Five ancient genomes from Britain (dating rom the Iron Age to the Late and Post-Medieval Period) of individuals with aneuploidies.
Ancient DNA is a valuable tool for investigating genetic and evolutionary history but can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes (~0.0001X-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first prehistoric case of mosaic Turner syndrome (45,X0/46,XX) in an Iron Age individual sequenced to average 9-fold coverage, as well as new cases of Down syndrome (47,XY,+21) and Klinefelter syndrome (47,XXY). Overall, our approach provides the first accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can provide new interpretations of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.