Shipwrecks provide invaluable insights into human society and trade. Their unique preservation conditions also mean that they can serve as exceptional biobanks, recording traces of organisms carried aboard or arriving post wreck. Yet only limited research has explored the genetic potential of onboard sediments. Here, the authors present environmental and metagenomic analyses of sediments contained in a large amphora from the 150-year-old Yangzi Estuary II shipwreck. Weaving the results with historic texts, they reconstruct part of the history of the wrecked vessel, elucidating cargo-packing techniques, its likely season and port of sailing, and its ultimate submersion within the estuarine environment.

The Gansu-Qinghai (GQ) region is a critical Eurasian contact zone with exceptional linguistic and genetic diversity. However, genomic studies integrating genetic and linguistic evidence in areas with intensive language mixing remain limited. We conducted fine-scale genomic analyses on 153 new samples from four linguistically mixing or mixed regions: Linxia and Xiahe in Gansu, and Gan’gou and Wutun in Qinghai. Our findings reveal three primary ancestral components: Yellow River, western Eurasian steppe, and Tibetan Plateau (TP)-related lineages. While non-Han populations show pronounced genetic heterogeneity and varying patterns of language maintenance, Han populations exhibit asymmetric convergence. Specifically, the Wutun Han show concordant genetic and linguistic shifts, whereas other Han groups exhibit linguistic structural convergence without corresponding gene flow. Widespread east-west admixture was detected in both Han Chinese and non-Han populations from the GQ region, primarily dating to the Tang/Song and Yuan Dynasties. Together, our interdisciplinary genetic-linguistic framework reveals complex and asymmetric processes underlying population interaction and language evolution in the GQ contact zone.

OBJECTIVE:To evaluate axial and peripheral joint lesions in a late adolescent/young adult skeleton and assess whether they support a diagnosis of juvenile-onset ankylosing spondylitis. MATERIALS:Individual M55, a possible male aged 16.5-20 years, recovered from a Ming-Qing period tomb (14th-20th century CE) at the Dabuzi cemetery, Shaanxi, China. METHODS:Macroscopic observation was used to record skeletal pathologies. Differential diagnosis focused on inflammatory spondyloarthropathies and related arthropathies. RESULTS:The preserved thoracic and lumbar vertebrae show multi-level posterior ankylosis of the zygapophyseal joints, with fusion of the costovertebral and costotransverse joints. Erosive and irregular lesions affect the shoulders, hips, knees, and other peripheral joints. Ossified ligamentous tissue occurs superior to the right auricular surface, although the sacroiliac joints are poorly preserved. Manubriosternal fusion and active periosteal reactions are also present. CONCLUSIONS:The lesion distribution is most consistent with possible juvenile-onset ankylosing spondylitis, but incomplete preservation prevents a definitive diagnosis. SIGNIFICANCE:This case provides a diagnostic model for evaluating juvenile inflammatory spondyloarthropathy in incomplete archaeological remains, especially when the sacroiliac joints, hands, and feet are absent or poorly preserved. LIMITATIONS:Observations are macroscopic and lack radiographic, CT, or biomolecular confirmation. SUGGESTIONS FOR FURTHER RESEARCH:Imaging, comparative screening, and biomolecular analysis may clarify disease attribution and broader patterns of inflammatory joint disease.

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.

