Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA

The study of how past societies dealt with disease is a key focus of biological anthropology. Disease can impact daily life and shape community responses. While studying pathologies in skeletal remains offers insights, osteological examinations are limited to skeletal manifestations and diagnoses can be ambiguous. Rare diseases are under-represented due to taphonomic, methodological, and visibility factors. This multidisciplinary study integrates genetic, anthropological, and archaeological data to understand disease and societal perceptions in the past. Chromosomal trisomies, involving three copies of a chromosome instead of two, are common genetic aberrations. Except for mosaicism or partial trisomy, full autosomal trisomies are rarely compatible with life. Trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome) are the only potentially non-fatal full autosomal trisomies, with trisomy 13 and 18 rarely surviving childhood without medical intervention. Each trisomy is associated with physical and neurodevelopmental symptoms, some of which might have been recognized by past societies. However, genetically identified prehistoric or historic cases of autosomal trisomies are lacking, likely due to the low prevalence of these conditions and the challenges in analyzing ancient DNA (aDNA) for copy number variations. This study aims to address this gap by employing a novel Bayesian method for analyzing aDNA.

Previous anthropological reports have documented only a handful of cases of Down syndrome. Recently, a genetically identified case of Down syndrome was reported in Neolithic Ireland, but lacked physical description. No prehistoric or historic cases of trisomy 13 or 18 have been genetically or osteologically identified. The scarcity of such cases is attributed to the low prevalence of these syndromes (1:705 for Down syndrome, 1:3226 for Edwards syndrome, and 1:7143 for Patau syndrome in modern populations) and the methodological difficulties in analyzing aDNA for copy number variations, which typically require long read lengths and high-depth coverage. This study aims to overcome these limitations by using a novel method designed for low-coverage aDNA data.

This study analyzed shotgun sequencing data from 9,855 prehistoric and historic individuals using a novel Bayesian method for detecting trisomies in low-coverage aDNA data. The method involves recording the number and proportion of reads mapping to each autosomal chromosome. A beta-binomial distribution was used to model the proportion of reads mapping to each chromosome, accounting for overdispersion due to various factors. The parameters of the beta distribution were estimated from a subset of samples with high read counts. The Z-score was calculated as the number of standard deviations of the observed proportion of reads, compared to the expectation from the beta-binomial distribution. Genetic sex was estimated by comparing the fraction of reads mapping to X and Y chromosomes. Osteological analyses were conducted by reviewing existing publications, photographs, and osteological reports; no new skeletal analyses were performed. The age at death was estimated using multiple methods. Statistical tests, such as the binomial test, were used to compare the observed prevalence rates of trisomies to modern rates.

The study identified six new cases of Down syndrome (trisomy 21) and one case of Edwards syndrome (trisomy 18) among the 9,855 individuals analyzed. An additional previously published case of Down syndrome was also confirmed. All cases were found in infant or perinatal burials. The proportion of reads mapping to chromosome 21 in the Down syndrome cases was approximately 1.5 times higher than in negative cases. Similarly, the proportion of reads mapping to chromosome 18 in the Edwards syndrome case was 1.47 times higher than in the negative group. The six new Down syndrome cases ranged from the Neolithic period to the 18th century CE, across various geographic locations. The Edwards syndrome case was from the early Iron Age in Spain. Osteological analyses revealed overlapping skeletal markers (such as cranial porosity, abnormal bone growth on the occipital bone, and in one case, inner ear bone malformation) consistent with trisomy 21 in some individuals. The Edwards syndrome case showed severe skeletal abnormalities, some previously unreported. Burial practices suggested that these individuals were treated with care and considered members of their communities, given intramural burials and sometimes elaborate grave goods.

The findings address the research question by providing the first large-scale genetic and osteological study of trisomies in prehistoric and historic populations. The detection of trisomies in various time periods and geographic locations demonstrates that these conditions were present in past populations. The lower observed prevalence of Down syndrome compared to modern rates might be due to underrepresentation of infant burials and differential preservation of skeletal remains. However, the clustering of trisomy 21 and trisomy 18 cases in Early Iron Age Spain warrants further investigation. The osteological findings highlight the limitations of relying solely on skeletal markers for diagnosing these conditions, given the variable presentation and the possibility of other contributing factors. The careful burial practices observed suggest that these individuals were not stigmatized and were acknowledged as members of their communities.

This study significantly expands our knowledge of the prevalence and impact of trisomies in past populations. The identification of multiple cases, combined with osteological and archaeological evidence, provides insights into the lives and societal perceptions of individuals with these genetic conditions. Future research should focus on increasing the size of ancient DNA datasets and refining analytical methods for the detection of rare genetic disorders. Further investigation into the unexpectedly high frequency of trisomy cases in Early Iron Age Spain is also needed.

The study's findings might be affected by the limitations of ancient DNA analysis and the preservation of skeletal remains. Infant and perinatal remains are more fragile and less likely to be preserved, potentially underrepresenting the true prevalence of trisomies in the past populations. Also, osteological diagnoses are limited by the incompleteness and preservation of many specimens, and may reflect other conditions beyond trisomy.