The Genetic Formation of the Han Chinese: Longshan Expansion and Early Homogenization
A new ancient DNA study, “Reconstructing the genetic formation of Han Chinese from ancient genomes”, provides one of the clearest pictures yet of how the Han Chinese formed. By sequencing 28 individuals from Han Dynasty cemeteries in Shandong (c. 100–200 BCE) and integrating them with previously published ancient genomes, the authors trace the demographic foundations of the Han back to the Late Neolithic, especially to populations associated with the Longshan horizon.
The results reveal a world that was genetically diverse at the start and consolidated around a single branch by the end: the Central Plain populations who would eventually become the demographic foundation of northern China.
To understand why that matters, we first need to clarify what “Longshan” actually was.
What Was the Longshan Culture?
The Longshan culture refers to a Late Neolithic archaeological horizon (c. 2500–2000 BCE) spanning much of the middle and lower Yellow River basin. It is named after Longshan town in Shandong, where distinctive thin-walled black pottery was first identified.
Archaeologically, Longshan is characterized by:
Highly refined black pottery
Increasing social stratification
Walled settlements
Early forms of urbanization
A transition toward Bronze Age political complexity
It represents the period immediately before the emergence of early dynastic states traditionally associated with the Xia and Shang.
An archaeological culture is defined by shared material features, not shared DNA. Two populations can use similar pottery, adopt similar ritual practices, and participate in the same exchange networks while remaining genetically distinct.
Central Plain Longshan populations and Shandong Longshan populations were not genetically identical. Shandong Longshan retained more ancestry from earlier local hunter-gatherers and showed more southeastern affinities. Central Plain Longshan groups were more homogeneous and lacked these additional components.
So “Longshan” describes a cultural sphere — a networked world — not a single biological population.
The Yellow River corridor and the demographic core of early China.
From Regional Diversity to Han Homogeneity
The critical shift occurs between the Longshan era and the Han Dynasty.
By ~100–200 BCE, individuals from Shandong sampled in this study are overwhelmingly derived from Central Plain Longshan–related ancestry. Most Xujiacundong individuals are ~94% Central Plain–related, and Zhouhe individuals can be modeled almost entirely as descending from that source.
This implies that between the Late Neolithic and the early imperial period, substantial demographic change occurred in Shandong. Earlier regional genetic distinctiveness was largely replaced by ancestry tracing back to the Central Plain.
The pattern extends beyond Shandong. Historical populations in the Upper Yellow River basin, parts of the West Liao River region, Southwest China all show substantial Central Plain Longshan–related ancestry.
By the Han Dynasty, the demographic core of northern China appears to have been largely consolidated.
Moreover, modern Shandong Han can be modeled directly from Han Dynasty individuals in the region, indicating remarkable genetic continuity over two millennia.
Why Did Central Plain Ancestry Expand So Successfully?
In other regions of the world, we can often identify structural advantages that explain demographic expansions.
Anatolian farmers expanded into Europe because agriculture supported higher population densities than foraging. Yamnaya pastoralists expanded across Eurasia with mobility advantages, possibly linked to horse traction and steppe ecology. Bantu-speaking populations expanded with agricultural and iron technologies.
What might have given Central Plain populations a comparable advantage?
1. Agricultural Productivity and Ecological Position
The Central Plain sits in a fertile zone of the middle Yellow River basin, well suited for millet agriculture. By the Late Neolithic, farming systems there were well established. A stable agricultural base supports higher population density, which in turn increases the likelihood of outward migration.
Population growth does not require conquest to produce demographic expansion. Over generations, even modest surplus growth can push settlement frontiers outward.
If Central Plain societies achieved higher carrying capacity earlier than peripheral regions, sustained outward movement would follow almost automatically.
2. Early Political Centralization
The Longshan period in the Central Plain shows stronger evidence of hierarchical organization and walled centers than some peripheral regions. This suggests increasing political coordination.
More centralized societies can:
Organize labor more effectively
Mobilize people for colonization or defense
Integrate conquered or absorbed groups
If the Central Plain became a nucleus of early state formation (later visible in Erlitou and Shang contexts), demographic consolidation may have accompanied political consolidation.
3. Network Centrality
Geographically, the Central Plain is not peripheral. It sits at the intersection of multiple ecological zones:
West toward the upper Yellow River
East toward Shandong and the coast
South toward the Yangtze system
North toward steppe and forest-steppe margins
The Central Plain occupied a structurally advantageous position. It lay at the intersection of multiple ecological and communication zones: westward toward the upper Yellow River, eastward toward Shandong and the coast, southward toward the Yangtze basin, and northward toward steppe and forest-steppe margins. Regions situated at such crossroads tend to accumulate demographic weight over time. Trade routes converge there, political authority stabilizes there, and cultural models radiate outward from there. Peripheral societies often orient themselves toward the center economically and symbolically, and as those ties deepen, migration follows exchange. Cultural centrality tends to become demographic centrality over time.