Human-animal interactions have a profound impact on animal evolution and reflect societal behaviors, yet direct molecular evidence from prehistoric contexts is limited. In this study, we utilize shotgun metagenomics on three paleofeces, dated to the Longshan Period (similar to 4000-3800 cal yr BP), excavated from the elite Huangchengtai platform at the Shimao site in Shaanxi, China. Our goal is to elucidate human-animal interactions, including host identity, diet, and gut microbiota. Genetic analyses indicate that the paleofeces originated from three unrelated female domestic dogs, closely related to modern Shaanxi dog populations. Dietary analysis reveals a diverse diet consisting of domesticated animals (cattle, sheep), deer, foxtail millet, and common millet, linking the dogs' feeding practices directly to human subsistence strategies rather than independent foraging. The presence of plant-based dietary components is further confirmed by phytolith analysis. Gut microbiome analysis shows a high abundance of lactic acid bacteria, consistent with prolonged consumption of carbohydrate-rich or fermented food provided by humans, suggesting intentional provisioning or scavenging of human food residues. Elevated levels of human-associated bacteria underscore close daily interactions, highlighting dogs' roles in ecological waste management and raising concerns about zoonotic transmission risks. Moreover, the dietary composition provides direct biological evidence of the elite status associated with the Huangchengtai platform, highlighting the higher societal hierarchies present at Shimao. This study demonstrates the value of ancient metagenomics in reconstructing past human-animal dynamics and social structures.

Seated burial is a rare funerary practice, often associated with social status, religious beliefs, or ethnic traditions, yet its underlying cultural motivations remain poorly understood. In this study, a multidisciplinary analysis was conducted on four seated burials dating to the Tang Dynasty, identified among more than 4,000 tombs from four sites in Xi'an, to investigate potential links to Buddhism or specific ethnic affiliations. The C-14 dating results indicate that these individuals lived between the 7th and 9th centuries AD, encompassing almost the entire Tang Dynasty. Ancient DNA analysis reveals that their genetic profiles are consistent with those of local ordinary residents. While one individual exhibits a mixed ANA-SEA-WSH ancestry-a combination not uncommon at the time-the other three show affinities primarily with the YR_MN population. Their dietary patterns, dominated by millet and supplemented with wheat and animal protein, align closely with those of the broader regional population. Taken together, these findings suggest that seated burials in the Chang'an region during the Tang Dynasty were neither tied to distinct genetic lineages nor indicative of unique ethnic or dietary identities. Although Buddhist symbolic artifacts, such as pagoda-shaped jars, were found in one tomb, isotopic evidence contradicts strict adherence to vegetarian Buddhist precepts. This discrepancy may imply a disconnection between biological characteristics and cultural symbols. The interpretation of the cultural connotations and practical motivations represented by special burials in ancient society requires further exploration in combination with a broader social and historical context.

The Shatuo Turks played a pivotal role in late Tang and Five Dynasties China. However, similar to other Turkic groups, the genetic history and population origins of the Shatuo remain poorly understood. This study presents a genomic investigation of a Shatuo leader through the analysis of ancient DNA from Li Keyong (856 CE-908 CE), founder of the Later Tang dynasty, providing an opportunity to elucidate the genetic composition and origins of this pivotal group. Through comprehensive population genetic analyses, including PCA, ADMIXTURE analysis, f-statistics, and qpAdm modeling, we found that Li Keyong had a nearly balanced admixture, with 53.4% Ancient Northeast Asian and 46.6% Western Steppe ancestry. Additionally, he carried a Western Eurasian paternal lineage (R1a1a1b2∼AM01870) and an Eastern Steppe maternal lineage (C4a1a+195). This genetic profile contrasts sharply with the predominantly Northeast Asian ancestry observed in the Ashina royal clan, highlighting significant genetic heterogeneity within Turkic confederations. Our results suggest that the Shatuo emerged from complex cross-Eurasian interactions, consistent with the hypothesis of a multi-ethnic origin.

The 13th-century Changzhou Mummy, from the Lower Yangtze region in China, is the earliest known East Asian case of an artificially mummified body employing mercury and cinnabar enema without evisceration. This study conducts multidisciplinary research, integrating paleo-radiological, paleo-pathological, paleo-genetic, and paleo-nutritional analysis to investigate the phenotype, genotype, individual life history, and the process of deliberate mummification performed on this individual. We generate a whole genome with 12.7× coverage, revealing potential genetic predisposition for several atherosclerotic cardiovascular diseases (ASCVD). Stable C and N isotope analysis of bones, teeth and hairs indicates high animal protein consumption as well as terminal illness. Hereditary and dietary risk factors are consistent with the diagnosis of atherosclerosis determined via postmortem examination. Our study, leveraging high-quality ancient DNA, provides a unique opportunity to challenge and rethink the widely accepted consensus on the relationship between atherosclerosis and post-industrial age lifestyles, uncovering unrecognized genetic polymorphisms of ASCVD among ancient individuals, and improving our understanding of the role of genetic factors in the development and evolution of ASCVD.

