Ancient proteins extracted from fossils in Southwest China’s Yunnan Province have identified Denisovan remains for the first time in the region. Published in Nature, the multidisciplinary study reconstructs a 190,000-to-70,000-year-old survival landscape on the southeastern margin of the Qinghai-Xizang Plateau, linking northern and southern Asian populations.
Unearthing the Bat Cave Site in Yunnan Province
Situated in the Heqing Basin at an altitude of 2,370 meters on the southeastern margin of the Qinghai-Xizang Plateau, the bat cave site in Heqing County contains a 6.6-meter-thick deposit. The stratigraphy comprises Holocene deposits, artifact-bearing cultural deposits, and underlying cave-fissure deposits. The cultural layer is divided into upper layers spanning layers three through six and lower layers spanning layers seven through twelve, according to excavation records. A Bayesian age model combining optically stimulated luminescence and U-series dates established a time range spanning approximately 190,000 to 70,000 years ago, establishing the location as the earliest Paleolithic site discovered in western Yunnan.
Excavations led by Chinese Academician Chen Fahu from the Institute of Tibetan Plateau Research at the Chinese Academy of Sciences, alongside the Yunnan Institute of Cultural Relics and Archaeology and cooperative institutes, recovered seven human fossils from the site. These include four teeth, two parietal fragments, and one proximal radius segment. Four hominin teeth were unearthed in the middle of layer seven between 148–139 ka and 142–134 ka, pointing to a high likelihood of finding additional hominin fossils at the location.
Proteomic Analysis Confirms Denisovan Taxa
To confirm the taxonomic attribution of the finds, researchers performed proteomic analysis on the fossils. An acid etch approach analyzed the enamel, while dentine powder was drilled for protein extraction, yielding one enamel fraction and three dentine fractions for liquid chromatography coupled with tandem mass spectrometry analysis.
The testing confirmed that three bones and two teeth belong to Denisovans, dating back to 167,000 to 134,000 years ago, as detailed by the international research team’s official release. Morphological analysis showed that the lower second molar teeth exhibited close morphological affinity with those of Xiahe and Laos Denisovans, as well as East Asian late Middle Pleistocene archaic Homo from Hualongdong.
Researchers also examined more than 60,000 fragmentary mammal bones recovered from the cultural layers, identifying 22 fragments as potential hominin remains. After ZooMS screening across 76 bone fragments in six batches, researchers submitted three additional hominin remains and 14 mammalian samples for liquid chromatography analysis. They also extracted proteins from the parietal fragment known as BFD767, yielding three additional fractions.
Stone Tool Industries and Specialized Subsistence Strategies
The site yielded 1,366 stone artifacts across its deep stratigraphic layers, demonstrating remarkable long-term technological stability. The tool assemblage is dominated by expedient flaking and retouching techniques, supplemented by organized centripetal flaking that demonstrates a flexible and pragmatic survival strategy.
Alongside lithic tools, archaeologists identified diverse bone tools, including retouchers, wedges, and opportunistic tools. Their technical combination resembles Middle Paleolithic Neanderthal bone industries, highlighting bone processing as a core component of early human behavior in East Asia. Faunal remains recovered from the site were dominated by deer and bovids, mostly prime-age adults, alongside small numbers of rhinoceros and hyenas.
Extensive cut marks and percussion marks across the bones indicate specialized hunting, butchering, and meat consumption of medium-to-large ungulates. The detailed site stratigraphy and sample data demonstrate that Denisovans adapted stably across glacial-interglacial climate fluctuations while inhabiting a pine-dominated forest or forest-steppe environment.
Geographic and Evolutionary Significance for East Asian Hominins
The dental morphology discovered in Yunnan exhibits a mix of primitive and derived Homo traits. While similar to the Xiahe Denisovan specimen found in Baishiya Karst Cave in Northwest China’s Gansu Province, the teeth remain distinct, suggesting regional morphological variation among Asian Denisovans.
This variation indicates that the bat cave group may represent a distinct regional type within the Homo longi lineage. Located in a critical geographic corridor between Siberia, the Qinghai-Xizang Plateau, Southeast Asia, and Oceania, the site serves as a vital bridge connecting northern and southern East Asian Denisovan records.
Analytical Insights and Future Horizons
It shows how Denisovans actually adapted to their surroundings across 100,000 years of cultural history.
The evidence provides direct context for explaining the relatively high proportions of Denisovan genetic ancestry found in modern Southeast Asian and Oceanian populations.
