A 190,000- to 10,000-year-old fossilized mandible found in the Penghu Channel, Taiwan, in the 2000s belonged to a male Denisovan, according to an analysis of ancient proteins. The finding provides direct evidence that Denisovans occupied diverse climates, from the cold Siberian mountains to the warm, humid subtropical latitudes of Taiwan.
An artist’s concept of a Penghu Denisovan walking under the bright Sun during the Pleistocene of Taiwan. Image credit: Cheng-Han Sun.
“Recent discoveries and reanalyses of fossil specimens, together with the application of molecular techniques and new dating methods, have revealed unexpected diversity among archaic hominins in eastern Asia during the Middle to Late Pleistocene, before the arrival of modern humans,” said Dr. Takumi Tsutaya, a researcher at the University of Copenhagen and the Graduate University for Advanced Studies (SOKENDAI), and colleagues.
“The identification of Denisovans is a crucial example of one such advancement.”
“Denisovans were recognized as a hominin group distinct from Neanderthals and modern humans by analyzing the DNA of fragmentary bones and teeth excavated from Denisova Cave in the Altai Mountains, Siberia.”
“Their nuclear genome shows that Denisovans form their own clade as a sister group to Neanderthals, with a calculated genomic divergence between the two clades occurring more than 400,000 years ago.”
“Genetic evidence also indicates gene flow between Denisovans, modern humans, and Neanderthals.”
“Studies of introgressed Denisovan DNA in modern human populations suggest the presence of multiple genomically distinct Denisovan populations, once distributed over a wide range across continental eastern Asia and possibly in some parts of insular Southeast Asia.”
“Outside Denisova Cave, however, direct molecular evidence of Denisovans has only been found from a single site on the Tibetan Plateau.”
“At Baishiya Karst Cave, Xiahe, a mandible and a rib have been identified as Denisovan on the basis of their protein sequences.”
Labeled Penghu 1, the new Denisovan fossil was collected in the 2000s through dredging activities associated with commercial fishing from the sea bottom (60 to 120 m deep) around 25 km off the western shore of Taiwan.
This area is located 4,000 km southeast of Denisova Cave and 2,000 km southeast of Baishiya Karst Cave.
It was part of the Asian mainland during episodes of low sea levels during the Pleistocene.
“Penghu 1 is dated as younger than 450,000 years, with a most likely age range of 10,000 to 70,000 years or 130,000 to 190,000 years, according to trace element contents, biostratigraphic evidence, and past sea-level changes,” the researchers said.
“Direct uranium dating of Penghu 1 was unsuccessful because of the influence of uranium from the seawater.”
Using ancient proteomic analysis, Dr. Tsutaya and colleagues extracted proteins from bone and dental enamel from the fossil and retrieved 4,241 amino acid residues, two of which were Denisovan-specific protein variants.
These variants are rare in modern human populations but have a higher frequency in regions associated with Denisovan genetic introgression.
What’s more, morphological analysis of the Penghu 1 remains reveals a robust jaw structure with large molars, and distinctive root structures, features that align with traits seen in the Tibetan Denisovan specimen, suggesting these traits were characteristic of the lineage and perhaps sex-specific.
“It is now clear that two contrasting hominin groups — small-toothed Neanderthals with tall but gracile mandibles and large-toothed Denisovans with low but robust mandibles (as a population or as a male character) — coexisted during the late Middle to early Late Pleistocene of Eurasia,” the scientists said.
“Because the latter morphologies are rare or absent in the late Early to early Middle Pleistocene fossils from Africa and Eurasia, they are not primitive retentions as previously suggested but probably developed or were enhanced in the Denisovan clade after their genetic separation from Neanderthals more than 400,000 years ago.”
“Recent discoveries from insular Southeast Asia (Homo floresiensis and Homo luzonensis) and South Africa (Homo naledi) highlight the diverse evolution of the genus Homo, contrasting with the lineage leading to Homo sapiens.”
“The dentognathic morphology of Denisovans can be interpreted as another such distinct evolution that occurred in our genus.”
The results were published today in the journal Science.
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Takumi Tsutaya et al. 2025. A male Denisovan mandible from Pleistocene Taiwan. Science 388 (6743): 176-180; doi: 10.1126/science.ads3888