The excavation of the tomb of Zhao Boyun, a seventh-generation grandson of Emperor Taizu of the Song Dynasty (960-1279), provides valuable material for studying the state of the Zhao-Song royal clan, who relocated to the south of China in the early years of the Southern Song Dynasty (1127-1279). This study collected tooth dentin, bone, and nail samples from Zhao Boyun's remains for isotopic analysis, attempting to outline his life history. Zhao Boyun's diet was characterized by a high intake of protein, likely in the form of large quantities of terrestrial animals and freshwater fishes, reflecting his adoption of a typical Jiangnan lifestyle. Dentin isotopic data indicated that Zhao had been weaned at similar to 2.7 years of age, experienced a further improvement in nutritional status at 7.5 years old, and maintained a stable nutritional level between 10 and 15.5 years old, higher than the level approximately 5 years before death. Ten weeks prior to death, a marked elevation in the carbon and nitrogen stable isotopes in his nails suggests sudden physical deterioration, which may be related to his death.

This study presents the first isotopic analysis from the skeletal remains of a Tang Dynasty Emperor, casting light on ninth-century imperial dietary patterns in Chang'an. Compared with northern Chinese populations, the diet of Emperor Xizong diet featured fewer mixed C-3/C-4-based agricultural products and animal protein than earlier Imperial elites, such as Emperor Wu of Northern Zhou and the Crown Prince of Sui. Poor nutrition in Xizong's later years may reflect contemporary sociopolitical turmoil, which unlike earlier Emperors clearly affected Xizong's diet and lifestyle. This essay offers new insights and an overview of the dietary shifts of Chang'an royals from the 6th to 9th centuries.

The border region, which lies between different regimes, is highly regarded because of its diverse population, dietary habits, and living conditions. The population around the Great Wall was particularly intriguing during the Ming Dynasty, but it remains unstudied archaeologically. The study uses a multidisciplinary approach that includes paleopathology, isotope analysis, and ancient DNA analysis to investigate two individuals found in a Ming Dynasty military fortress at Qingping Fort. Both individuals were middle-aged males. Pathological examinations revealed nasal bone fractures in both individuals, possibly indicating violent interactions within their group or small-scale inter-group conflict. Carbon isotope analysis indicated that their diet predominantly consisted of C4 plants, which reflected their dietary pattern of millet consumption. Nevertheless, the low δ¹⁵N values implied limited meat intake. The paleopathological evidence, in conjunction with these findings, suggests that the individuals lived in a harsh environment. Based on the analysis of ancient DNA and strontium isotopes, it seems that the individuals are most likely from the Yellow River Basin, and there is no evidence of Eastern steppe ancestry. These findings tentatively suggest that at least some residents of Qingping Fort during the Ming dynasty had close genetic connections with Central Plains populations. Given the small sample size, our conclusions are preliminary, and they emphasize the necessity for future studies with an expanded sample. This work offers a starting point for comprehending the lives of residents in Ming frontier societies and underscores the significance of integrating archaeology with a multidisciplinary approach.

