Data from: Proportion methylation at a set of CpGs from 4 amplicons

Description

The file cpg_wide_clock.csv is the proportion methylation at each CpG. Rows or columns with missing values have been removed because GLMnet does not accept them. The file cpg_counts.csv provides information on the number of C's and T's counted, and thus also depth of coverage at each CpG.

Abstract

The age structure of populations, or the ageing rate of individuals, impacts aspects of animal ecology, epidemiology and conservation. Yet for many wild organisms, age is an inaccessible trait. In many cases measuring age or ageing rates in the wild requires molecular biomarkers of age. Epigenetic clocks based on DNA methylation have been shown to accurately estimate the age of humans and laboratory mice, but they also show variable ticking rates that are associated with mortality risk above and beyond that predicted by chronological age. Thus, epigenetic clocks are proving to be useful markers of both chronological and biological age, and they are beginning to be applied to wild mammals and birds. We have acquired strong evidence that an accurate clock will be possible for the wood mouse Apodemus sylvaticus by adapting epigenetic information from the laboratory mouse. Apodemus sylvaticus is a well-studied field system that is amenable to experimental perturbations and longitudinal sampling of individuals across their lives, and these features of the wood mouse offer opportunities to disentangle causal relationships between ageing rates and environmental stress. Our wood mouse epigenetic clock is PCR-based, and so requires tiny amounts of tissue and non-destructive sampling. We quantified methylation using Oxford Nanopore sequencing technology and present a new bioinformatics pipeline for data analysis. We thus describe a new and generalizable system that should enable ecologists and other field biologists to go from tiny tissue samples to an epigenetic clock for their study animal.