Detection of chromosomal aneuploidy in ancient genomes

Abstract

Ancient DNA is a valuable tool for investigating genetic and evolutionary history that 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 ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.

Juvenile sex estimation using the elevation of the auricular surface: A systematic review and meta‐analysis

“…For example, intersex traits due to chromosomal variations (e.g., XXX, XO, and XYY and others) or androgen insensitivity are present in approximately 1.7% of living populations (Dreger, 1998;Sax, 2002). At present, it is rare-though possible-for intersex individuals to be identified in archaeological skeletal remains through the use of aDNA analysis (Anastasiadou et al, 2024;Garofalo & Garvin, 2020;Roca-Rada et al, 2022). Nevertheless, evaluating sex estimation methods as diagnostic tests allows for the use of appropriate statistical approaches from the biomedical field.…”

Advancing Sex Estimation from Amelogenin: Applications to Archaeological, Deciduous, and Fragmentary Dental Enamel

“…Currently proteomic-based techniques have only provided binary sex estimates from dental enamel (Stewart et al, 2017). Recent palaeogenomic advances in identifying chromosomal polymorphisms are promising in highlighting the potential to provide insight into this level of sexual diversity (Anastasiadou et al, 2024;Roca-Rada et al, 2022), and Stewart and colleagues (2017) note the potential of peptide quantitation for future proteomic development along these lines. Recent years have seen the burgeoning application of proteomic-based techniques to archaeological and palaeoanthroplogical samples of various preservation levels and temporal distribution (Buonasera et al, 2020;Cappellini et al, 2019;Castiblanco et al, 2015;Demarchi et al, 2016;Froment et al, 2020;Hodgkins et al, 2021;Lugli et al, 2019Lugli et al, , 2020Nogueira et al, 2021;Parker et al, 2019;Porto et al, 2011;Rebay-Salisbury et al, 2020;Stewart et al, 2016Stewart et al, , 2017Wasinger et al, 2019;Welker et al, 2019Welker et al, , 2020, but as with any new field there is the need for further methodological testing, validation, and ultimately standardisation.…”