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Genetic population structure of the Xiongnu Empire at imperial and local scales


The Xiongnu established the first nomadic imperial power, controlling the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies identified extreme levels of genetic diversity across the empire, corroborating historical records of the Xiongnu Empire being multiethnic. However, it has remained unknown how this diversity was structured at the local community level or by sociopolitical status. To address this, we investigated aristocratic and local elite cemeteries at the western frontier of the empire. Analyzing genome-wide data from 18 individuals, we show that genetic diversity within these communities was comparable to the empire as a whole, and that high diversity was also observed within extended families. Genetic heterogeneity was highest among the lowest-status individuals, implying diverse origins, while higher-status individuals harbored less genetic diversity, suggesting that elite status and power was concentrated within specific subsets of the broader Xiongnu population.


The Xiongnu Empire was the first of many historically documented steppe empires to arise in Eurasia, and its formation foreshadowed the rise of subsequent nomadic imperial powers, including the Mongol Empire, whose reach a millennium later stretched from the East Sea to the Carpathian Mountains (1). Centered on the territory of present-day Mongolia, the Xiongnu empire controlled the Eastern Eurasian Steppe and surrounding regions in northern China, southern Siberia, and Central Asia for nearly three centuries, starting from ca. 209 BCE until their eventual disintegration in the late first century CE. At its height, the Xiongnu profoundly influenced the political economies of Central, Inner, and East Asia, becoming a major political rival of imperial China and establishing far-flung trade networks that imported Roman glass, Persian textiles, Egyptian faience, Greek silver, and Chinese bronzes, silks, and lacquerware deep into the heart of their empire (2).

The Xiongnu represented a radically new kind of political entity that incorporated heterogeneous nomadic and sedentary groups spanning the Eastern Steppes and as far west as the Altai Mountains, under a single authority. As the Xiongnu expanded their empire from its core in central and eastern Mongolia, they conquered and integrated numerous neighboring groups. They successfully expanded into western Mongolia and southern areas of Lake Baikal, while winning decisive victories in northern China (3). However, the Xiongnu were much more than just experts in mobilizing cavalry forces for conquests. They were also shrewd trade partners who exerted considerable influence over the Silk Road kingdoms of Central Asia (4), with even greater control over Eurasian exchange networks during the late Xiongnu period (ca. 50 BCE to 100 CE). Nevertheless, a detailed understanding of their internal social and political organization is lacking (5).

Historical narratives of the Xiongnu were largely authored by their Han Chinese political rivals, who repeatedly and dismissively characterized their polity as a “simple body” of nomadic elites (3, 6). Much of what is now known about Xiongnu sociopolitical organization has been gleaned from textual evidence alongside a growing body of archaeological sites throughout Inner Asia, consisting primarily of cemeteries (2, 79). The mortuary record indicates that there is a sociopolitical hierarchy among the Xiongnu, with clear differences between individuals in terms of burial type, investment in construction, and offerings. Most identified graves of the late Xiongnu period are shaft pits set beneath thick stone rings on the surface. These conspicuous burials represent the vast network of regional and local elites of Xiongnu society, while commoners were likely buried under less conspicuous stone piles or in unmarked pits (10). The uppermost aristocratic ruling elites of the empire were buried in large square stone tombs, often flanked by satellite burials of lower-status individuals, forming a mortuary complex (11). Elites in square tombs and large circular graves were richly buried, typically in decorated wood-plank coffins and accompanied by foreign luxury goods, gold, or gilt objects, and sacrifices of horses and other valuable livestock. Metal discs and crescents representing the sun and moon, a symbol of the Xiongnu empire, are also frequently found in such elite graves. Because of their wealth and conspicuous appearance on the landscape, many Xiongnu graves have been looted since antiquity, but the differences in grave forms nevertheless reflect clear social gradations, with the square tombs as an exclusive political faction within the empire (2).

Previous archaeogenetics studies have sought to identify the people who made up the Xiongnu and have found an extremely high level of genetic diversity across the Xiongnu empire (1216). Recently, a genome-wide study of 60 individuals from 27 Xiongnu sites found that this diversity was initially formed by the unification of two genetically distinct pastoralist populations in Mongolia—one descending from groups associated with the Deerstone Khirigsuur, Mönkhkhairkhan, and Sagly/Uyuk cultures in the west and the other the descendants of the Ulaanzuukh and Slab Grave cultures in the east—followed by additional population influx from other regions, most likely Sarmatia (near present-day Ukraine) and imperial China (14). However, while this evidence supports previous claims that the Xiongnu Empire was likely a multiethnic, multicultural, and multilingual entity, until now, it has not been possible to determine whether such diversity was composed of a heterogeneous patchwork of locally homogenous communities or whether local communities themselves were also internally diverse. Moreover, many aspects of Xiongnu political constituencies still remain unknown, such as who made up the imperial elite occupants of the square tombs, and what their relationship was to lower-status individuals, including those buried in satellite graves within their elaborate tomb complexes. It also remains unclear whether high-status square tomb elites and local elites in the standard circular graves were drawn from the same segments of the Xiongnu population, or whether local elites were more likely to genetically resemble prior local populations than their incoming imperial counterparts, which would suggest that demographic processes associated with empire formation may have been stratified by status and origin.

