The Shimao site in Shaanxi Province, hailed as a "groundbreaking" site, was first built around 4,300 years ago. It is a super-large stone-built city site, showcasing typical early state characteristics with its grand defensive facilities and diverse sacrificial remains. It is currently the largest prehistoric city site discovered in China. However, issues such as the origin of its population, its social structure, and its relationship with the surrounding population have long been controversial.
The Paper learned from a press conference held by the State Administration of Cultural Heritage that a research team led by Fu Qiaomei from the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, in collaboration with the Shaanxi Provincial Institute of Archaeology and other institutions, conducted a large-scale, high-resolution nuclear genome study over 13 years on 169 ancient human bone samples from the Shimao site, surrounding sites, and southern Shanxi. This study provides conclusive genetic evidence that the main body of the Shimao culture population originated from the late Yangshao culture in northern Shaanxi, providing solid genetic evidence for the continuous evolution of Chinese civilization within its own territory. This research on the hierarchical society of the ancient city of Shimao, characterized by its large scale and diverse and complex burial practices, is the first of its kind in the world.
The relevant research findings were published online in the journal *Nature* on November 27 and received a key recommendation from *Nature*. Experts highly praised it for "revealing a new chain of evidence for early Chinese civilization"; "pioneering research in East Asia using ancient DNA methods to reveal prehistoric social class differentiation and human sacrifice phenomena"; and "demonstrating the population history and genetic structure of the first national civilization, which is of crucial significance for understanding the early forms of civilization in China and even the whole of East Asia."
Shimao City
At a special press conference held in Beijing by the State Administration of Cultural Heritage on November 27, Fu Qiaomei, deputy director of the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, introduced the latest scientific research results of the Shimao site.
According to reports, the research team led by Fu Qiaomei from the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, in collaboration with the Shaanxi Provincial Institute of Archaeology and other institutions, conducted nuclear genomic studies on 169 ancient human bone samples from the Shimao site, surrounding sites, and southern Shanxi. This research not only provides genetic evidence confirming that the main body of the Shimao culture originated from the late Yangshao culture in northern Shaanxi, establishing the continuity of its culture and population development, but also reveals close connections between the Shimao culture and the Taosi culture in southern Shanxi, related populations of the Yumin group in the north, and rice-farming populations in the south, showcasing a broad historical scene of interaction and exchange among prehistoric agricultural and pastoral populations. By reconstructing a family genealogy spanning four generations within the ancient city of Shimao, the study clearly reveals its patrilineal social hierarchy, providing a social organization model for understanding the formation and development of early Chinese states, and offering the first direct genetic evidence for exploring the power succession patterns, ruling families, and social class composition of early East Asian states.
National Cultural Heritage Administration press conference
Next, the National Cultural Heritage Administration will continue to advance the project to trace the origins of Chinese civilization and the major project of "Archaeological China," strengthen multidisciplinary cooperation, leverage the supporting role of scientific archaeology, and continuously deepen the research on the origins of Chinese civilization.
Located at the junction of the Loess Plateau and the Mu Us Desert, the Shimao site is the largest known prehistoric city site in China. Its complex defensive layout, diverse sacrificial remains, and high-level cultural relics demonstrate a typical early state structure and a high degree of social complexity. However, scientific questions regarding the genetic origins of the site and its related cultural populations, their connections with surrounding Yellow River basin and grassland populations, and their forms of social organization have long been controversial. Therefore, large-scale, systematic, and detailed nuclear genomic studies of the Shimao site and surrounding ancient populations have become a crucial means of exploring these questions.
In recent years, using ancient DNA to reveal the kinship lineage and social organization of large settlements has become a cutting-edge field in paleogenetics. However, accurately interpreting the kinship network of a large settlement requires not only a sufficient number of representative samples and high-coverage ancient genome data, but also complex data modeling and analysis based on the deep integration of multi-dimensional archaeological information such as settlement structure, burial style, burial objects, and dwelling sites. Therefore, related research worldwide remains relatively limited, and studies of prehistoric societies with more than 100 individual genomes are extremely rare. Furthermore, research on the hierarchical society of Shimao Ancient City, with its extremely large scale and complex and diverse forms of human sacrifice or burial, is a world first.
