The Central Plain of China, the cradle of Chinese civilization, experienced major demographic upheavals during the Qing era (1644-1912 AD), yet its population's genetic history during this critical period remains largely uncharacterized. Here, we generated genome-wide data for 46 Qing Dynasty individuals from the Sanzhiyuan cemetery in Sanmenxia, Henan province. The Sanzhiyuan population exhibits remarkable genetic homogeneity and shows substantial genetic continuity with preceding populations of the Yellow River region dating back to the Late Neolithic. We successfully model them as direct descendants of Tang Dynasty populations. Notably, despite the Qing being ruled by the ethnically distinct Manchu elite, we detected no evidence of large-scale genetic admixture with Manchu, Mongol, or other northern or West Eurasian groups. Furthermore, we demonstrate that these Qing-era individuals are direct ancestors of the modern Han population in Henan, completing an unbroken multi-millennial genetic lineage. Our findings further demonstrate the stability of the genetic profile of the Central Plains population-a stability that has persisted for millennia and remained profoundly unaffected by major historical upheaval.

Dietary differences across social strata have a direct impact on the oral health of a population. This research explores the relationship between oral health, diet, and social stratification in the Guo State ((sic)) during the Spring-Autumn Period of the Eastern Zhou Dynasty (771-476 bce). A total of 887 teeth and 1213 alveoli from 57 individuals in the Shangshihe Cemetery in Yima County, Henan Province, China were included in this study. Dental wear severity and the prevalence of dental caries, dental calculus, periapical lesions, antemortem tooth loss (AMTL), linear enamel hypoplasia (LEH), temporomandibular joint osteoarthritis (TMJ-OA), and periodontal disease were analyzed and integrated with previously recorded isotope data. Our results revealed oral health and dietary differences related to social class, age, and sex at Shangshihe. First, as social class declined, there was an increase in dental wear severity and a significant increase in LEH prevalence associated with coarser diets and lower protein consumption. A gradual decline in the proportion of middle-aged individuals was observed as social class decreased. Second, for the commoner class, an increase in protein intake for middle adults compared to their young adult counterparts suggests age-based privileges that transcended typical class barriers. Lastly, pronounced sex-based differences in oral pathologies emerged for the commoner class under conditions of resource disparity. Males had a more protein-rich diet, potentially contributing to the significantly higher prevalence of dental calculus and PD observed in male commoners. These findings align with historical documents demonstrating how the social, age-related, and gendered hierarchies of the Eastern Zhou were materially manifested through oral health and diet.

Abstract As a pivotal cradle of East Asian civilization, the middle Yellow River region has long been a focal point for studying human cultural and biological evolution. However, its peopling history and kinship practices remain unclear due to a lack of ancient genomic data. In this study, we present 112 newly sequenced ancient genomes from eight archaeological sites in the middle Yellow River region, dating from 6,200 to 100 years ago. Our analyses reveal that all later individuals ultimately traced their primary ancestry to local early populations represented by our newly generated 6,200-year-old genomes from western Henan—the earliest genomes from the core area of the Yangshao culture. We also identified two major subsequent demographic transformations. The first was a cultural transition-associated genetic shift around 4,500 years ago in western Henan during the Longshan period that may be linked to the spread of Shaanxi-Shanxi populations. This was followed by a two-millennia-long expansion of central Henan-related ancestry that homogenized the genetic landscape across the entire Yellow River basin, independent of significant genetic contributions from the Eurasian Steppe or other adjacent foreign regimes. Beyond demographic history, we provide insights into ancient social structures through two case studies. At the 2,500-year-old Shangshihe site, evidence suggests that the social status was stably inherited within families and among close biological kin. The society represented by the 2,000-year-old Dongxiaoli-Bailong site appears to have placed greater emphasis on the relationships forged through marriage alliances rather than on ancestral lineage inheritance. Collectively, our study illuminates the complex interplay between local continuity and long-distance population connectivity in one of the world’s earliest agricultural heartlands and provides new insights into social structure in Iron Age northern China.