To address these questions, here, we genetically investigate in detail a range of burials from the aristocratic elite cemetery of Takhiltyn Khotgor (TAK) and the local elite cemetery of Shombuuzyn Belchir (SBB), located at the far western frontier of the empire in Mongolia’s present-day Khovd province. Analyzing the genome-wide data of 18 individuals from high and low-status burials, we show that both communities harbored an extremely high level of genetic diversity that is comparable to that of the Xiongnu Empire as a whole. High genetic diversity is reflected within individual tomb complexes and burial clusters and even extended family groups. Thus, we find that the same sociopolitical processes that produced a genetically diverse empire on a vast scale also operated at the smallest scale, creating highly diverse local communities over the span of only a few generations. There are also discernable genetic patterns with respect to social and political status at TAK and SBB, where individuals of the lowest status (based on grave form and mortuary remains) have the highest degree of genetic heterogeneity. In contrast, higher-status individuals are less genetically diverse and have high levels of eastern Eurasian ancestry. This further suggests the existence of an aristocracy in the Xiongnu empire, that elite status and power was concentrated within specific subsets of the broader population.


Generation of genome-wide data from Xiongnu aristocratic elites, local elites, and subordinates

Before this study, two archaeogenetic studies had intensively investigated Xiongnu-era cemeteries in the political core of the Xiongnu empire at Egyin Gol (12) and Tamir Ulaan Khoshuu (16), but these studies did not generate genome-wide data and thus they have limited capacity to trace individual ancestries and relationships. Other studies have focused on producing genome-wide datasets (1315), but the small number of individuals they analyzed per site make these data insufficient to explore genetic diversity within Xiongnu communities or potential associations with sociopolitical status. To address this, we conducted an intensive genome-wide archaeogenetic investigation of two Xiongnu cemeteries, the aristocratic elite cemetery of TAK and the local elite cemetery of SBB, which are located at the far western frontier of the Xiongnu empire in the Altai mountains. These cemeteries include the full social spectrum of individuals from exclusive square tombs to standard circular graves to meager pit graves. This dataset helps to better understand the genetic diversity, heterogeneity, and relationships among elites and subordinates at Xiongnu communities in the social and spatial edges of their empire. We then compared these frontier Xiongnu communities to previously published archaeogenomic data for 29 additional Xiongnu sites across Mongolia (Fig. 1A) (13, 14).

Fig. 1. Map of Xiongnu sites in this study, and burial plans of the TAK and SBB cemeteries.

(A) Geographic locations of the sites analyzed in the study are presented with the cultural affiliation and the time period. Newly sequenced individuals were excavated from the aristocratic elite cemetery of Takhiltyn Khotgor (TAK) (yellow square) and the local elite cemetery of Shombuuzyn Belchir (SBB) (red circle) in western Mongolia. Previously reported Xiongnu sites with five or more sequenced individuals are also labeled in the figure: Salkhityn Am (SKT), Uguumur Uul (UGU), and the Il’movaya Pad (IMA) (14). Other Xiongnu sites are indicated with white diamonds (early Xiongnu) or black diamonds (late Xiongnu). Sites of the preceding Early Iron Age (EIA) associated with the Sagly/Uyuk (pink triangle) and Slab Grave (green down-pointing triangle) archaeological cultures are also shown. (B) Plan detail of the TAK cemetery indicating the square tomb complexes and associated graves (yellow). See fig. S1 for a full cemetery plan. (C) Plan of the SBB cemetery indicating stone circle and stone pile graves. Excavation focused on a dense grave cluster (pink) and a selection of other representative graves (red). See fig. S2 for a full cemetery plan. For both sites, tomb or grave numbers are indicated in bold red; each analyzed individual is numbered in black.

