Promises and limitations of current ancient human epigenetic clocks

Age-at-death estimation of archaeological human remains is central to paleodemographic research yet remains particularly challenging for adults, where osteological methods often produce imprecise age ranges. Epigenetic clocks can accurately predict chronological age in modern humans, but their applicability to ancient human DNA is unclear due to data limitations and indirect methylation inference. Here, we evaluate existing epigenetic clocks on ancient human methylomes combining high-coverage genomic data and a correction framework. Using DNA methylation estimates inferred across different CpG window sizes, neither direct clock application nor regression-based retraining produced reliable age-at-death estimates, and adult-subadult classification did not return statistically supported age classes. In contrast, X chromosome methylation separated males and females, suggesting that broad biological signals remain detectable at sufficient sequencing depth. These results indicate that current approaches can recover global biological signals but remain insufficiently sensitive to capture gradual age-related variation. Estimating age-at-death from ancient methylomes will therefore require methodological advances beyond correction alone, including reference data and improved models for inferring damage-derived epigenetic signals.