Denisovans: The Lost Human Species Revealed by Ancient DNA

The Denisovans are an extinct group of humans known first not from a skeleton but from their DNA. In 2010 geneticists sequencing a tiny finger bone from Denisova Cave in the Altai Mountains of Siberia found that it belonged to a previously unknown branch of humanity, closely related to the Neanderthals. Since then a handful of fossils, sediment DNA and the genomes of living people have shown that Denisovans were spread widely across Asia and left a lasting genetic mark on populations from Tibet to Papua New Guinea.

Background: Denisova Cave

Denisova Cave lies in the valley of the Anui River in the Altai Mountains of southern Siberia, close to where Russia, Kazakhstan, Mongolia and China meet. It is named after Dionisij (Denis), a hermit said to have lived there in the 18th century. The cave’s cool, stable conditions have helped preserve ancient DNA unusually well.

Archaeologists from the Institute of Archaeology and Ethnography in Novosibirsk, led over the years by Anatoly Derevianko and Michael Shunkov, have excavated the cave systematically since the late 1970s. Its layers span roughly 300,000 years and contain thousands of stone tools, animal bones and, in the upper levels, ornaments such as bone pendants and a polished stone bracelet. The cave was also used at times by Neanderthals and, later, by modern humans.

The finger bone and the DNA

In 2008 excavators recovered a small fragment of a finger bone, the tip of the little finger of a young girl, catalogued as Denisova 3. It was too small and incomplete to identify by its shape alone. A sample was sent to Svante Pääbo’s ancient DNA laboratory at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

In March 2010 a team led by Johannes Krause and Pääbo published the complete mitochondrial genome from the bone. Mitochondrial DNA, inherited through the mother, showed a lineage that had split from the ancestors of both Neanderthals and modern humans around a million years ago. It was the first time a new kind of human had been recognised from DNA rather than anatomy.

In December 2010 a larger team including David Reich published a draft of the nuclear genome, which carries DNA from both parents. It told a more nuanced story: the Denisovans were a sister group of the Neanderthals, sharing a common ancestor with them after their joint line had separated from that of modern humans. The researchers named the group “Denisovans” after the cave. In 2012 a high-quality genome was produced from the same tiny bone, one of the most complete genomes of any ancient human.

Key people

• Svante Pääbo, the Swedish geneticist who pioneered the study of ancient human DNA, received the 2022 Nobel Prize in Physiology or Medicine for his work on the genomes of extinct humans, including the Denisovans.
• Johannes Krause led the analysis of the mitochondrial genome published in 2010.
• David Reich, a geneticist at Harvard, helped show how Denisovans were related to other humans and how their DNA entered living populations.
• Anatoly Derevianko and Michael Shunkov directed the excavations at Denisova Cave.

What the fossils show

Physical remains of Denisovans are scarce. From Denisova Cave they include the finger bone and several large molars, among them Denisova 2, 4 and 8. The molars are strikingly large, larger than those of Neanderthals or modern humans and closer in size to much older species.

In 2018 researchers reported Denisova 11, nicknamed Denny: a bone fragment from a girl about 13 years old whose mother was a Neanderthal and whose father was a Denisovan. She is the only first-generation offspring of two different ancient human groups yet identified.

The first Denisovan fossil found outside Siberia was the Xiahe mandible, a jaw from Baishiya Karst Cave on the Tibetan Plateau in China, identified in 2019 using ancient proteins. It is at least about 160,000 years old. In 2022 a child’s molar from Tam Ngu Hao 2 (Cobra Cave) in Laos was reported as probably Denisovan, dated to roughly 164,000 to 131,000 years ago.

In 2025 two further fossils were linked to Denisovans using ancient proteins and DNA. A jaw dredged from the sea floor off Taiwan, known as Penghu 1, was identified as a Denisovan male. Separately, researchers recovered mitochondrial DNA and proteins from the Harbin skull, a large cranium from north-eastern China that had been named Homo longi (“dragon man”) in 2021, and concluded that it too was Denisovan. If accepted, the Harbin skull gives the first clear picture of a Denisovan head: long and broad, with heavy brows and a large brain.

How Denisovans lived

Because so few Denisovan bones have been found, their way of life has to be pieced together from the places they occupied. They clearly coped with very different environments: the cold, mountainous Altai, the high, dry Tibetan Plateau at more than 3,000 metres, and the warm, forested karst landscapes of Laos. That range suggests they were adaptable hunter-gatherers rather than specialists of a single habitat.

