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5 recordsLinked to original sources
PubMed2026

The Oral Microbiome of King Richard III of England.

OBJECTIVES: Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452-1485). MATERIALS AND METHODS: Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of nearly 400 million reads. The metagenomic data were taxonomically profiled and compared to new and previously published dental calculus metagenomes from England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Sequencing data were de novo assembled, and metagenome-assembled genomes assigned to the genus Tannerella were investigated for phylogenetic relatedness and virulence. Putative dietary DNA was assessed for authenticity. RESULTS: The dental calculus of King Richard III was well-preserved and yielded an exceptionally high quantity of DNA. Oral microbiome species diversity fell within the range previously observed among other northern European populations, suggesting that a royal lifestyle and a rich diet did not substantially impact his oral microbiota. The reconstructed Tannerella genomes contained many virulence factors found today among oral Tannerella species. No putative dietary DNA could be authenticated. DISCUSSION: The dental calculus of King Richard III produced one of the richest ancient oral metagenomes published to date, yet the species diversity was indistinguishable from that of commoners living in northern Europe over the last 7000 years. Insufficient plant and animal DNA were recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA even when exceptionally well-preserved.

Humans↗
PubMed2025

Leprosy in skeletons from archaeological sites: A systematic review.

BACKGROUND: Leprosy (Hansen's disease) is an ancient stigmatising infectious disease that remains endemic in many countries. Leprosy-related bone changes that cause disabilities in affected persons are evident in skeletons from archaeological sites. The aim of our synthesis of paleopathological data was to gain insights into the disease's historical distribution and presentation. METHODOLOGY: Systematic review of paleopathological studies describing human remains with signs of leprosy published up to December 2023. Extracted data on bone features from skulls and limbs, including rhinomaxillary syndrome (RMS) in cranial bones and post-cranial bone changes (PCBC) in hands and feet, were summarised, together with genomic data from studies of Mycobacterium leprae ancient DNA. FINDINGS: The 297 skeletons described in 67 studies comprised 264 skeletons from sites in modern-day Europe (117 from England, 68 from Denmark); 23 skeletons from Asia (10 from India), 5 from The Americas, and 4 from the African continent (all from Egypt); 174 (58.6%) were from leprosaria, 255 (85.9%) were adults, 28 (9.4%) adolescent, 14 (4.7%) of indeterminate age. Skeletons dated from 3715 BCE to 1839 CE, peaking around the 15th Century. Probable and possible RMS were identified in 85 (30.5%) and 153 (54.8%) of 279 skeletons with cranial data, respectively. Lower limb pathological PCBC were most prevalent in tarsals (76.6%), metatarsals (81.5%), and feet phalanges (85.6%). In upper limbs, 75.8% of humeri, 65.8% of radii, 61.0% of ulnae and 75.8% of hand phalanges exhibited pathological alterations. From 73 skeletons from 19 genomic studies, M. leprae single nucleotide polymorphism (SNP) type 3 was identified in 59 skeletons (80.8%), SNP type 2 in 11 (15.1%), type 4 in two, and type 1 in one. CONCLUSIONS: Four out of five archaeological skeletons with leprosy exhibited some degree of RMS, which is pathognomonic of the most severe form of the disease, irrespective of whether the skeleton was excavated from a leprosarium (leprosy hospital) or from a public cemetery or other burial site. The relatively small numbers of remains excavated over a wide geographical area and a long time period, and the focus of archaeological studies on skeletons already identified as having leprosy, mean that it is difficult to prove or disprove theories that aim to explain the decline and eventual disappearance of leprosy as a disease in Europe.

Humans↗
PubMed2026

Chronic disease in a 15th-century skeleton from the first European settlement of the Canary Islands: Early evidence in the colonial Atlantic expansion (San Marcial de Rubicón, Lanzarote).

