Age estimation based on blood DNA methylation levels in brown bears

Abstract

Age is an essential trait for understanding the ecology and management of wildlife. A conventional method of estimating age in wild animals is counting annuli formed in the cementum of teeth. This method has been used in bears despite some disadvantages, such as high invasiveness and the requirement for experienced observers. In this study, we established a novel age estimation method based on DNA methylation levels using blood collected from 49 brown bears of known ages living in both captivity and the wild. We performed bisulfite pyrosequencing and obtained methylation levels at 39 cytosine‐phosphate‐guanine (CpG) sites adjacent to 12 genes. The methylation levels of CpGs adjacent to four genes showed a significant correlation with age. The best model was based on DNA methylation levels at just four CpG sites adjacent to a single gene, SLC12A5, and it had high accuracy with a mean absolute error of 1.3 years and median absolute error of 1.0 year after leave‐one‐out cross‐validation. This model represents the first epigenetic method of age estimation in brown bears, which provides benefits over tooth‐based methods, including high accuracy, less invasiveness, and a simple procedure. Our model has the potential for application to other bear species, which will greatly improve ecological research, conservation, and management.

Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species

“…Age structure is being recognized as an important source of information about long-lived species (Dolan et al, 2023; Holmes & York, 2003). Although age information is rarely readily available for empirical populations, it is sometimes possible to approximate an individual’s age from their phenotype (e.g., turtle scutes and carapace length (Jensen et al, 2018; Wilson et al, 2003), rattlesnake rattles (Heyrend & Call, 1951), tree rings (Shroder, 1980), otoliths (Campana, 1999), tooth wear (Hinton et al, 2023), telomere length (Haussmann & Vleck, 2002), DNA methylation (Nakamura et al, 2023), coloration (Pyle, 1997) etc.) or population monitoring (Eaton & Link, 2011)).…”

“…On the other hand, Schmidt et al (2018) did not find a relationship between heterozygosity and age in the long-lived Australian lungfish ( Neoceratodus forsteri ), despite habitat degradation and suspected decline. The development of new methods for estimating individual age non-invasively, for example using telomere length (Haussmann & Vleck, 2002), DNA methylation levels (Nakamura et al, 2023), and radiocarbon dating (Fallon et al, 2019), expands the applicability of age comparisons in long-lived organisms of high conservation concern. However, to understand the utility of using genetic differences and age structure within contemporary populations as evidence of demographic decline, we need to investigate the relationship between age and genetic patterns in a system where the true timing and severity of the decline is known.…”

A cost‐effective blood DNA methylation‐based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models

“…feature selection) together with regression. Elastic net regression is widely adopted in many DNA methylation-based age estimation studies (Bors et al, 2021;Lu et al, 2023;Nakamura et al, 2023;Raj et al, 2021;Thompson et al, 2017;Vidaki et al, 2021).…”

“…As shown in Figure 1, after feature selection, we created regression models with elastic net regression and support vector machine radial (SVMr) in the training data. SVMr, similar to elastic net regression, has been found to produce high estimation accuracy (Krivonosov et al, 2022;Nakamura et al, 2023;Qi et al, 2021;Xu et al, 2015). We performed elastic net regression and its hyperparameter tuning with cv.glmnet in the R package glmnet 4.1-8 (Friedman et al, 2010).…”

Editorial 2024

“…Studies into methylation patterns are progressing rapidly in the field of molecular ecology, with guidance for ecological studies outlined in Laine et al. (2023) and powerful examples of non‐invasive ageing of non‐model organisms through methylation patterns (Nakamura et al., 2023; Parsons et al., 2023).…”