Multiple osteochondromas (MO) is a rare bone disease with variable manifestations that make it difficult to distinguish from phenotypically similar diseases, both morphologically and radiologically. As a monogenic disorder associated with mutations in EXT1 or EXT2, ancient DNA analysis can provide genetically confirmed diagnoses and insights into the pathogenesis of suspected cases. To further investigate a previously reported suspected MO case from Qing-period Shandong, China, we generated ancient whole-exome sequencing data from the individual’s petrous bone, yielding a mean sequencing coverage of 27.172×. We identified a pathogenic heterozygous mutation in the ligand-binding site Rossmann-2 subdomain of EXT1 (c.791T > C; p.Leu264Pro) with a sequencing depth of 17×, a mutation also found in an unrelated modern Latin American patient. Additionally, by predicting and analyzing the 3D structure of the EXT1 protein, we detected structural and functional damage. Our findings expand the known spectrum of EXT1 mutations and enhance the comprehensive genotype–phenotype map of rare MO, providing insights into its genetic pathology from a historical perspective. Furthermore, this research expands the understanding of disease landscapes in Northern China, both paleopathologically and paleogenetically.

Objects associated with oral cavities in archaeological contexts may reflect antemortem dental intervention, deliberate postmortem treatment, or taphonomic movement. This study examines a cylindrical object reported within a pathological alveolar cavity in the right maxillary second molar region of the individual from Burial M280, a Warring States-period Qin grave at Beishenjiaqiao cemetery in Xi’an. Compositional and density data were consistent with a carbonate-rock composition. Macroscopic, radiographic, microscopic, and contextual analyses revealed no fixation features, masticatory wear, artificial preparation, or adaptive osseous response. Together with severe alveolar abscess formation and loss of the buccal root, these observations strongly argue against sustained antemortem use as a prosthesis or implant. Deliberate postmortem placement remains plausible, but non-intentional postmortem entry or later displacement cannot be excluded because the original object–sediment–bone relationship was not documented before removal. The case illustrates a structured differential approach to evaluating comparable object–oral associations in archaeological contexts.

Punitive nasal amputation was an irreversible punishment in ancient times as a form of punitive body reduction. Though it had been listed as one of the major punishments in the penal system of early ancient China, and there had been many records of nasal punitive amputation cases in ancient texts, there have been no skeletal discoveries of this practice in archaeological settings in China. This study reports a case of a female individual with signs of midfacial disfigurement, dated 1298–1404 CE and possibly from the Yuan-Ming Dynasties. The female buried in a prone position was recovered from the Sanzhiyuan Cemetery in Sanmenxia City, Henan Province. The facial skeleton of the adult female individual carried signs of bony damage, healing, and bone spurs around the piriform aperture. Considering the broad antemortem destruction of piriform aperture structures and the historical background of this individual, the most possible reason for midface disfigurement was punitive nasal amputation. The post-procedure patient care had allowed the individual to survive for years. This individual was the only person in this cemetery buried in a prone position, indicating a special funeral treatment to cover for the facial disfiguration due to criminal punishment. If confirmed, this is the first archaeological case of punitive nasal amputation from ancient China, which enriches our knowledge of the penal system and medical care system in antiquity. The discovery and bioarchaeological study of the first nasal punitive amputation case helps enrich our knowledge of the penal system, medical system, patient care, and social outlook in antiquity.

Ancient lead mining and smelting activities caused significant environmental heavy metal contamination and human lead exposure. This study investigates the lead exposure dynamics from the Neolithic period to the Han Dynasty (ca. 6000 BCE-AD 220) by systematically analyzing 140 human dental enamel and bone samples from six archaeological sites in the central northern Shandong ((sic)(sic)): Houli, Dinggong, Huangtuya, Bianxianwang, Zonglvcheng, and Xiangjianan. Results from ICP-OES and MC-ICP-MS analyses reveal a marked increase in lead levels in human remains, correlating with intensified bronze production and the expanding circulation of lead-containing artifacts. During the Han Dynasty (202 BCE-AD 220), lead exposure fluctuated between the Western and Eastern Han periods, influenced by governmental policies and changes in the use of lead-based products, ultimately peaking in the Eastern Han. Lead isotopic evidence further indicates that pollution was mainly derived from the nearby copper and lead mines in Zouping and Zichuan, with the Tai-Yi Mountains HRL Cu-Pb Ore Belt contributing partially to highly radiogenic lead exposure. This study establishes the first continuous 6000-year record of human lead exposure in East Asian, spanning from the Neolithic to the Iron Age, providing critical evidence for understanding ancient human health and the historical dynamics of heavy metal pollution.