Shimao Ancient City
Local genetic continuity: the diverse genetic makeup of the Shimao population
According to Fu Qiaomei's team, previous mitochondrial studies of the population at the Shimao ancient city and its satellite sites inferred that they originated from the local Yangshao culture. However, recent whole-genome studies of the Shimao satellite settlement (Xinhua site) have revealed a high proportion of agricultural populations from the middle and lower reaches of the Yellow River in Henan province, suggesting that their genetic ancestry originated from the Central Plains. This makes the genetic structure and specific compositional origins of the Shimao culture population even more complex. Due to the limited scope of mitochondrial genome studies and whole-genome sampling, a series of questions remain unanswered, such as whether there are differences between populations at different levels of the Shimao culture sites, whether the local Yangshao culture population is completely identical to the agricultural populations of the middle and lower reaches of the Yellow River in Henan province during the same period, and whether there are other ancient population components besides the local Yangshao culture population.
Stone carvings of Shimao Ancient City
Analysis of 144 nuclear genome samples covering the Shimao ancient city and surrounding areas, as well as multiple settlements in southern Shanxi, revealed a high degree of genetic consistency among the main populations. These populations, whether from different social strata within the Shimao ancient city's Huangchengtai (palace city), inner city, and outer city, or from surrounding satellite settlements, were identical to those of the late Yangshao population in northern Shaanxi (represented by the population at the Wuzhuang Guoliang site). While the late Yangshao population in northern Shaanxi showed high genetic similarity to contemporary agricultural populations in Henan (represented by the populations at the Wanggou site in Xingyang and the Xiaowu site in Lingbao), certain differences remained. The late Yangshao population in northern Shaanxi possessed an additional, unique ancestral source, exhibiting a genetic ancestor compared to agricultural populations in Henan. This ancestor showed high genetic similarity to ancient populations in the Heilongjiang River basin, early Neolithic populations in Shandong, or related ancient populations in Tibet. However, no population representing this ancestral component has been found among the published genomic data of East Asian ancient populations.
Furthermore, the study revealed that some outliers among the Shimao culture population also carried a certain proportion of ancestral components related to the Yumin population of the northern grasslands of China and rice-growing populations of the southern coastal areas, but this did not affect the genetic continuity of the main population in northern Shaanxi. These results strongly support the continuity of local genetics among the Shimao culture population, demonstrating the profound local roots of the Shimao culture.
Agricultural and pastoral integration zone: the migration and exchange of people across the Yellow River and grasslands
As a core city located in an agro-pastoral transition zone, Shimao Ancient City, despite its predominantly local population, exhibits close connections between its culture and surrounding archaeological cultures. For example, the pottery unearthed at Shimao is highly similar to the Taosi culture of southern Shanxi in the Central Plains; bronze remains and metallurgical techniques show connections to the Eurasian Steppe; stone statues may be related to the Okunev culture of southern Siberia; and the discovered crocodile bone plates may originate from the Yangtze River basin culture. So, did the Shimao culture interact and exchange with these ancient populations in the surrounding areas during its formation? Ancient genomic evidence provides the answer.
In the Central Plains region, the Taosi culture population (represented by the Taosi and Zhoujiazhuang sites) from the same period as the Shimao site share a similar ancestral origin with the Shimao culture population and have a very strong genetic connection with the late Yangshao population in northern Shaanxi, indicating that the Shimao culture population and the Taosi culture population are homologous.
In the northern grasslands, the exchange exhibited a different pattern. Although the genetic components of the Yumin population from the northern grasslands did not leave a widespread imprint on the main population of the Shimao culture, the analysis of outliers provided important clues. From the Wuzhuang Guoliang site of the late Yangshao period (containing 50% Yumin-related components) to the Shimao city site and surrounding wooden pillar beams and Xinhua site of the Longshan period (containing a few individuals with 100% Yumin-related components), outliers carrying a very high proportion of Yumin-related genetic components were discovered. Clearly, since the middle and late Neolithic periods, there has been a long-term migration and interaction between the local populations of northern Shaanxi and the Yumin populations of the northern grasslands, with occasional periodic genetic exchange events, but this did not affect the continuity of the main population.
In the southern coastal region, a small number of isolated individuals from several Shimao cultural sites were found to possess 10%-30% genetic material from ancient southern populations, which can be represented by components related to southern rice-farming populations from over 4,000 years ago. This discovery broadens our understanding of the northward influence of rice-farming populations and provides strong genetic evidence for the northward spread of prehistoric rice agriculture.
Apart from the aforementioned genetic components, the main cultural population of Shimao did not show any related components from ancient populations in the western Eurasian steppe, Central Asia, North Asia, or the coastal areas of Shandong.
