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

The study investigates how often and in what contexts autosomal trisomies, especially trisomy 21 (Down syndrome) and trisomy 18 (Edwards syndrome), occurred in historic and prehistoric populations, and how past societies may have responded to affected individuals. Understanding disease in past communities has long been a focus of biological anthropology, but osteological diagnoses are limited because many pathologies do not manifest uniquely in bone, rare diseases are underrepresented, and skeletal lesions can have multiple causes. Trisomies 21, 18, and 13 are the only full-autosomal trisomies compatible with live birth, though survival into childhood without modern interventions is rare for trisomy 13 and 18. Phenotypic variability and age-dependent manifestations can hinder osteological recognition. The authors aim to integrate genetic screening of ancient DNA with osteological and archaeological context to identify cases of trisomy and evaluate mortuary treatment, thereby providing insights into prevalence, recognition, and social responses in past societies.

Few clear historic or prehistoric cases of autosomal trisomies have been documented osteologically, with only a handful of Down syndrome cases suggested in anthropological literature. A recent genetic identification of trisomy 21 was reported for Neolithic Ireland (3629–3371 BCE), though without a detailed physical description. The rarity of genetically identified cases in the past likely reflects (1) low baseline prevalence (modern birth prevalence approximately 1:705 for trisomy 21, 1:2500 for trisomy 18, and 1:471 for trisomy 13 among live births) making discoveries unlikely until datasets became large, and (2) methodological constraints for ancient DNA (short reads, low coverage) that limit traditional copy-number analyses. These gaps motivate development of methods suited to aDNA and large-scale screening to uncover rare disorders in the archaeological record.

• Sampling and sequencing: The study screened shotgun sequencing data from 9,855 prehistoric and historic individuals, primarily generated between 2016 and 2022 at the Max Planck Institute for Evolutionary Anthropology. Reads were adaptor-trimmed and aligned to the human reference genome GRCh37 using the Burrows-Wheeler Aligner. Autosomal reads were retained after filtering for minimum length (≥35 bp) and mapping quality (≥25).
• Trisomy detection approach: A novel Bayesian framework was developed to detect autosomal trisomies in low-coverage aDNA by modeling the proportion of reads mapping to each chromosome c (1–22). For each chromosome and library type, a beta prior was estimated for the binomial mapping probability θ using a filtered subset of samples with at least 10,000 reads (n=7103) to account for overdispersion from differing library protocols, sequencing runs, and preservation. Posterior probabilities for overrepresentation consistent with trisomy were computed, enabling confident detection with as few as ~1,000 mapped reads.
• Z-scores: For each individual and chromosome, Z-scores quantify the deviation of observed mapping proportions from expectation under the beta-binomial model (derivation in Supplementary Methods). Individuals with significant overrepresentation for a single chromosome and sufficient reads were flagged as positives.
• Statistical testing and software: Beta-binomial parameters were estimated via maximum likelihood (R package aod’s beta.mb()), densities via extraDistr::dbinom(), comparisons of observed versus expected prevalence via stats::binom.test(), and visualization via ggplot2.
• Genetic sex estimation: Genetic sex was inferred by comparing fractions of reads mapping to X and Y chromosomes; individuals within female-range cutoffs were assigned genetically female, others male.
• Osteological assessment: No new reanalysis of remains was conducted; osteological traits were compiled from previous publications, reports, and photographs. For infants/perinates, multiple skeletal indicators and limb bone lengths were used to approximate age-at-death, with caution due to potential growth abnormalities in trisomies.
• Validation: The method was applied to reanalyze a previously published Neolithic Irish case of trisomy 21 to confirm portability across datasets and laboratories.