The Eastern Zhou period (770-256 BCE) was a transformative era in ancient China, marked by intensified social stratification, frequent warfare, and increased population movements. The Western Guo State, as an important vassal state during the Western Zhou period, migrated eastward with King Ping of Zhou and was eventually conquered by the Jin State. Due to limited genomic data, the genetic history of the Guo State population remains unclear. The Shangshihe cemetery, located in Yima City, Henan Province, is hypothesized to be associated with the Guo State and provides an opportunity to understand the genetic dynamics of this period. In our study, we successfully obtained 13 ancient genomes from the Shangshihe cemetery. Our findings suggest notable maternal and paternal genetic diversity within the Shangshihe population, although this observation is limited by the small sample size. Population genomic analysis shows that the Shangshihe individuals are predominantly of Yellow River Basin-related ancestry, with minor contributions from Southern East Asian-related and Eurasian Steppe-related sources. This genetic profile reflects extensive interactions between the Central Plains and surrounding populations during the Eastern Zhou period. Additionally, while distinct Y-chromosome haplogroups were observed among individuals with different burial orientations, autosomal analysis did not detect significant genetic differentiation, indicating overall genetic homogeneity within the population. These results not only elucidate the genetic characteristics of the Guo State population but also provide a new genetic perspective on the population dynamics and cultural exchanges in the Central Plains during the Eastern Zhou period.

The Yellow and Yangtze river basins in China are among the world's oldest independent agricultural centers, known for the domestication of millet and rice, respectively, yet their genetic history is poorly understood. Here, we present genome-wide data from 74 Middle Neolithic genetic samples from these regions, showing marked genetic differentiation but bidirectional gene flow, supporting a demic diffusion model of mixed farming. Yellow River populations exhibit distinct genetic substructures resulting from interactions with surrounding groups during the mid-Neolithic expansion of millet agriculture. Upper Yellow River populations are genetically linked to Tibetan Plateau populations and possess the earliest adaptive EPAS1 haplotype (∼5,800 BP) among modern humans. Meanwhile, Yangtze River rice farmers show genetic affinity with Neolithic to present-day southeast coastal China and Austronesian populations, tracing the origins of proto-Austronesians farther north to the Yangtze River. These findings offer new insights into the impact of mid-Neolithic agricultural expansion on human genetic history.

The Yellow River (YR) Basin is a pivotal region for understanding the origins and evolution of Chinese civilization. Previous genomic data here suggest a temporal shift in population genetics towards southern Chinese profiles, possibly due to the introduction of rice agriculture and climatic shifts in the Holocene. Here, we report the ancient genomes of two individuals from the Dahecun site during the Yangshao and transitional YangshaoLongshan (Longshanization) periods. We found a genetic homogeneity in the Middle Neolithic YR basin, but we have not detected a southern-related ancestry among YR farmers in our sample of the Longshanization period compared with the Middle Neolithic YR farmers. Our results indicate a genomic substructure in YR Basin farmers during the transitional Yangshao-Longshan periods. The initial introduction of rice farming into the Central Plain might not be always accompanied by demic diffusion. The Neolithic Yellow River farmers were suggested to significantly contribute to the formation of modern Han Chinese.

