Scientists recently discovered various Denisovan remains in Southwest China dating back to the late Middle Pleistocene, including the first Denisovan radius—one of two long bones in the forearm.
Denisovans are a genetically identified archaic hominin group believed to have been widely distributed across Asia. However, due to the limited number of fossil remains, especially postcranial bones—those below the skull—a distribution gap has long existed in Southwest China. Therefore, little is known about the physical traits that allowed Denisovans to adapt to different environments.
In a new study, researchers employed a novel proteomic strategy to identify additional hominin bones from a Paleolithic site called Bianfu Cave in Southwest China’s Yunnan Province. Paleoproteomic analysis confirmed five hominin remains as Denisovans, helping fill the distribution gap of Denisovans in Southwest China.
According to the researchers, the discovery of the first Denisovan radius provides crucial insights into Denisovan postcranial phenotype.
The study, published in Nature on September 9, was conducted by a research team led by Professor FU Qiaomei from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences (CAS), in collaboration with multiple institutions.
New Strategy
ZooMS (Zooarchaeology by Mass Spectrometry) has recently become an important tool for large-scale screening of hominin fossils due to its advantages of micro-invasive sampling, methodological simplicity, rapid identification, and low cost. However, the recovery rate of hominin fossils has been extremely low—only 0.1% at sites such as Denisova Cave and Baishiya Karst Cave. Given that Bianfu Cave yielded more than 60,000 bone fragments, conducting ZooMS analysis on all specimens would be both costly and inefficient.
To overcome this challenge, the researchers developed a novel “morphological pre-screening + ZooMS identification” strategy. This combined approach significantly improved screening efficiency and provided a replicable methodological framework for discovering hominin remains at similar Paleolithic sites with abundant bone fragments.
Through morphological pre-screening, the researchers selected 22 potential hominin remains from the large assemblage of bone fragments. Subsequent ZooMS analysis confirmed that two parietal bone fragments (BFD767 and BFD769) and one proximal radial fragment (BFD771) were derived from hominins.
Among the three newly identified hominin specimens, BFD767 and BFD771 originated from Layer 7, which also contained four hominin teeth. This layer was dated to approximately 148,000–134,000 years ago. BFD769 came from the older Layer 9, dated to approximately 167,000–150,000 years ago.
In addition to the three hominin bones, the research team also analyzed two hominin teeth excavated from Layer 7, including a lower fourth premolar (YHB3518) and a lower second molar (YHB3075).
To obtain comprehensive proteomic profiles of the five specimens, the team extracted and analyzed proteins from multiple fractions of different tissues, including bone, dentine, and enamel. Six to 16 endogenous proteins were identified from each specimen, covering 1,972 to 4,076 amino acid residues. Notably, abundant specific peptides from the amelogenin Y isoform were identified in the enamel of the two teeth, indicating that both teeth belonged to male individuals.
Population A ssignment
To determine the population assignment of these hominin specimens, the research team systematically screened for single amino acid polymorphisms (SAPs) within the endogenous proteomes.
They found that all five samples carried the Denisovan-specific variant COL1A2 R996K, indicating their Denisovan identity. Three additional informative SAPs were identified in the enamel of two Bianfu Cave teeth: the Denisovan-related variant AMBN M273V; AMELY 179L, a variant shared by modern humans, Neanderthals, and Denisovans; and AMBN 253A, a variant that distinguishes the Bianfu Cave individuals from Middle Pleistocene Homo erectus in East Asia.
Using the consensus sequences of endogenous proteins from each sample, the researchers constructed Bayesian phylogenetic trees with topologies highly consistent with those obtained from nuclear genome studies. The trees placed modern humans as the sister group to the Neanderthal-Denisovan clade. Each Bianfu Cave sample formed a monophyletic clade with Denisova 3, with a posterior probability of 100 percent. This result aligns with the SAP assignments, supporting the reliable attribution of these specimens as Denisovans.
M orphological Phenotype
Comprehensive morphological analysis was conducted on the two Denisovan parietal bones (BFD767 and BFD769) and one partial radius (BFD771). The cranial vault thickness pattern of Bianfu Cave hominins is most similar to that of H. heidelbergensis and East Asian late Middle Pleistocene archaic Homo .
Notably, BFD771 is the only confirmed Denisovan radius to date. Although it has large proximal dimensions and a likely medially oriented radial tuberosity, similar to Neanderthal radii, its overall external shape and mid-neck cross-sectional geometry align more closely with modern humans. According to the researchers, the first identified Denisovan radius fragment is of exceptional importance. Its mosaic features indicate unique biomechanical demands and behavioral adaptations in Denisovans, differing from those inferred for Neanderthals and modern humans.
Based on their results, Bianfu Cave has the richest Denisovan fossil record currently known outside Denisova Cave. The study fills a critical geographical gap in the known distribution of Denisovans. The Denisovan remains were derived from two different stratigraphic layers dating to Marine Isotope Stage 6. During this glacial period, the relatively warmer climate and abundant food resources may have enabled the Yunnan-Guizhou Plateau to serve as a favorable habitat for hominins and supported the long-term survival of the Bianfu Cave population.
Nature
Ancient proteins identify various Denisovan remains from Southwest China
9-Sep-2026