Complete Guide to the Denisovans, a Newer Hominid Species

The Denisovans are a recently identified hominin species, related to but different from the other two hominid species (early modern humans and Neanderthals) who shared our planet during the Middle and Upper Paleolithic periods. Archaeological evidence of the existence of Denisovans is so far limited, but genetic evidence suggests they were once widespread across Eurasia and interbred with both Neanderthals and modern humans.

The earliest remains were tiny fragments found in the Initial Upper Paleolithic layers of Denisova Cave, in the northwestern Altai Mountains some four miles (six kilometers) from the village of Chernyi Anui in Siberia, Russia. The fragments held 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.

Denisova Cave

The first remains of the Denisovans were two teeth and a small fragment of finger-bone from Level 11 at Denisova Cave, a level dated between 29,200 to 48,650 years ago. The remains contain a variant of initial Upper Paleolithic cultural remains found in Siberia 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 the results of the examination of one of the small fragments, a phalanx (finger bone) of a child aged between 5 and 7, found within Level 11 of Denisova Cave. The mtDNA signature from the phalanx from Denisova Cave was significantly different from both Neanderthals or early modern humans (EMH). A complete mtDNA analysis of the phalanx was reported in December of 2010, 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 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 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 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 Denisova Cave, as were two fragments of a stone bracelet made of dark green chlorite. The Denisovan levels contain the earliest use of an eyed-bone needle known in Siberia to date.

Genome Sequencing

In 2012, Pääbo's team reported the mapping of the complete genome sequencing of the tooth. 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 southeast Asian 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, Denisovan DNA, and Xiahe

A DNA study published by population geneticist Emilia Huerta-Sanchez and colleagues in the journal Nature 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 to 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. Denisova Cave is only about 2,300 feet above sea level; the Tibetan Plateau averages 16,400 ft asl.

A team led by paleontologist Jean-Jacques Hublin (Chen 2019) searched through archived Tibetan paleontological remains and identified a mandible which had been discovered in Baishiya Karst Cave, Xiahe, Gansu province, China in 1980. The Xiahe mandible is 160,000 years old and it represents the earliest known hominin fossil found on the Tibetan Plateau—the cave's elevation is 10,700 ft asl. Although no DNA remained in the Xiahe mandible itself, there was extant proteome in the dentine of the teeth—albeit highly degraded, it was still clearly distinguishable from contaminating modern proteins. A proteome is the set of all expressed proteins in a cell, tissue, or organism; and the observed state of a particular single amino acid polymorphisms within the Xiahe proteome helped establish the identification of the Xiahe as Denisovan. 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.

Now that researchers have an indication of what Denisovan jaw morphology looks like, it will be easier to identify possible Denisovan candidates. Chen et al. also suggested two more East Asian bones which fit the morphology and time frame of Xiahe cave, Penghu 1 and Xuijiayo.

Family Tree

When anatomically modern humans left Africa about 60,000 years ago, the regions they arrived in were already populated: by Neanderthals, earlier Homo species, Denisovans and possibly Homo floresiensis. To some degree, the AMH interbred with these other hominids. The most current research indicates that all of the hominid species are descended from the same ancestor, a hominin in Africa; but the exact origins, dating, and spread of hominids throughout the world was a complex process that needs much more research to identify.

Research studies led by Mondal et al. (2019) and Jacobs et al. (2019) have established that modern populations containing admixtures of Denisovan DNA are found throughout Asia and Oceania, and it is becoming clear that interbreeding between anatomically modern humans and Denisovans and Neanderthals occurred several times over the course of our history on planet earth.

Selected Sources

• Árnason, Úlfur. "The Out of Africa Hypothesis and the Ancestry of Recent Humans: Cherchez La Femme (Et L'homme)." Gene 585.1 (2016): 9–12. Print.
• Bae, Christopher J., Katerina Douka, and Michael D. Petraglia. "On the Origin of Modern Humans: Asian Perspectives." Science 358.6368 (2017). Print.
• Chen, Fahu, et al. "A Late Middle Pleistocene Denisovan Mandible from the Tibetan Plateau." Nature (2019). Print.
• Douka, Katerina, et al. "Age Estimates for Hominin Fossils and the Onset of the Upper Palaeolithic at Denisova Cave." Nature 565.7741 (2019): 640–44. Print.
• Garrels, J. I. "Proteome." Encyclopedia of Genetics. Eds. Brenner, Sydney and Jefferey H. Miller. New York: Academic Press, 2001. 1575–78. Print
• Huerta-Sanchez, Emilia, et al. "Altitude Adaptation in Tibetans Caused by Introgression of Denisovan-Like DNA." Nature 512.7513 (2014): 194–97. Print.
• Jacobs, Guy S., et al. "Multiple Deeply Divergent Denisovan Ancestries in Papuans." Cell 177.4 (2019): 1010–21.e32. Print.
• Mondal, Mayukh, Jaume Bertranpetit, and Oscar Lao. "Approximate Bayesian Computation with Deep Learning Supports a Third Archaic Introgression in Asia and Oceania." Nature Communications 10.1 (2019): 246. Print.
• Slon, Viviane, et al. "The Genome of the Offspring of a Neanderthal Mother and a Denisovan Father." Nature 561.7721 (2018): 113–16. Print.
• Slon, Viviane, et al. "A Fourth Denisovan Individual." Science Advances 3.7 (2017): e1700186. Print.