This study investigates the population history and subsistence of farming communities at the Erdaojingzi site (ca. 3700-3330 cal. BP), a well-preserved Bronze Age settlement located in the agro-pastoral transition zone of the West Liao River Basin in northern China. We apply a multidisciplinary approach, combining ancient DNA, carbon and nitrogen stable isotope analysis, zooarchaeological data and archaeobotanical evidence, to evaluate population affinities at the site and to characterise subsistence practices in relation to environmental and cultural conditions. Ancient DNA from two individuals shows ancestry profiles closely related to farming populations of the Yellow River Basin, rather than to previously published Neolithic groups from the western Liao region, indicating strong genetic connections with Central Plains related farming communities. Stable isotope results from 43 animal and two human bone samples demonstrate that millet and its by-products formed dietary staples for both humans and domestic animals. Humans, pigs and dogs primarily relied on C4 plants, whereas cattle and sheep consumed mixed diets of C3 and C4 plants. Nitrogen isotope values point to a diet rich in animal protein for humans. Combined age at death and isotopic data from pig remains further indicate that young pigs constituted an important component of meat consumption. Variation in nitrogen isotope values among sheep suggests differences in grazing and foddering regimes, and may also reflect localised soil enrichment by dung and other management practices. Taken together, these results provide new insight into how farming communities organised their subsistence and how population history and economic strategies were intertwined in an agro-pastoral transition zone of prehistoric East Asia.

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.

BACKGROUND:As a key region in the lower Yellow River Basin, Shandong Province plays a central role in understanding the genetic history of East Asia. However, detailed ancient DNA data across its historical periods remains limited. This study aims to characterise the genomic profiles of Shandong populations during the Western Han Dynasty and trace their genetic connections with neighbouring regions. RESULTS:Here, we newly generated 14 ancient genomes from the Wenshaobei site of the Western Han dynasty in Shandong Province. Genetic analyses, including principal component analysis (PCA), ADMIXTURE, and f-statistics, revealed that the Wenshaobei population was genetically distinct from Early Neolithic Shandong hunter-gatherers but closely aligned with Middle Neolithic to Iron Age populations from the middle and lower Yellow River Basin. This indicates strong genetic continuity with millet-farming societies from the middle Yellow River, supplemented by minor influences from southern rice-farming groups. Modern Han Chinese in Shandong share a core genetic foundation with ancient populations, such as Wenshaobei. CONCLUSIONS:Our findings highlight the role of the lower Yellow River Basin as a nexus of genetic exchange between northern millet-farming and southern rice-farming cultures, with sustained genetic influences from the middle Yellow River shaping the demographic landscape from the Neolithic to the Han Dynasty. The study provides critical insights into the formation of East Asian populations, underscoring the interplay between agriculture, migration, and genetic diversity in this cradle of ancient Chinese civilization.

The Eastern Zhou period (771-221 BC), characterized by social stratification, was marked by important inequality. Here the authors analyse 32 skeletons from Songzhuang Cemetery in Henan Province using sex-specific peptides, ancient DNA and isotopes to explore multidimensional inequality in sexes, diet and mobility. DNA and proteomic analyses show that young women were marginalized as sacrificial victims (22 out of 26 human sacrifices were female). Carbon and nitrogen isotopic analyses suggest dietary differences by social class, with the nobility consuming more high-protein and millet-based diets than sacrificial companions, who themselves show intra-group dietary variation (δ13Cbone,nobles = -8.6‰; δ13Cbone,human sacrifice group one = -10.9‰; δ13Cbone,human sacrifice group two = -14.1‰; δ15Nbone,nobles = 11.6‰; δ15Nbone,human sacrifice group one = 8.5‰; δ15Nbone,human sacrifice group two = 7.7‰). Enamel and dentin isotope data indicate that these dietary inequalities were established from childhood (δ13Cenamel,nobles = -1.5‰; δ13Cenamel,human sacrifice group one = -3.8‰; δ13Cenamel,human sacrifice group two = -6.9‰). Strontium and oxygen isotope evidence shows that a high proportion of the nobles were non-local migrants. Genetic analysis reveals a genealogy linking four noblewomen to a sacrificial victim, highlighting the importance of kinship and marital alliances in maintaining social status. Despite class rigidity, dental isotope sequences in M18 reveal that two individuals experienced childhood dietary shifts, indicating rare class mobility.

