Detection of chromosomal aneuploidy in ancient genomes.

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.

Dental calculus in the industrial age: Human dental calculus in the Post-Medieval period, a case study from industrial Manchester.

The analysis of dental calculus (mineralised dental plaque) has become an increasingly important facet of bioarchaeological research. Although microscopic analysis of microdebris entrapped within dental calculus has revealed important insights into the diet, health, and environment of multiple prehistoric populations, relatively few studies have examined the contributions of this approach to more recent historical periods. In this study, we analyze dental calculus from an English Post-Medieval, middle-class urban skeletal assemblage from Manchester, England using light microscopy. We characterize all types of microremains, observing heavily damaged starch and plant material, high quantities of fungal and yeast spores, the presence of wood particles, plant (cotton) and animal (wool) fibres, as well as limited quantities of microcharcoal and burnt debris. We observe the presence of non-native, imported plant products, including New World maize and potentially tapioca starch. We compare our results to similar studies from earlier time periods to reveal the impacts of the significant economic, social and environmental changes occurring during the Industrial period in England, including changes in food processing, food access, food storage, and air quality. We conclude by outlining important methodological considerations for the future study of Post-Medieval dental calculus and propose potential areas of future research.