Data from: 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
trajectories, indicating potential inter-individual variation in ageing
dynamics. Functional enrichment analyses revealed that age-associated CpGs
were enriched in genes and pathways related to development, neurogenesis,
metabolism, and social or physiological regulation, including oxytocin,
apelin, and melanogenesis signalling. Age-related methylation changes were
characterised by predominant hypermethylation in CpG islands and genic
regions, consistent with patterns reported across mammals. Together, these
findings demonstrate that epigenetic clocks capture biologically
meaningful features of ageing linked to life-history traits.  As
a long-lived mammal with extended reproductive capacity and complex social
systems, the Asian elephant represents an informative comparative system
for investigating the molecular architecture of ageing. This study
contributes to the growing field of comparative epigenetic ageing and
highlights the potential of DNA methylation–based approaches to inform
evolutionary and conservation-relevant research when applied in
appropriate ecological and methodological contexts.