Tawfik, Y. | bioRxiv Science

bioRxiv2026

Promises and limitations of current ancient human epigenetic clocks

Age-at-death estimation of archaeological human remains is central to palaeodemographic 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 limitation and indirect methylation inference. Here, we evaluate the performance of existing epigenetic clocks on reconstructed ancient human methylomes combining high-coverage genomic data and a correction framework adapted to mitigate damage-derived sequence bias. Across multiple CpG window sizes, neither direct clock application nor regression-based retraining produced reliable continuous age-at-death estimates. Reframing age inference as adult-subadult classification did not return statistically supported age classes either. In contrast, sex estimation based on X-chromosome methylation achieved perfect accuracy, before and after correction. Together, these results indicate that current palaeo-epigenetic approaches reliably recover global biological signals but are not sufficiently sensitive to capture gradual, age-related variation in humans. 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.

genomics↗

bioRxiv2025

Historic Genomes Uncover Demographic Shifts and Kinship Structures in Post-Roman Central Europe

Many European towns and villages trace their origins to Early Medieval foundations. In former Roman territories, their emergence has traditionally been linked to mass migrations from outside the Roman Empire. However, recent studies have emphasised local continuity with some individual-level mobility. We generated and analysed 248 historic genomes from Late Roman (3rd and 4th century CE) and Early Medieval (5th-8th century CE) burial sites in southern Germany, comparing them to over 2,500 contemporary and Iron Age genomes in addition to 1,344 modern-day genomes from Germany, Italy and Great-Britain. Despite small inferred Early Medieval period community sizes, genetic diversity exceeded that of modern German cities. In the Altheim graveyard, established in the 5th century by a group of Northern European descent, we inferred a demographic shift in the 6th century with the integration of newcomers with ancestry typical of a nearby Roman military camp, likely as a result of the collapse of Roman state structures. We reconstructed multigenerational pedigrees and, using a novel approach to infer ancestry of unsampled relatives, inferred immediate intermarriage between incoming and local groups, with a distinct tendency for men from former Roman background marrying women of northern descent. Burial proximity correlates strongly with kinship, in some cases spanning six generations. These communities were organized around small family units, exhibited loosely patrilineal or bilateral descent patterns, practiced reproductive monogamy, and avoided close-kin marriages. Such practices reflect broader transformations in family structures that began during the Late Roman period, were transferred to small agrarian societies in the Early Medieval period, and continued to shape European societies. By the 7th century, ongoing admixture had shaped genetic diversity patterns into those resembling Central Europe today.

genetics↗