The core area of the Central Plains is one of the crucial regions for the origin of Chinese civilization, and the settlement site cluster in the mid-late Yangshao period (6000-5000 BP) provides a unique opportunity to investigate the human dietary pattern in the Central Plains for the origin of Chinese civilization. However, previous studies have not yet been able to adequately explain why the Central Plains has developed into an area in which the process of social complexity has accelerated significantly and the emergence of early Chinese civilization based on the development of millet agriculture in the core area of the Central Plains in the mid-late Yangshao period. In this case study, stable isotope analysis of the human bone collagen from the Shanggangyang site was conducted. The isotopic data showed that the majority of the Shanggangyang inhabitants (-8.0 +/- 0.7%o, 9.0 +/- 0.8%o, n = 24) were on a C4 millet-based diet, while the M13 individuals (-15.9 +/- 0.1%o, 6.5 +/- 0.1%o, n = 2) was on a C3 and C4 mixed diet. Furthermore, temporal investigations of the development of millet agriculture from isotopic perspective during the middle to late Neolithic period (9000-5000 BP) in the Central Plains comprehensively and explicitly revealed that millet agriculture developed and matured, and became the predominant subsistence economy in the mid-late Yangshao period (6000-5000 BP). This prosperous subsistence economy based on millet farming of the mid-late Yangshao period not only played an important role in generally accelerating the process of social complexity in the Central Plains, but also provided a substantial economic foundation for the emergence of early Chinese civilization in the core area of the Central Plains.

Limb amputation is a surgical procedure used during a medical operation or to manage trauma. Besides its therapeutic potential, amputation is a cruel punishment, with punitive body reduction practiced in ancient societies and even some modern ones. Victims of punitive amputation would face impaired locomotion and public shame. In this study, two individuals with signs of lower limb amputation were excavated from the Xiagantang site in Sanmengxia, Henan Province, China. The two skeletons were studied using bioarcheological approaches to determine consequences of amputation, identify possible patient care, and reconstruct circumstances of the amputation events. M693 had a lower limb amputation on the left side, while M432 was amputated on the right. Macroscopic observations and image analyses indicated healing and functional adaptations. Grave goods and the isotopic analysis suggested that the amputees had relatively high socioeconomic status. It is postulated that M693 and M432 had punitive amputation for felonies; this bioarchaeological evidence corroborated with historic written records of law and punishment from the penal system of the Zhou Dynasty. Post-execution, the individuals were allowed to recover, and they continued to live for years. These cases enrich our understanding of the physical consequences of lower limb amputation and illuminate the social context of amputation during ancient times.

Ancient Chang’an in the Tang Dynasty (618–907 AD) was one of the world’s largest and most populated cities and acted as the eastern end of the world-famous Silk Road. However, little is known about the genetics of Chang’an people and whether the Western Regions-related gene flows have been prevalent in this cosmopolitan city. Here, we present seven genomes from Xingfulindai (XFLD) sites dating to the Tang Dynasty in Chang’an. We observed that four of seven XFLD individuals (XFLD_1) were genetically homogenous with the Late Neolithic Wadian, Pingliangtai, and Haojiatai populations from the middle reaches of the Yellow River Basin (YR_LN), with no genetic influence from the Western Eurasian or other non-Yellow River-related lineages. The remaining three XFLD individuals were a mixture of YR_LN-related ancestry and 3–15

In the Central Plains of China during the Zhou Dynasty (1046-256 BCE), the social hierarchy gradually solidified, accompanied by frequent wars and the phenomena of multicultural and multi-ethnic integration. These social phenomena collectively influenced the population’s genetic structure at that time. However, our understanding of the genetic history of this period remains largely unknown owing to limited ancient DNA studies. In this study, we successfully obtained 11 ancient genomes from the Guanzhuang site during the Zhou Dynasty on the central plain of China. Our findings revealed remarkable genetic continuity with the Neolithic populations of the Yellow River Basin and emphasized genetic diversity through the analysis of uniparental genetic markers. Population structure analysis further confirmed the genetic similarity between the Guanzhuang population and ancient populations of the Yellow River Basin and indicated genetic exchanges with ancient populations from surrounding regions. Intriguingly, signs of inbreeding within the Guanzhuang community cast doubt on the stringent enforcement of the contemporary marital regulations against consanguineous marriages within the same surname or clan. These revelations significantly enhance our insight into the complex interplay of ancient demography and societal organization, concurrently presenting a genetic perspective to view the complex evolution of Chinese civilization’s multiethnic.