Excavations at Baishiya Karst Cave published in 2024 showed that its occupants, identified as Denisovans by DNA in the sediments and by a rib fragment, hunted or scavenged blue sheep, wild yaks, wild horses and woolly rhinoceroses, and also took smaller animals such as marmots and birds. Bones were cut and broken for meat and marrow.

At Denisova Cave the stone tools associated with Denisovan layers belong to the Middle Palaeolithic, similar to tools made by Neanderthals. Whether Denisovans also made the bone points, beads and the famous stone bracelet found in the upper layers is disputed, because modern humans and Neanderthals used the cave around the same time and the layers are not always easy to separate.

Denisovan genes in living people

The most surprising discovery came from comparing the Denisovan genome with those of people alive today. Populations in Papua New Guinea, Aboriginal Australians and some groups in Island South-East Asia carry roughly 3 to 6 per cent Denisovan DNA, depending on the study and the method. Among the highest levels found so far are in the Ayta Magbukon people of Luzon in the Philippines. Much smaller traces, well under one per cent, are found across mainland East and South Asia and among Native Americans.

This means modern humans met and had children with Denisovans after leaving Africa, probably on several occasions and with several distinct Denisovan populations. Analyses of these segments suggest that some Denisovan groups were genetically quite different from one another and from the Altai Denisovans, implying a long and widespread history across Asia.

Some of the inherited genes appear to have been useful. The best-known example is a version of the EPAS1 gene, which helps the body cope with low oxygen. It is common among Tibetans, who live at high altitude, and was inherited from Denisovans. Other Denisovan gene variants may have affected immunity and fat metabolism.

Interbreeding among ancient humans

The genomes show a tangled web of contacts. Denisovans interbred with Neanderthals, as Denny demonstrates, and the Denisovan genome itself contains a small amount of DNA from a still older, unidentified human group, sometimes called a “superarchaic” population. Modern humans in turn received DNA from both Denisovans and Neanderthals, a story explored in Neanderthal interbreeding.

Mitochondrial DNA from 430,000-year-old fossils at Sima de los Huesos in Spain, published in 2013, turned out to be closer to Denisovans than to Neanderthals, even though the nuclear DNA from the same site is closer to Neanderthals. This puzzle shows how mixing between populations can make family trees look different depending on which part of the genome is studied.

Myths and facts

• Myth: Denisovans are known from just one finger bone. Fact: The finger bone came first, but teeth, a jaw, a skull and other fragments have since been assigned to them, and their DNA has been recovered from cave sediments.
• Myth: Denisovans lived only in Siberia. Fact: The cave gave them their name, but fossils from Tibet, Laos, Taiwan and north-eastern China, along with modern genetic evidence, show they ranged widely across Asia.
• Myth: Denisovans and modern humans never met. Fact: Their genes in living people prove that the two groups interbred repeatedly.

Timeline

• c. 400,000-450,000 years ago: Estimated split between the ancestors of Denisovans and Neanderthals, based on genetic studies.
• c. 200,000 years ago or earlier: Denisovans are present at Denisova Cave.
• At least c. 160,000 years ago: A Denisovan jaw is left in Baishiya Karst Cave on the Tibetan Plateau.
• c. 90,000 years ago: Denny, the daughter of a Neanderthal mother and a Denisovan father, lives in the Altai.
• c. 76,000-52,000 years ago: Estimated age of the Denisova 3 finger bone.
• 2008: The finger bone is found in Denisova Cave.
• 2010, March: The mitochondrial genome reveals an unknown human lineage.
• 2010, December: The nuclear genome is published and the group is named Denisovans.
• 2019, May: The Xiahe mandible becomes the first Denisovan fossil identified outside Siberia.
• 2025: Ancient proteins and DNA link the Penghu jaw and the Harbin skull to Denisovans.

Why it matters

The Denisovans changed how the study of human origins is done. They were the first human group discovered through DNA, proving that genetics can reveal populations that fossils alone had missed. Their legacy lives on in the genomes of millions of people, and they show that our species did not replace other humans cleanly but mixed with them. Much remains unknown, from their full appearance to the time of their disappearance, which makes the Denisovans one of the most active fields in palaeoanthropology.