An epigenetic aging clock for dogs and wolves

Age structure is a fundamental aspect of animal population biology. Age is strongly related to individual physiological condition, reproductive potential and mortality rate. Currently, there are no robust molecular methods for age estimation in birds. Instead, individuals must be ringed as chicks to establish known‐age populations, which is a labour‐intensive and expensive process. The estimation of chronological age using DNA methylation (DNAm) is emerging as a robust approach in mammals including humans, mice and some non‐model species. Here, we quantified DNAm in whole blood samples from a total of 71 known‐age Short‐tailed shearwaters (Ardenna tenuirostris) using digital restriction enzyme analysis of methylation (DREAM). The DREAM method measures DNAm levels at thousands of CpG dinucleotides throughout the genome. We identified seven CpG sites with DNAm levels that correlated with age. A model based on these relationships estimated age with a mean difference of 2.8 years to known age, based on validation estimates from models created by repeated sampling of training and validation data subsets. Longitudinal observation of individuals re‐sampled over 1 or 2 years generally showed an increase in estimated age (6/7 cases). For the first time, we have shown that epigenetic changes with age can be detected in a wild bird. This approach should be of broad interest to researchers studying age biomarkers in non‐model species and will allow identification of markers that can be assessed using targeted techniques for accurate age estimation in large population studies.

Section: Discussionsupporting

confidence: 85%

Age estimation in a long‐lived seabird (Ardenna tenuirostris) using DNA methylation‐based biomarkers

Paoli-Iseppi

Deagle

Polanowski

et al. 2019

“…This is the first epigenetic age assay developed for monitoring bats, a taxon which forms a third of all mammalian species, and only the third designed for use on a wild species after humpback whales (Polanowski et al., ) and wolves ( Canis lupus ) (Thompson, vonHoldt, Horvath, & Pellegrini, ). The age prediction model developed explained 64% of the variance and predicted age from wing punches with a standard deviation of 1.52 years.…”

Section: Discussionmentioning

confidence: 99%

Application of a novel molecular method to age free‐living wild Bechstein's bats

Wright

Mathews

Schofield

et al. 2018

The age profile of populations fundamentally affects their conservation status. Yet, age is frequently difficult to assess in wild animals. Here, we assessed the use of DNA methylation of homologous genes to establish the age structure of a rare and elusive wild mammal: the Bechstein's bat (Myotis bechsteinii). We collected 62 wing punches from individuals whose ages were known as a result of a long-term banding study. DNA methylation was measured at seven CpG sites from three genes, which have previously shown age-associated changes in humans and laboratory mice. All CpG sites from the tested genes showed a significant relationship between DNA methylation and age, both individually and in combination (multiple linear regression R = 0.58, p < 0.001). Despite slight approximation around estimates, the approach is sufficiently precise to place animals into practically useful age cohorts. This method is of considerable practical benefit as it can reliably age individual bats. It is also much faster than traditional capture-mark-recapture techniques, with the potential to collect information on the age structure of an entire colony from a single sampling session to better inform conservation actions for Bechstein's bats. By identifying three genes where DNA methylation correlates with age across distantly related species, this study also suggests that the technique can potentially be applied across a wide range of mammals.

“…Because the basic features of DNA methylation are conserved at least in closely related species or even taxa, the epigenetic clock based on the same informative CpGs identified in humans was found to also work reasonably well in chimpanzees (Pan troglodytes) (Horvath, 2013). Since then, species-specific epigenetic clocks have been constructed in chimpanzees (Ito, Udono, Hirata, & Inoue-Murayama, 2018), mice (Han et al, 2018), humpback whales (Megaptera novaeangliae) (Polanowski, Robbins, Chandler, & Jarman, 2014), Bechstein's bats (Myotis bechsteinii) (Wright et al, 2018), dogs and wolves (Janowitz Koch et al, 2016;Thompson, vonHoldt, Horvath, & Pellegrini, 2017) and in a long-lived seabird (Ardenna tenuirostris) (Paoli-Iseppi et al, 2019). Epigenetic clocks are characterized by very high accuracy when compared to more traditional methods of age estimation.…”

mentioning

confidence: 99%

A clockwork fish: Age prediction using DNA methylation‐based biomarkers in the European seabass

Anastasiadi

Piferrer

2019

Age‐related changes in DNA methylation do occur. Taking advantage of this, mammalian and avian epigenetic clocks have been constructed to predict age. In fish, studies on age‐related DNA methylation changes are scarce and no epigenetic clocks have been constructed. However, in fisheries and population dynamics studies there is a need for accurate estimation of age, something that is often impossible for some economically important species with the currently available methods. Here, we used the European sea bass, a marine fish the age of which can be determined with accuracy, to construct a piscine epigenetic clock, the first one in a cold‐blooded vertebrate. We used targeted bisulfite sequencing to amplify 48 CpGs from four genes in muscle samples and applied penalized regressions to predict age. We thus developed an age predictor in fish that is highly accurate (0.824) and precise (2.149 years). In juvenile fish, accelerated growth due to elevated temperatures had no effect on age prediction, indicating that the clock is able to predict the chronological age independently of environmentally‐driven perturbations. An epigenetic clock developed using muscle samples accurately predicted age in samples of testis but not ovaries, possibly reflecting the reproductive biology of fish. In conclusion, we report the development of the first piscine epigenetic clock, paving the way for similar studies in other species. Piscine epigenetic clocks should be of great utility for fisheries management and conservation purposes, where age determination is of crucial importance.