• Screening outcome: Among 9,855 individuals, six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome) were identified. All positive cases had normalized posterior probabilities of 1.0 (machine precision) for the implicated chromosome.
• Signal magnitude: Trisomy 21 cases showed ~1.5-fold higher proportions of reads mapping to chromosome 21 compared to negatives (range 1.44–1.52). The Edwards syndrome case (CRU013) had a 1.47-fold elevation for chromosome 18.
• Genetic sex: The Edwards syndrome case was genetically female, consistent with the higher frequency of trisomy 18 in females (modern ratio ~3:2). The trisomy 21 set included both genetically male and female infants.
• Temporal and geographic distribution: Newly identified trisomy 21 cases largely date to 5000–2400 years ago, with one post-medieval Finnish case (17th–18th century CE). Notably, three trisomy 21 cases and one trisomy 18 case were from two contemporaneous early Iron Age sites in Navarra, Spain (ca. 800–400 BCE). A previously published Down syndrome case from Neolithic Ireland (Poulabone) was confirmed.
• Archaeological contexts: All cases were infant or perinatal burials. Bronze/Iron Age instances were intramural domestic burials; the Finnish case received a standard Christian burial. Some Iron Age burials included grave goods (e.g., bronze rings at La Estrella).
• Osteological observations: Across cases, overlapping skeletal markers included cranial and mandibular porosity, porosity of frontal/parietal/occipital bones, and abnormal bone growths on the occipital pars lateralis. Additional findings included occipital squama protrusion, inner ear malformation, enamel hypoplasia, and femoral morphological changes. LAZ019 (12–16 months) and YUN039 (~6–16 months) survived postnatally; comorbidities in Down syndrome could explain care needs, with mortuary treatment suggesting social inclusion and care.
• Prevalence context: The observed frequency of Down syndrome in the screened ancient sample is lower than modern birth prevalence, likely reflecting non-random sampling and preservation biases, especially the underrepresentation and poor preservation of perinatal/infant remains.

The study demonstrates that autosomal trisomies can be confidently detected in low-coverage ancient DNA using a chromosome-level mapping proportion model, enabling discovery of rare genetic disorders in archaeological contexts. Identification of six trisomy 21 and one trisomy 18 cases among nearly 10,000 individuals, including clusters at two Iron Age Iberian sites, shows that such conditions occurred across diverse times and places. Osteological traits overlapped with known clinical features but remained non-specific, underscoring the necessity of genetic confirmation. Mortuary evidence suggests that infants with trisomy 18 and 21 were buried according to prevailing customs, occasionally with grave goods, indicating community acknowledgment rather than stigmatization. The lower observed frequency relative to modern prevalence is plausibly explained by biases in sampling strategies and preservation, especially for fetuses, neonates, and infants whose remains are fragile and often absent from cemeteries. The findings highlight the value of integrating genetics with osteology and archaeology to interpret health, care, and social attitudes in past societies, while cautioning against osteology-only diagnoses and emphasizing the need for larger datasets to assess spatial-temporal variation in prevalence.

This work provides the first systematic genetic screening for autosomal trisomies in ancient individuals, identifying six Down syndrome and one Edwards syndrome cases across Neolithic to post-medieval contexts and confirming a previously reported Neolithic case. A Bayesian beta-binomial framework enables robust detection from low-coverage shotgun data (~1,000 mapped reads), overcoming limitations of traditional copy-number approaches in aDNA. Osteological markers consistent with trisomy were observed but remained non-diagnostic, reinforcing the importance of genetic confirmation. Mortuary practices indicate social inclusion of affected infants. Future research should expand sample sizes, refine statistical models for ultra-low coverage data, and deepen integration with osteological and archaeological context to assess prevalence variation, maternal-age effects, and cultural responses across regions and periods.

• Osteological diagnosis: No single osteological marker is pathognomonic for trisomy 21 or 18; many observed traits (e.g., porosity, enamel hypoplasia) are non-specific and can reflect diverse developmental or environmental factors.
• Preservation and sampling biases: Perinatal and infant remains are fragile, often poorly preserved, and underrepresented archaeologically, likely leading to underestimation of prevalence. Sampling across sites is non-random.
• Data constraints: The approach relies on low-coverage shotgun data and read-mapping proportions, which, while powerful, may be affected by library-specific biases and coverage heterogeneity (mitigated via beta-binomial modeling). No new osteological reanalysis was performed; age-at-death estimation in growth-disordered bones is uncertain.
• Scope: Only autosomal trisomies detectable via overrepresentation of whole-chromosome reads were targeted; mosaicism and segmental aneuploidies are not reliably addressed by this method.