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Blood DNA methylation-based age estimation in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species using machine learning models
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  • Huiyuan Qi,
  • Qi Luan Lim,
  • Kodzue Kinoshita,
  • Nobuyoshi Nakajima,
  • Miho Inoue-Murayama
Huiyuan Qi
Kyoto University Wildlife Research Center
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Qi Luan Lim
Kyoto University Wildlife Research Center
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Kodzue Kinoshita
Kyoto University Wildlife Research Center
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Nobuyoshi Nakajima
National Institute for Environmental Studies
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Miho Inoue-Murayama
Kyoto University Wildlife Research Center

Corresponding Author:murayama.miho.5n@kyoto-u.ac.jp

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Abstract

Knowledge of individual age can help both in-situ and ex-situ conservation programs to design more efficient and suitable management plans for targeted wildlife species. DNA methylation is one of the epigenetic aging markers that has emerged as a promising tool that can estimate age with high accuracy using only a tiny amount of biological material, which can be collected in a minimally invasive way. Although the conservation of Felidae species has received great attention, studies rarely focus on the development of age estimation models. Here, we sequenced five genetic regions and used 4–25 selected CpG sites to build age estimation models with several machine learning methods, using blood samples of seven Felidae species—ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples), and five Panthera species (96 samples). The models built achieved satisfactory accuracy—the mean absolute deviation of the best models was 1.80, 1.30, and 1.55 years in domestic cats, Tsushima leopard cats, and Panthera spp., respectively. Our models in domestic cats and Tsushima leopard cats were applicable to all individuals regardless of health conditions and sex, indicating high applicability of our models to samples collected from diverse situations, e.g., rescued individuals in the context of conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using two of the five genetic regions, suggesting an even lower cost to use our models for future applications.