Historical migration activities have played a crucial role in the exchange and dissemination of populations and cultures, leading to significant cultural transformations in certain regions. Previous research has often focused on historical documents and archaeological materials, with less emphasis on integrating genetic evidence for a more comprehensive analysis. The Shengjizui cemetery, located in Bishan District, Chongqing, is characterized by its row-style stone chamber tombs and has yielded numerous burial artifacts and human remains. In this study, we conducted a comparative analysis of some of the burial artifacts unearthed from the Shengjizui cemetery with those from tombs in the same region and period, determining that the cemetery dates back to the mid to late Ming Dynasty. The results also revealed that the granary jar culture of the Shengjizui population was influenced by the Huguang region. Furthermore, the analysis of uniparental genetic markers from human bone samples indicated that the cemetery was likely a clan burial site predominantly featuring the paternal genetic lineage D1ala1a1b-Z31611, while the maternal lineage was more akin to the Han population in Southeastern China. By combining archaeological typological comparisons with historical literature, these findings suggest that the Shengjizui population was influenced by migration activities during the Ming Dynasty, providing valuable genetic evidence for the study of local and migration history in Southwest China.

OBJECTIVE:This paper evaluates evidence of trauma observed on a skeleton of a child from Ningxia, China in order to assess the potential cause of the lesions. MATERIALS:Skeletonized remains of Individual M26:R3 from the site of Yaoheyuan in Western Zhou, dated 1046-771 BCE. METHODS:Standard osteological methods were carried out. Nano-CT scans were used to determine possible endocranial trauma and to reconstruct the crania. Ancient DNA analysis was conducted on the remains of the three individuals interred in burial M26 to determine possible kinship relationships. RESULTS:A total of 59 individuals were studied. The individual under examination was a male with an estimated age of 6-9 years old. The child was found alongside two adult females. The osteological analysis and CT scans indicated two perimortem injuries and one possible perimortem sharp force cutmark on his cranium. Ancient DNA analysis performed on the three individuals in burial M26 revealed no familial relatedness. CONCLUSIONS:The multiple strike marks on the remains of the child, along with the fact that he was the only individual in this burial ground showing clear evidence of sharp force cranial injuries, might suggest a unique incident of violence. SIGNIFICANCE:This paper demonstrates how the integration of osteoarchaeological observation with ancient DNA analysis can provide insight and contextualization of perimortem events. LIMITATIONS:Post-depositional disturbance affecting the archaeological contexts of this cemetery complicates the interpretation of this case. SUGGESTIONS FOR FUTURE RESEARCH:Systematic archaeological and historical data are needed to understand reasons behind violent episodes in ancient China.

The relationship between culture and ancestry is complex. Since the 2nd century, the Silk Road has facilitated human mobility across continents, complicating the determination of ancestry based on cultural traits, as evidenced by archaeological findings and historical accounts. In 2005, a 6th-century couple's joint tomb was found east of Northern Zhou's Chang'an city. According to conflicting epitaph texts, the male, Li Dan, has an ambiguous ancestry, possibly from East or South Asia. Archaeological materials blend Eastern and Western influences, posing challenges for researchers. In this study, we generated high-coverage genomes on the 1240k panel for the couple, covering 1,057,118 and 1,048,087 SNPs with average depths of 3.53x and 4.10x, respectively, revealing distinct northern South Asian and northern China-related ancestries. For Li Dan, genetic analysis reveals a close relationship with modern Brahmins, supporting his Brahmin status and his biography as the progeny of Brahmanic descent. Alongside the eclectic archaeological culture, we believe Li Dan preserved his ethnic heritage while forming an integrated Chinese cultural identity. This study highlights the value of integrating genetic studies with archaeological and historical research, providing the first genomic evidence of a cross-border couple between South Asia and East Asia in the 6th century.