The Harbin skull confirms Denisovan ancestry and expands their known range using protein and DNA analysis from dental calculus.
What did Denisovans look like, despite their known genetic contributions to modern East Asian and Oceanian populations? This question has remained one of the most important since Denisovans were first discovered 15 years ago.
Recent research by a team led by Qiaomiei Fu of the Institute of Vertebrate Paleontology and Paleoanthropology at the Chinese Academy of Sciences, and Qiang Ji of Hebei GEO University, has helped provide an answer. The researchers confirmed that a nearly complete hominin skull found near Harbin belongs to the Denisovan lineage and dates back at least 146,000 years.
The team developed a method to automatically identify human populations using ancient proteins, producing the most informative ancient human proteome to date. They also improved extraction techniques and created bioinformatic tools to trace the evolution of ancient human DNA from Pleistocene dental calculus, successfully retrieving host mitochondrial DNA from the Harbin cranium.
Fossil link to Denisovan ancestry
These findings suggest that the Harbin cranium does belong to the Denisovan lineage and is connected to the early Denisovan population from Siberia. The results were recently published online in the journals Science and Cell.
The Harbin cranium, which is at least 146,000 years old, offers important insight into the broad geographic range of Denisovans in Asia. Prior to this discovery, Denisovan fossils were limited and fragmentary, complicating our understanding of their morphology and evolutionary history. The Harbin fossil, previously proposed as a new species named Homo longi—giving it the nickname “Dragon Man” from the region’s “Dragon River”—shares significant morphological similarities with Denisovan remains found at other locations.
The research team carried out separate paleoproteomic studies and innovative ancient DNA analyses on both the cranium and dental calculus. For the first time, they were able to directly link a nearly complete skull to the Denisovan population, resolving a long-standing question since Denisovans were first identified using ancient DNA in 2010.
Protein analysis confirms Denisovan identity
Using a newly established paleoproteomic system, the team analyzed mass spectrometric data from the Harbin cranium, identifying over 308,000 peptide-spectrum, more than 20,000 peptides, and confirming 95 endogenous proteins. This extensive dataset surpasses previous results from contemporaneous fossils.
The team also discovered 122 single amino acid polymorphisms (SAPs) unique to Hominidae species, confirming the Harbin individual’s classification within the Homo genus.
Notably, they identified three variants unique to Denisovans, establishing a phylogenetic link between the Harbin individual and Denisova 3.
DNA evidence expands Denisovan range
Despite the challenges of ancient DNA research, the team successfully retrieved mitochondrial DNA from dental calculus samples with a lot of effort. They optimized extraction methods and constructed multiple libraries, ultimately identifying Denisovan-specific mutations for further analysis.
The results confirmed that the Harbin individual belongs to an early mtDNA lineage of Denisovans, suggesting a wide distribution from Siberia to Northeast China during the late Middle Pleistocene. This study highlights the potential of dental calculus for preserving ancient human DNA, opening a new window into the genetic research of Middle Pleistocene hominins.
The two studies not only resolve the classification controversy surrounding the Harbin cranium and reveal the relatively complete skull morphology of Denisovans, but also provide important references for identifying other ancient human fossils in East Asia that may belong to the Denisovan lineage, such as those from Dali and Jinniushan.
References:
“The proteome of the late Middle Pleistocene Harbin individual” by Qiaomei Fu, Fan Bai, Huiyun Rao, Shaokun Chen, Yannan Ji, Aoran Liu, E. Andrew Bennett, Feng Liu and Qiang Ji, 18 June 2025, Science.
DOI: 10.1126/science.adu9677
“Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium” by Qiaomei Fu, Peng Cao, Qingyan Dai, E. Andrew Bennett, Xiaotian Feng, Melinda A. Yang, Wanjing Ping, Svante Pääbo and Qiang Ji, 18 June 2025, Cell.
DOI: 10.1016/j.cell.2025.05.040
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