Epigenetic signatures of ageing in Asian elephants revealed by reduced representation bisulphite sequencing

Accurate age estimation is essential for understanding life-history variation, modelling population dynamics, and informing conservation strategies, yet remains challenging for long-lived species. Here, we developed a genome-wide, DNA methylation-based epigenetic clock for Asian elephants (Elephas maximus), an endangered species, using reduced representation bisulphite sequencing (RRBS). Genome-wide methylation profiles were generated from 91 blood samples, yielding 144,611 candidate CpG sites, of which 389 CpG sites were identified as strongly associated with chronological age. The final model predicted age with high accuracy (r = 0.96, MAE = 4.82 years), corresponding to a relative error of 6.06 %, comparable to epigenetic clocks developed for humans and other non-model species. Longitudinal analyses revealed heterogeneous epigenetic ageing trajectories, with most individuals showing increases in epigenetic age over time, while others exhibited relatively neutral or decelerated trajec..., , # Data from: Epigenetic signatures of ageing in Asian elephants revealed by reduced representation bisulphite sequencing Dataset DOI: [10.5061/dryad.ksn02v7kp](https://doi.org/10.5061/dryad.ksn02v7kp) ## Description of the data and file structure * merged_methratio.txt Data filtered CpG methylation ratios (methylated reads divided by total reads) across all samples and chromosomes, where CpG sites were retained based on mean methylation (0.1–0.9) and average coverage (>5). This matrix includes missing values for sites not detected in all samples. Depending on downstream handling of methylation values and the desired use of these data, these cases can be excluded, ignored, or one can simply set \"effective CT count\" to the methylated count for those small subsets of sites. * all_methratios_imputedall.txt To prepare the data for downstream modelling, CpG sites with excessive missingness (>5 missing samples) were removed, and the remaining missing values were imputed using k-nearest ..., ,