The Denisovans - The Third Species of Human

Newly Discovered Hominids of Siberia

Entrance to the Denisova cave in southern Siberia, Russia.
Entrance to the Denisova cave in southern Siberia, Russia. Image courtesy of Max Planck Institute for Evolutionary Anthropology

The Denisovans are a recently identified hominid species, related to but different from the other two hominid species who shared our planet during the Middle and Upper Paleolithic periods, early modern humans and Neanderthals. The only archaeological evidence of Denisovans recovered to date are a few tiny fragments of bone. Those were found in the Initial Upper Paleolithic layers of Denisova Cave, in the northwestern Altai Mountains some six kilometers (~four miles) from the village of Chernyi Anui in Siberia, Russia.

But those fragments hold DNA, and the sequencing of that genetic history and the discovery of remnants of those genes in modern human populations has important implications for the human habitation of our planet.

Human Remains at Denisova

The only remains of the Denisovans identified to date are two teeth and a small fragment of finger-bone from Level 11 at Denisova Cave, a level dated between ~29,200-48,650 years ago and containing a variant of initial Upper Paleolithic cultural remains found in Siberiai called Altai. Discovered in 2000, these fragmentary remains have been the target of molecular investigations since 2008. The discovery came after researchers led by Svante Pääbo at the Neanderthal Genome Project at the Max Planck Institute for Evolutionary Anthropology successfully completed the first mitochondrial DNA (mtDNA) sequence of a Neanderthal, proving that Neanderthals and early modern humans are not very closely related at all.

In March 2010, Pääbo's team reported (Krause et al.) the results of the examination of one of the small fragments, a phalanx (finger bone) of a child aged between 5 and 7, and found within Level 11 of Denisova Cave. The mtDNA signature from the phalanx from Denisova Cave is significantly different from both neanderthals or early modern humans (EMH).

A complete mtDNA analysis of the phalanx was reported in December of 2010 (Reich et al.), and it continued to support the identification of the Denisovan individual as separate from both neanderthal and EMH.

Pääbo and colleagues believe that the mtDNA from this phalanx is from a descendant of people who left Africa a million years after Homo erectus, and half a million years before the ancestors of Neanderthals and EMH. Essentially, this tiny fragment is evidence of a human migration out of Africa that scientists were completely unaware of before this discovery.

The Molar

The mtDNA analysis of a molar from Level 11 in the cave and reported in December 2010 (Reich et al.) revealed that the tooth was likely from a young adult of the same hominid as the finger bone: and clearly a different individual, since the phalanx is from a child.

The tooth is an almost complete left and probably third or second upper molar, with bulging lingual and buccal walls giving it a puffy appearance. The size of this tooth is well outside the range for most Homo species, in fact, it is closest in size to Australopithecus: it is absolutely not a neanderthal tooth. Most importantly, the researchers were able to extract DNA from the dentin within the root of the tooth, and preliminary results reported (Reich et al.) its identification as a Denisovan.

The Culture of the Denisovans

What we know about the culture of the Denisovans is that it was apparently not much different from other Initial Upper Paleolithic populations in the Siberian north. The stone tools in the layers in which the Denisovan human remains were located are a variant of Mousterian, with the documented use of parallel reduction strategy for the cores, and a large number of tools formed on large blades.

Decorative objects of bone, mammoth tusk, and fossilized ostrich shell were recovered from the cave, as were two fragments of a stone bracelet made of a dark green chloriolite. The Denisovan levels contain the earliest use of an eyed-bone needle known in Siberia to date.

  • Read more about the Upper Paleolithic cultural component of Denisova Cave

Genome Sequencing

In 2012 (Meyer et al.), the mapping of the complete genome sequencing of the tooth was reported by Pääbo's team (Meyer et al.).

Denisovans, like modern humans today, apparently share a common ancestor with Neanderthals but had a completely different population history. While Neanderthal DNA is present in all populations outside of Africa, Denisovan DNA is only found in modern populations from China, island Southeast Asia and Oceania.

According to the DNA analysis, the families of present-day human and Denisovans split apart about 800,000 years ago and then reconnected some 80,000 years ago. Denisovans share the most alleles with Han populations in southern China, with Dai in northern China, and with Melanesians, Australian aborigines, and other southeast Asia islanders.

The Denisovan individuals found in Siberia carried genetic data that matches that of modern humans and is associated with dark skin, brown hair and brown eyes.

Tibetans and Denisovan DNA

A DNA study published in the journal Nature in 2014 (Huerta-Sánchez et al.) focused on the genetic structure of people who live on the Tibetan Plateau at 4,000 meters above sea level  and discovered that Denisovans may have contributed to the Tibetan ability to live at high altitudes. The gene EPAS1 is a mutation which reduces the amount of hemoglobin in blood required for people sustain and thrive at high altitudes with low oxygen. People who live at lower altitudes adapt to low-oxygen levels at high altitudes by increasing the amount of hemoglobin in their systems, which in turn increases the risk of cardiac events. But Tibetans are able to live at higher elevations without increased hemoglobin levels. The scholars sought for donor populations for EPAS1 and found an exact match in Denisovan DNA.

The scholars believe that this human adaptation to extraordinary environments may have been facilitated by gene flow from Denisovans who had adapted to the climate first.

  • Read more about How the Tibetan Plateau was Settled


Derevianko AP, Shunkov MV, and Volkov PV. 2008. A Paleolithic Bracelet From Denisova CaveArchaeology, Ethnology and Anthropology of Eurasia 34(2):13-25

Gibbons A. 2012. A crystal-clear view of an extinct girl's genome. Science 337:1028-1029.

Huerta-Sanchez E, Jin X, Asan, Bianba Z, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M et al. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNANature advance online publication.

Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, and Paabo S. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464(7290):894-897.

Martinón-Torres M, Dennell R, and Bermúdez de Castro JM. 2011. The Denisova hominin need not be an out of Africa story. Journal of Human Evolution 60(2):251-255.

Mednikova MB. 2011. A proximal pedal phalanx of a Paleolithic hominin from Denisova cave, Altai. Archaeology, Ethnology and Anthropology of Eurasia 39(1):129-138.

Meyer M, Fu Q, Aximu-Petri A, Glo cke I, Nickel B, Arsuaga JL, Martinez I, Gracia A, Bermúdez de Castro JM, Carbonell E et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los HuesosNature 505(7483):403-406. doi: 10.1038/nature12788

Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C et al. 2012. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science Express.

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Bence V, Briggs AW, Stenzel U, Johnson PLF et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.