This article aims to understand the impact of a condition causing multiple benign neoplasms on a historical individual, and increase understanding of disease processes using a paleopathological case. We present the case of an adult male from the Balizhuang site in Weifang City, Changle County, Shandong Province, China, dated by the burial artifacts to the Qing period (1644–1911 CE). The individual has multiple bony growths found on both long and flat bones, which were also observed radiographically. Imaging revealed that the lesions show continuity with the medullary cavity of the host bone. The individual also exhibited short stature, upper limb length asymmetry, and hip and ankle deformities. Conditions included in a differential diagnosis are myositis ossificans, parosteal osteosarcoma, and osteochondroma, with multiple osteochondromas (MO) being the most likely diagnosis. We also present historical texts suggesting the presence of osteochondromas in China. This may be the first case of adult MO reported in Chinese bioarcheology, helping to expand paleopathological data on benign tumors.

Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.

Skeletal fluorosis is a systemic chronic disease caused by long-term intake of excessive fluoride, which accumulates in bone tissue and causes changes to the bone and periosteal tissue. Skeletal fluorosis is rarely considered in paleopathological analyses, but in areas with relatively high fluoride in the environment, it may be an important cause of bone hyperplasia. In this study, we observed pathological lesions consistent with fluorosis on two human skeletons from the Ming Dynasty (1368-1644 CE) excavated from a cemetery in western Henan Province. By using an electron microprobe to measure the fluoride content in the teeth, and by considering the living conditions in the area during the Ming Dynasty, we conclude that the remains show evidence of skeletal fluorosis. We also consider the content of fluoride in the local groundwater, the local way of life, and other factors, to identify potential causes of skeletal fluorosis in this population and demonstrate that environmental factors were the main cause. This offers insight into the relationship between humans and their environments in China, especially western Henan Province, in the historical past. It also demonstrates the unique contributions bioarchaeology can make to environmental health studies and studies of the history of health.

Cattle are one of the six livestock species that have occupied an important place in Chinese history. Previous ancient DNA studies have indicated that Chinese taurine cattle (Bos taurus taurus) are exotic, but the exact route and diffusion by which they were introduced to China is unknown. In this study, we extracted the mitochondrial genomes of 34 cases of ancient taurine cattle (from the late Neolithic to Qin and Han dynasties) excavated from sites in northern China and the eastern Eurasian steppe, and successfully obtained 14 mitochondrial genome sequences. The results of ancient DNA analysis reveal that with cultural exchange and trade, there was close genetic exchange between domestic taurine cattle in different regions. The haplotypes shared by domestic cattle have genetic continuity, reflecting the strong cultural influence of the large capital city sites such as Taosi, Shimao and Erlitou on the surrounding areas. This study suggests that ancient northern Chinese taurine cattle may have accompanied the westward transmission of agricultural or painted pottery culture and thus had a maternal genetic contribution to modern Tibetan cattle.

The turbulent stage before the unification of China under the first Empire, the Qin Dynasty (221-207 BC), witnessed remarkable changes in economic livelihood and social conditions. This study aims to investigate the subsistence strategies of humans living in the Guanzhong Plain during the Late Qin State (350-221 BC) by using carbon and nitrogen isotope analysis on animal and human bone collagen, as well as starch grain analysis of human dental calculus, from Podi cemetery, Shannxi Province, China. We argue that Podi humans likely relied on a mixed subsistence strategy based on animal husbandry practices and diverse crop agricultural pattern which consist of millet, soybean, wheat, and probably supplemented by hunting and gathering (Job's tears, nuts and tubers) economy. Combined with bioarcheological studies on Qin humans, we infer that previously traditional animal husbandry economy was still being practiced in the Qin period along with the inclusion of a newly introduced agricultural economy.