It is evident that the Shimao culture and its related populations exhibit a dynamic formation process characterized by "a clear main lineage and diverse integration." The local Yangshao population serves as a stable genetic backbone, while maintaining varying degrees of long-term interaction and exchange with agricultural and pastoral populations in the Central Plains, grasslands, and the south. This provides crucial empirical evidence for understanding the early evolution of the "pluralistic unity" pattern of Chinese civilization.
Patriarchal Society: Kinship and Social Institutions under Diverse Forms of Funerary Sacrifice
The diverse forms of burial in the Shimao ancient city, including the "skull pits" of public ceremonies and the practice of human sacrifice in aristocratic tombs, reflect the significant class differentiation and strict hierarchical system of its society. Did this prehistoric hierarchical society rely on kinship for its structure? What were the characteristics of the selection of human sacrifices? How did the wealth inheritance system and marriage system operate under a clear hierarchical structure? These are also long-standing but unresolved mysteries in academia. Based on samples from tombs of different social classes in Shimao and its satellite city of Zhaishan, this study reveals the unique social organizational structure of Shimao from three dimensions: lineage transmission, marriage patterns, and residential rules.
Geographical location and era of sample source
Research has revealed a clear gender preference among the sacrificial victims or those buried alive in different areas of the Shimao ancient city. The "skull pit" at the eastern gate of the outer city was predominantly male, while the high-ranking nobles or elites were predominantly female. Furthermore, comparative analysis of the genetic components among the sacrificial victims, commoners, and high-status tomb owners in Shimao society showed no significant differences in the main genetic components across different social classes, except for a very small number of individuals possessing a certain proportion of Yumin (wealthy) characteristics. No clear kinship (within two generations) was detected between the sacrificial victims and the tomb owners in the high-ranking tombs of Shimao and Zhaishan. However, in the highest-ranking Shimao culture site currently known—the Huangchengtai cemetery (possibly the tombs of rulers)—multiple pairs of sacrificial victims were found to have second-degree kinship, suggesting that some families or communities may have been selected by the ruling class for sacrificial burial. Furthermore, in the analysis of homozygous fragments from numerous individuals, including high- and low-ranking tomb owners or sacrificial victims, across seven sites, only one case of inbreeding was found among the sacrificial victims at Zhaishan Ancient City. This phenomenon suggests that inbreeding may have been consciously avoided or was relatively rare among families of higher social status in the Shimao culture.
Schematic diagram of the genetic structure of the main population and outliers of the Shimao culture.
Human sacrifice and human burial were the two main forms of human sacrifice found within the Shimao ancient city: human sacrifice during public ceremonies (foundation laying) and human burial in aristocratic tombs. Human sacrifice in public ceremonies was concentrated in the outer city's east gate and the Huangchengtai square area; this ritualistic violence often preserved a large number of concentrated skulls. Human sacrifice in aristocratic tombs was often buried alongside the deceased; such tombs were common in the Hanjiagedan, Huangchengtai, and Zhaishan sites within the inner city of Shimao. The gender ratio of those buried in these two types of burial differed: the "skull pit" at the outer city's east gate did not show a predominantly female human sacrifice pattern, which differs from the physical anthropology conclusion that it was predominantly female; however, the final DNA analysis, through direct detection of sex chromosomes (XY or XX), provided a more reliable conclusion. Conversely, the Huangchengtai cemetery and the Hanjiagedan aristocratic cemetery in the inner city showed almost exclusively female burial victims, the latter representing a significant class differentiation pattern within the Shimao culture.
Sacrificial pits at the Shimao site
Schematic diagram of kinship and social organization forms within the Shimao site
A diagram illustrating the reconstructed family genealogy of the Hanjiagedan Cemetery and Zhaishan Site in Shimao, along with the corresponding tomb locations.
Further kinship analysis of the tomb owners at Shimao Huangchengtai, Hanjiagedan, and its satellite city Zhaishan revealed a family genealogy spanning up to four generations. The main founders of these genealogies were all high-ranking male tomb owners, whose spouses came from different biological families. Furthermore, among all the Shimao cultural sites examined so far, the paternal Y-chromosome haplotype structure is relatively homogeneous, while the maternal mitochondrial haplotype is highly diverse. In addition, the spatial layout of the tombs and family relationships at Zhaishan also support a potential paternally-dominated residential system.
(This article is primarily based on research articles by Researcher Fu Qiaomei from the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences; Associate Researcher Chen Zehui from the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences; and Researcher Sun Zhouyong from the former Shaanxi Provincial Institute of Archaeology/Northwest University. This research was supported by grants from the Chinese Academy of Sciences, the National Key Research and Development Program of China, and the National Natural Science Foundation of China.)