An international team of scientists examined the DNA of three individuals who lived between 11,000 and 9,000 years ago at the Donghulin archaeological site, situated in the area of modern western Beijing. The findings, published in the journal Current Biology, suggest that one of these individuals either had no previously identified ancestry, or represented a mix of already extinct genetic lineages.
The Donghulin archaeological site, located on the North China Plain, is one of the few locations documenting the transition from hunter-gatherer societies to the first agricultural communities. Archaeologists unearthed remains of permanent dwellings, polished stone tools, pottery, and, critically, evidence marking the initial cultivation of millet. Scientists successfully isolated and sequenced the genomes of two individuals buried onsite with clear archaeological context, along with the mitochondrial DNA of a third.
The oldest specimen, labeled DHL_M1, lived between 11,170 and 10,700 years ago, right at the conclusion of the last Ice Age. The second, DHL_M2, is approximately 2,000 years younger, dated from 9,263 to 9,027 years ago, during the warming climate of the early Holocene. The third, DHL_M02, lacks a definitive stratigraphic context but is dated between 10,200 and 9,300 years ago.
Genetic scrutiny of the most ancient individual, DHL_M1, revealed an unexpected discovery. His lineage does not align with any known groups from Northeast Asia identified to date. Researchers categorize him as an “early diverging lineage,” meaning a line that split from the common trunk of Northeast Asian populations a very long time ago.
The paper’s authors clarify that they uncovered an early diverging Northeast Asian lineage represented by DHL_M1, approximately 11,000 years in age. This lineage is as ancient and deeply rooted as that of the earliest known individual to date, named AR19K, who resided around 19,000 years ago in the Amur River basin, thousands of kilometers to the northeast. Nevertheless, despite such distant origins, DHL_M1 and AR19K followed divergent genetic paths, implying that multiple distinct lineages inhabited northern East Asia at the close of the Ice Age.
Surprisingly, DHL_M1 is not a direct ancestor to later populations in the area. In fact, he shares fewer genetic similarities with other North Asian groups than AR19K or later individuals. Scientists attempted to model his genetic composition by blending known sources, yet no single combination fully accounted for his DNA. This suggests he might represent a previously unrecognized origin or a combination of lines that have since vanished.
Concerning the maternal lineage, both DHL_M1 and the DHL_M02 individual belong to mitochondrial haplogroup D4h, a group that originated in Northeast Asia and experienced two major expansion periods in the late Pleistocene era. Analysis using molecular clocks indicates that the divergence of their subpopulations occurred around 14,000 and 13,000 years ago, respectively, supporting the notion that these populations existed and diversified long before the onset of the Neolithic transition.
The youngest individual, DHL_M2, living about 2,000 years after DHL_M1, exhibits a completely different genetic signature. Analyses clearly demonstrate that he is not a direct descendant of DHL_M1. Ancient DNA statistical tests suggest that DHL_M2 shares more total alleles with another individual named Yumin, a hunter-gatherer from the Inner Mongolian Plateau dating to around 8,400 years ago, than with his local Donghulin predecessor.
The authors note that they found a specific genetic connection between DHL_M2 and the source related to Yumin. However, he cannot be simply described as a mixture of Yumin and other known populations either. DHL_M2 appears to possess an additional component that doesn’t match any previously documented Northeast Asian lines. This notable genetic shift at the same site over a relatively short time span points to substantial population mobility during the post-glacial warming period.
The researchers hypothesize that the indigenous population, represented by DHL_M1, was not entirely supplanted but may have contributed partially to DHL_M2’s ancestry. Nevertheless, the genetic profile clearly underwent a significant transformation. This finding is consistent with observations from physical anthropologists: the skulls of the two individuals display marked morphological differences, more pronounced than those seen between later Neolithic populations. It also aligns with the distinctions in pottery discovered between the lower and upper strata of the site.
Despite the genetic shifts, one element remained constant: the gradual incorporation of Neolithic practices. Botanical evidence shows that the proportion of domesticated millet increased progressively from the lower level to the upper. In other words, as populations succeeded one another, technology and subsistence farming continued their evolution toward agriculture.
The study’s core conclusion is that the transition from Paleolithic to Neolithic in Northeast Asia did not mirror the developments in the Near East or Europe. In the Near East, local hunter-gatherers adopted farming without substantial shifts in population numbers. In Europe, conversely, the arrival of agriculture involved a massive population turnover, as Anatolian farmers expanded their territory and displaced European hunter-gatherers.
The situation in northern China diverged. The researchers observed heterogeneous Northeast Asian lineages undergoing a transition, concurrently detecting population changes at the Donghulin site despite continuous Neolithic practices. This pattern contrasts with the agriculture-driven population booms seen in Southwest Asia and Europe during the early Holocene, indicating a unique trajectory for the Paleolithic-Neolithic shift in northern East Asia, the authors state.
The research also revealed long-distance interactions. DHL_M1 shares alleles with later populations from the Amur River basin (like AR14K), while DHL_M2 shares affinities with populations from the Mongolian Plateau (Yumin). Furthermore, the researchers found ornamentation at the site crafted from marine snail shells of the Neritina violacea species and ostrich eggshell fragments—exotic materials demonstrating exchange networks connecting this community with very distant regions.
Despite their role in the transition process, neither the DHL_M1 nor the DHL_M2 lineage left a deep imprint on modern populations. Analysis shows that DHL_M2 shares more alleles with contemporary populations than DHL_M1, but overall, his contribution was modest. DHL_M2’s mitochondrial haplogroup is G4, a very rare line sporadically documented in modern individuals from China and Japan. His Y-chromosome belongs to lineage N-F1360, but occupies a basal position, having not branched into the subclades seen today.
The scientists also found that both individuals exhibited a similar level of archaic ancestry (i.e., DNA inherited from Neanderthals and Denisovans) compared to other East Asians from the same period and later. This suggests that admixture with archaic hominins occurred earlier and became stabilized.
The work conducted by the Qiaomei Fu laboratory at the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, marks a significant advancement because it links ancient genomes in this critically important region with detailed archaeological context for the first time. Previously, the limited genomes recovered from Northeast Asia older than 10,000 years often came from remains lacking clear cultural context, hindering a direct correlation between genetic shifts and lifestyle changes.
The Donghulin archaeological site is unique in documenting two millennia of continuous change in a single location, spanning from the end of the last Ice Age to the climatic optimum of the early Holocene. The integration of genetic, archaeological, and paleoecological data allows for a much more nuanced picture of how humans adapted following the glacial retreat.
Until now, the prevailing hypothesis suggested that Neolithicization in Northeast Asia was a gradual process carried out by small, diverse groups of hunter-gatherers who independently adopted farming without major migration waves. The Donghulin data support this view: genetic diversity exists, population turnover occurs, but there is no complete replacement driven by immigrant farmers. Millet agriculture evolved locally, and the practicing populations changed over time, yet always within the broad spectrum of Northeast Asian ancestry.
The authors conclude that while various genetic lines were present across Northeast Asia around 10,000 years ago, they all fall within a wide bracket of Northeast Asian heritage, lacking substantial influence from external genetic components. This reinforces the notion that North China was an independent center of Neolithicization with its own population dynamics distinct from other regions globally.
The study leaves many questions unanswered. The scientists acknowledge that more ancient DNA samples from the early and middle Neolithic periods are required to accurately gauge the extent to which the impact of lineages like DHL_M2 was widespread. What is clear at present is that the story of the emergence of farmers in China is far richer and more varied than previously understood.
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