Epigenetic Clock in Bears: A Simple Cost‐Effective Blood DNA Methylation‐Based Age Estimation Method Applicable to Multiple Bear Species

ABSTRACT Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear‐specific age estimation model to other b...

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Published inEcology and evolution Vol. 15; no. 5; pp. e71424 - n/a
Main Authors Shimozuru, Michito, Nakamura, Shiori, Yamazaki, Jumpei, Yanagawa, Yojiro, Tamatani, Hiroo, Kuroe, Misako, Yamazaki, Koji, Koike, Shinsuke, Goto, Yusuke, Naganuma, Tomoko, Tochigi, Kahoko, Inagaki, Akino, Takekoshi, Naoki, Baek, Seungyun, Sato, Nobutaka, Honda, Yusuke, Tsubota, Toshio, Ito, Hideyuki
Format Journal Article
LanguageEnglish
Published England John Wiley & Sons, Inc 01.05.2025
John Wiley and Sons Inc
Wiley
Subjects
Accuracy
Age
Age determination
age estimation
Aging
Animal research
bear
Bears
Bisulfite
Blood
carnivore
Chronology
CpG islands
Cytosine
Deoxyribonucleic acid
DNA
DNA methylation
epigenetic clock
Epigenetics
Females
Genes
Genetic testing
Laboratory animals
Life history
Males
Methods
Ursus thibetanus
Wildlife
Wildlife conservation
Japan
DNA methylation
carnivore
bear
aging
age estimation
epigenetic clock
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Abstract ABSTRACT Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear‐specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine‐phosphate‐guanine (CpG) sites adjacent to a single gene, SLC12A5. The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear‐specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan‐bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave‐one‐out cross‐validation (LOOCV). In addition, the best pan‐bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan‐bear age estimation model using the aging marker (CpG sites adjacent to SLC12A5) is a simple, highly accurate, and cost‐effective tool that is applicable to Ursidae. Age is an essential factor to understand the life history and demographic parameters of wildlife. In this study, we built a common epigenetic clock model for multiple bear species, including brown, Asian black, polar, sun, and Andean bears. The model will contribute to ecological research, conservation, and management of bear species.
AbstractList Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear‐specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine‐phosphate‐guanine (CpG) sites adjacent to a single gene, SLC12A5 . The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear‐specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan‐bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave‐one‐out cross‐validation (LOOCV). In addition, the best pan‐bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan‐bear age estimation model using the aging marker (CpG sites adjacent to SLC12A5 ) is a simple, highly accurate, and cost‐effective tool that is applicable to Ursidae. Age is an essential factor to understand the life history and demographic parameters of wildlife. In this study, we built a common epigenetic clock model for multiple bear species, including brown, Asian black, polar, sun, and Andean bears. The model will contribute to ecological research, conservation, and management of bear species.
Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear-specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine-phosphate-guanine (CpG) sites adjacent to a single gene, SLC12A5. The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear-specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan-bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave-one-out cross-validation (LOOCV). In addition, the best pan-bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan-bear age estimation model using the aging marker (CpG sites adjacent to SLC12A5) is a simple, highly accurate, and cost-effective tool that is applicable to Ursidae.Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear-specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine-phosphate-guanine (CpG) sites adjacent to a single gene, SLC12A5. The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear-specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan-bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave-one-out cross-validation (LOOCV). In addition, the best pan-bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan-bear age estimation model using the aging marker (CpG sites adjacent to SLC12A5) is a simple, highly accurate, and cost-effective tool that is applicable to Ursidae.
ABSTRACT Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear‐specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine‐phosphate‐guanine (CpG) sites adjacent to a single gene, SLC12A5. The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear‐specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan‐bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave‐one‐out cross‐validation (LOOCV). In addition, the best pan‐bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan‐bear age estimation model using the aging marker (CpG sites adjacent to SLC12A5) is a simple, highly accurate, and cost‐effective tool that is applicable to Ursidae.
Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear‐specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine‐phosphate‐guanine (CpG) sites adjacent to a single gene, SLC12A5 . The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear‐specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan‐bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave‐one‐out cross‐validation (LOOCV). In addition, the best pan‐bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan‐bear age estimation model using the aging marker (CpG sites adjacent to SLC12A5 ) is a simple, highly accurate, and cost‐effective tool that is applicable to Ursidae.
ABSTRACT Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear‐specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine‐phosphate‐guanine (CpG) sites adjacent to a single gene, SLC12A5. The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear‐specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan‐bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave‐one‐out cross‐validation (LOOCV). In addition, the best pan‐bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan‐bear age estimation model using the aging marker (CpG sites adjacent to SLC12A5) is a simple, highly accurate, and cost‐effective tool that is applicable to Ursidae. Age is an essential factor to understand the life history and demographic parameters of wildlife. In this study, we built a common epigenetic clock model for multiple bear species, including brown, Asian black, polar, sun, and Andean bears. The model will contribute to ecological research, conservation, and management of bear species.
Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown bears based on blood DNA methylation level. In this study, we first applied the brown bear-specific age estimation model to other bear species, including Asian black, polar, sun, and Andean bears. Using blood DNA, we performed bisulfite pyrosequencing to determine the methylation levels at four cytosine-phosphate-guanine (CpG) sites adjacent to a single gene, . The best model specific to brown bears estimated their ages with satisfactory accuracy, with mean absolute error (MAE) of 1.5, 2.1, 2.2, and 0.4 years for Asian black (52 samples from 16 captive and 36 wild bears), polar (27 samples from 21 captive bears), sun bears (11 samples from 8 captive bears), and Andean bears (one captive bear), respectively. Then, we established an Asian black bear-specific age estimation model and a common age estimation model applicable for other bear species (i.e., a pan-bear model) using the methylation levels of the four CpG sites. The best model specific to Asian black bears had high accuracy with MAE of 1.1 after leave-one-out cross-validation (LOOCV). In addition, the best pan-bear model achieved accuracy with MAE of 1.3, 1.2, 2.1, and 2.2 years after LOOCV for brown, Asian black, polar, and sun bears, respectively. The results suggested that the pan-bear age estimation model using the aging marker (CpG sites adjacent to ) is a simple, highly accurate, and cost-effective tool that is applicable to Ursidae.
Author Yamazaki, Jumpei
Kuroe, Misako
Sato, Nobutaka
Yanagawa, Yojiro
Inagaki, Akino
Baek, Seungyun
Takekoshi, Naoki
Shimozuru, Michito
Nakamura, Shiori
Tochigi, Kahoko
Goto, Yusuke
Honda, Yusuke
Ito, Hideyuki
Yamazaki, Koji
Tamatani, Hiroo
Koike, Shinsuke
Naganuma, Tomoko
Tsubota, Toshio
AuthorAffiliation 9 Asahikawa City Asahiyama Zoo Asahikawa Hokkaido Japan
10 Noichi Zoological Park of Kochi Prefecture Konan Kochi Japan
12 Kyoto City Zoo Kyoto Japan
11 Wildlife Research Center Kyoto University Kyoto Japan
4 Nagano Environmental Conservation Research Institute Nagano Japan
1 Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
2 One Health Research Center Hokkaido University Sapporo Hokkaido Japan
5 Tokyo University of Agriculture Tokyo Japan
3 Department of Bear Management Picchio Wildlife Research Center Nagano Japan
8 Obihiro University of Agriculture and Veterinary Medicine Obihiro Hokkaido Japan
6 Zoological Laboratory Ibaraki Nature Museum Ibaraki Japan
7 Tokyo University of Agriculture and Technology Tokyo Japan
AuthorAffiliation_xml – name: 4 Nagano Environmental Conservation Research Institute Nagano Japan
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/40330099$$D View this record in MEDLINE/PubMed
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IsDoiOpenAccess true
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Issue 5
Keywords DNA methylation
carnivore
bear
aging
age estimation
epigenetic clock
Language English
License Attribution
2025 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley & Sons Ltd.
This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
LinkModel DirectLink
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Notes Michito Shimozuru and Shiori Nakamura should be considered joint first author.
Funding
This work was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (16H04932, 21H02351, 22K14910, 25H01002) and the Environment Research and Technology Development Fund of the Environmental Restoration and Conservation Agency provided by Ministry of the Environment of Japan (JPMEERF20254002).
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content type line 14
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Funding: This work was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (16H04932, 21H02351, 22K14910, 25H01002) and the Environment Research and Technology Development Fund of the Environmental Restoration and Conservation Agency provided by Ministry of the Environment of Japan (JPMEERF20254002).
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Snippet ABSTRACT Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method...
Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method for brown...
ABSTRACT Age is an essential factor to understand the life history and demographic parameters of wildlife. Previously, we established an age estimation method...
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SubjectTerms Accuracy
Age
Age determination
age estimation
Aging
Animal research
bear
Bears
Bisulfite
Blood
carnivore
Chronology
CpG islands
Cytosine
Deoxyribonucleic acid
DNA
DNA methylation
epigenetic clock
Epigenetics
Females
Genes
Genetic testing
Laboratory animals
Life history
Males
Methods
Ursus thibetanus
Wildlife
Wildlife conservation
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Title Epigenetic Clock in Bears: A Simple Cost‐Effective Blood DNA Methylation‐Based Age Estimation Method Applicable to Multiple Bear Species
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fece3.71424
https://www.ncbi.nlm.nih.gov/pubmed/40330099
https://www.proquest.com/docview/3212479209
https://www.proquest.com/docview/3201116913
https://pubmed.ncbi.nlm.nih.gov/PMC12055220
https://doaj.org/article/4bb7634ca16541e0b6764dd99d36e8f5
Volume 15
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