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The aristocratic cemetery of TAK, dating to ca. 40 BCE to 50 CE (17, 18), is notable not only for its large circular graves of local elites but also for its numerous square tombs (Fig. 1B and fig. S1), which were reserved for individuals of the highest status within the imperial Xiongnu hierarchy. Flanking many of these tombs are low-status “commoner” graves consisting of simple stone piles over stone cist or earthen pit burials. Together, these square tombs and satellite graves form extended mortuary complexes. At TAK, two complete square tomb mortuary complexes have been excavated, THL-82 and THL-64, and a third complex, THL-25, has been partly excavated (fig. S1). THL-82 consists of a large central elite square tomb flanked by two satellite graves to its east and west (Fig. 1B). The tomb contained the remains of an adult female, TAK001, who was buried in a decorated wood-plank coffin with six horses, Chinese bronze chariot pieces, and a bronze spouted pot (19). The use of a wood-plank coffin, in strict adherence with elite Xiongnu political culture and rituals, is particularly noteworthy in this frontier context, as the large larch wood planks must have been imported at great effort and expense into this largely treeless mountain region (20). The satellite graves each contained an adult male interred in an earthen pit burial (TAK008 and TAK009), one of whom (TAK008) was interred in a prone (face-down) position, which differs from the supine (face-up) position that is more typical of Xiongnu burials. THL-64 consisted of a large central elite square tomb with two satellite graves on its eastern side (Fig. 1B). Like THL-82, the tomb also contained the remains of an adult female, TAK002, who was buried in a wood-plank coffin with one horse, four caprines (either sheep or goat), and a golden disc and crescent, representing the sun and moon (17). The satellite graves each contained an adolescent male (TAK003 and TAK004) buried in simple stone cists in a semi-flexed position, a position consistent with long-standing local mortuary traditions in western Mongolia (21). Tomb complex THL-25, for which only the satellite graves have been excavated to date, consisted of a large central square tomb flanked by three satellite graves on its eastern side (Fig. 1B). The three satellite graves consisted of simple earthen pit burials, marked only by small piles of stones, containing the remains of a child (TAK005) and two adult males (TAK006 and TAK007). In total, we genetically investigated eight individuals from TAK cemetery, seven new to this study and one (TAK001) published in a previous study (14).

Located approximately 50 km to the southwest of TAK, the local elite cemetery of SBB is situated along a strategic high mountain pass and spans a period from ca. 50 BCE to 210 CE (18, 20). Consistent with other local elite Xiongnu cemeteries, it consists primarily of circular graves containing the remains of both adult females and males, as well as children (data file S1A). Fifteen of the 33 graves have been excavated to date, of which 11 were genetically screened in this study and 10 of 11 were sufficiently preserved for genome-wide analysis (Fig. 1C and fig. S2). The analyzed individuals span the full spectrum of marked social status, from individuals in large stone-encircled graves with decorated wood-plank coffins and elaborate grave goods to humble burials consisting of small stone cists (fig. S2). Five of the analyzed graves were arranged into a cluster (graves 12, 13, 14, 15, and 18), while the others were spatially dispersed and selected as a representative sample of the remainder of the cemetery (graves 2, 7, 8, 19, 26, and 29). Graves 7, 8, 15, and 19 were the highest-status graves analyzed in this study, and each consisted of an adult female buried in a wood-plank coffin surrounded by a stone ring. Grave 7 contained the remains of an older adult female (SBB002) buried with a disassembled wooden cart, a bronze cauldron, a ceramic cooking pot, and a golden sun disc and moon crescent nailed to the wood-plank coffin. Grave 8 contained the remains of an older adult female (SBB003) buried in a quatrefoil-decorated coffin and interred with gilded glass beads and a Chinese mirror fragment, as well as a large deposit of livestock offerings consisting of at least 12 caprines (sheep or goats). Grave 15 contained the remains of an adult female (SBB007) buried in a decorated wood-plank coffin overlain with wooden cart pieces, as well as horse-riding tack, a gilded iron belt clasp, and a Han Dynasty–painted lacquer cup. Grave 19 contained the remains of a young adult female (SBB008) who had apparently died in childbirth; she was buried alongside an infant and wore a paste-bead necklace containing a faience bead depicting the phallus of Bes, an Egyptian god associated with the protection of children. Like SBB003, this woman was also buried with Chinese mirror fragments. The remaining graves were simpler, consisting of a small stone circle or stone pile overlying a stone cist. Grave 13 contained the remains of a middle-aged adult male (SBB001) buried with a bow, arrows, and spear. An adolescent (SBB011) buried in grave 12 was also buried with a bow, arrows, and spear, and a child (SBB009) buried in grave 26 was buried with a child-sized bow. Three additional children were buried in graves 14 (SBB005), 18 (SBB006), and 29 (SBB004), and grave goods consisted of varied glass beads in graves 14 and 18, while the child in grave 29 was buried with silk, leather, and felt. Last, grave 2 (SBB010) contained the remains of an older adult male buried with an iron sun disc and moon crescent. Screening of burial sediments recovered traces of silk clothing in all SBB burials.

For this study, we generated new genome-wide data for 19 individuals from TAK and SBB, of which 17 yielded sufficient human DNA for analysis (>0.1% human DNA), and we further enriched these DNA libraries for a panel (“1240K”) of 1,233,013 ancestry-informative single-nucleotide polymorphisms (SNPs) using an in-solution DNA capture method (