2. One Health Research Center, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Hokkaido, Japan

    Jumpei Yamazaki & Michito Shimozuru

  3. Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara, 252-5201, Kanagawa, Japan

    Naoya Matsumoto

  4. Noboribetsu Bear Park, 224 Noboribetsuonsencho, Noboribetsu, 059-0551, Hokkaido, Japan

    Kyogo Hagino & Hideyuki Sakamoto

  5. Shiretoko Nature Foundation, 531 Iwaobetsu, Shari, 099-4356, Hokkaido, Japan

    Masami Yamanaka & Masanao Nakanishi

  6. Hokkaido Research Organization, Sapporo, 060-0819, Hokkaido, Japan

    Mina Jimbo

  7. Kyoto City Zoo, Okazaki Hosshojicho, Kyoto, 606-8333, Japan

    Hideyuki Ito

Authors

  1. Shiori Nakamura
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  2. Jumpei Yamazaki
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  3. Naoya Matsumoto
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  4. Kyogo Hagino
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  5. Hideyuki Sakamoto
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  6. Masami Yamanaka
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  7. Masanao Nakanishi
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  8. Mina Jimbo
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  9. Yojiro Yanagawa
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  10. Hideyuki Ito
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  11. Toshio Tsubota
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  12. Michito Shimozuru
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S.N. designed the study, performed laboratory work, and constructed each age estimation model. S.N., N.M., K.H., H.S., M.Y., M.N., M.J., Y.Y., and M.S. were involved in sample collection. J.Y. and H.I. supported with the technical aspects of the experiment. S.N. and M.S. wrote the article with inputs from J.Y., H.I., and T.T. All authors reviewed the article.

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Michito Shimozuru.

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The authors declare no competing interests.

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All procedures involved in sample collection from animals were conducted in accordance with the Guidelines for Animal Care and Use, Hokkaido University, and were approved by the Animal Care and Use Committee of the Graduate School of Veterinary Medicine, Hokkaido University (Permit Number: 1152, 15009, 17005, 18–0083, 19–0021, 20–0146, and 23 − 0014). In addition, all methods were carried out in compliance with ARRIVE guidelines.

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Nakamura, S., Yamazaki, J., Matsumoto, N. et al. Less-invasive age estimation using hair based on DNA methylation in brown bears.
Sci Rep (2025). https://doi.org/10.1038/s41598-025-27455-2

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  • DOI: https://doi.org/10.1038/s41598-025-27455-2

Keywords

  • Epigenetic clock
  • Age estimation
  • Brown bear
  • DNA methylation
  • Wildlife management
  • Aging

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