4. Gradual Assimilation Rather Than Abrupt Replacement
The genetic data do not imply a single violent replacement event. Instead, they point to centuries of migration, intermarriage, and assimilation.
Peripheral populations likely adopted Central Plain cultural forms first, and demographic integration followed gradually. This is similar to what is observed in other expansions, where cultural convergence precedes or accompanies genetic homogenization.
A Familiar Pattern in World History
The Central Plain expansion resembles other cases where agricultural cores radiate outward and become demographic anchors for large civilizations.
In Europe, Neolithic farmers created a genetic substrate that persists to this day. In parts of Africa, Bantu-speaking agriculturalists became the dominant demographic layer across vast regions. In each case, the key driver was not simply cultural prestige but sustained demographic growth linked to agricultural systems and social organization.
Northern China appears to follow a similar structural logic. By the Han Dynasty, the demographic groundwork laid in the Late Neolithic had matured into a largely homogenized northern population. The Han ethnic identity that emerged during the imperial period did not create this substrate; it formalized and institutionalized it.
Conquest, Consolidation, and Why the Central Plain Won
The genetic evidence does not point to a single dramatic replacement event. Instead, it reveals something more historically interesting: by the Han Dynasty, regions such as Shandong were already overwhelmingly derived from Central Plain Longshan–related ancestry. Earlier regional differentiation visible in the Late Neolithic had largely dissolved. Moreover, modern Shandong Han can be modeled directly from Han-period individuals in the same region , implying long-term continuity rather than repeated waves of genetic upheaval.
On the imperial frontiers, the Han state clearly expanded through military campaigns. Wars against the Xiongnu, annexations in the south, and the establishment of commanderies in newly secured territories were unmistakably coercive processes.
But inside the northern heartland, the mechanism looks different. The genetic transformation of Shandong is unlikely to have resulted from a sudden violent replacement. Instead, it is more consistent with long-term demographic consolidation driven by population density, administrative integration, and sustained migration from a high-density core. Centralized governance increases mobility, standardizes institutions, and links regional marriage markets. Over centuries, even modest but continuous migration from a demographic center can overwhelm earlier regional genetic differences without requiring dramatic episodes of extermination or expulsion.
Conquest opened space at the periphery; state capacity and demographic gravity reshaped the core.
That still leaves the deeper question: why was the Central Plain the demographic center in the first place?
In other regions of the world, demographic expansions often correlate with structural advantages. Anatolian farmers expanded into Europe because agriculture supported higher population densities than foraging societies. The Yamnaya expansion appears linked to steppe mobility, possibly reinforced by stature and martial organization. In each case, ecological productivity, social organization, and potentially trait distributions interacted to produce durable demographic advantage.
The Central Plain may represent a parallel case.
By the Late Neolithic, millet agriculture in the middle Yellow River basin supported relatively dense and stable populations. Archaeological evidence from the Longshan horizon indicates increasing social stratification and political centralization. A fertile ecological position at the intersection of multiple regions likely reinforced this centrality. Higher carrying capacity alone can generate expansion over time: when population density rises in one region faster than in surrounding areas, outward movement becomes structurally inevitable.
A genetic advantage?
But ecological productivity may not be the entire story. With larger ancient genomic datasets, it would become possible to test whether Central Plain populations differed systematically in polygenic profiles relative to peripheral Longshan groups. Domains such as cognitive-related traits, height and body composition, immune function under dense settlement conditions, and metabolic adaptation to cereal-based diets are all empirically testable with time-series data.
This bears on the long-standing wheat/millet versus rice divide within China. Northern China, including the Central Plain, was historically dominated by millet (and later wheat) agriculture—dry grain systems compatible with household-level production and large-scale storage. Southern China developed intensive wet-rice systems requiring irrigation coordination and dense cooperative labor. If northern millet-based societies consolidated demographically earlier, while southern rice ecologies remained more regionally diverse, then the modern north–south genetic gradient among Han Chinese may reflect layered processes: early homogenization of a northern core followed by later southward expansion into rice-dominated regions accompanied by admixture and potentially distinct selective pressures.
The genetic evidence establishes the demographic framework: Central Plain Longshan–related ancestry became dominant across much of northern China by the Han period.
What it does not yet establish is whether this success was purely ecological and institutional, or whether it was reinforced by systematic differences in trait distributions that amplified long-term reproductive success.
Future datasets spanning the Neolithic through the imperial era will allow us to test that possibility directly. The most defensible conclusion is also the most striking: the rise of the Han was not merely the story of armies expanding borders, but of a densely populated agrarian heartland projecting its demographic weight outward through the machinery of state formation. Conquest shaped the frontiers; demography shaped the civilization.