OBJECTIVE: This study seeks to evaluate morphological changes in a skeleton recovered from San Marcial de Rubicón, the earliest permanent European settlement in the Canary Islands. MATERIALS: The individual derives from a primary inhumation dated to the early fifteenth century. METHODS: Macroscopic observation was combined with conventional radiography, computed tomography, and mitochondrial DNA analysis. A systematic differential diagnosis considered metabolic, infectious, inflammatory, neoplastic, and degenerative conditions. RESULTS: The individual under investigation is an adult male with evidence of diffuse cortical thickening, periosteal new bone formation, heterogeneous radiodensity, cranial diploic expansion, long-bone bowing, severe degenerative joint disease, sacroiliac ankylosis, and elongated thoracic vertebral defects. Mitochondrial DNA analysis identified haplogroup X2c1, consistent with European maternal ancestry. CONCLUSIONS: The overall pattern is most consistent with polyostotic Paget disease of bone, although coexisting axial ankylosis and vertebral defects complicate the interpretation. These additional lesions are insufficient to support an alternative primary diagnosis. SIGNIFICANCE: This case provides an early extra-European archaeological example of Paget disease in the context of Atlantic colonial expansion. Rather than simply extending the geographic record of the disease, it shows how chronic skeletal conditions with strong European clinical and archaeological associations may be identified in frontier populations formed through mobility, settlement and colonial interaction. LIMITATIONS: The diagnosis is based on a single individual, and nuclear DNA data were insufficient to assess genetic susceptibility. SUGGESTIONS FOR FURTHER RESEARCH: Further radiological, genomic, and isotopic analyses of early colonial skeletal assemblages are needed to evaluate chronic disease, mobility, and biological diversity in Atlantic frontier populations.

Male↗
PubMed2026

Transmission history of major China-prevalent Mycobacterium tuberculosis sub-lineages in East Asia.

Mycobacterium tuberculosis complex (MTBC) is distributed globally and has posed a severe threat to human health throughout history. In this study, we analyzed whole-genome data from the four major MTBC sub-lineages prevalent in China (L2.2, L4.2, L4.4, and L4.5) to reconstruct their transmission and expansion histories across East Asia and parts of Central Asia. We found that L2.2 has established a highly connected transmission network centered in Southern China, whereas L4.2 is characterized by cross-border transmission between Central Asia and Western China, and L4.4 and L4.5 exhibit repeated transmission events between Southeast Asia and Southern China. By reconstructing their population histories, we demonstrated that these sub-lineages have experienced multi-stage expansions since the 15th century, accompanied by a recent rapid proliferation of evolutionary clades. These findings reveal that the MTBC epidemic in East Asia may follow a pattern of long-term historical adaptation superimposed with recent concentrated outbreaks, providing potential genomic evidence to inform precise regional tuberculosis control strategies in China.

Mycobacterium tuberculosis↗
PubMed2025

Nested Admixture During and After the Trans-Atlantic Slave Trade on the Island of São Tomé.

Human genetic admixture, involving the contact between two or more previously isolated populations, can be a complex process influenced by social dynamics. In this study, we aim to reconstruct complex admixture histories in São Tomé, an island in the Gulf of Guinea where the Portuguese established one of the first plantation-based slave societies. Since the 15th century, migration waves from Africa and Europe, slavery, marooning, and indentured labour led to profound demographic shifts and social stratification on the island. Examining 2.5 million SNPs newly genotyped in 96 São Toméans, we observed patterns of genetic differentiation that were more complex than those of other populations descended from enslaved Africans on either side of the Atlantic. Using local ancestry inference and Identical-by-Descent methods, we identified five genetic clusters in São Tomé and reconstructed shared ancestries between each cluster and 70 African and European population samples, including an extensive sample from the Cabo Verde archipelago. Our findings align with historical records, retracing the major slave trade routes and labour-driven migrations after the abolition of slavery. We also identified gene flow between recently admixed groups that were previously isolated on the island. We call this process, creating multiple layers of genetic ancestry in admixed genomes, nested admixture. We suggest that changing social structures in São Tomé transformed the genetic structure of its population and influenced the admixture process. This study demonstrates how successive admixture and isolation events during and after the Trans-Atlantic Slave Trade shaped extant genetic diversity patterns at local scale in Africa.

Humans↗