The Denisovans

In 2008, a distal manual phalanx of from a hominin little finger was recovered from Denisova Cave in the Altai Mountains of southern Siberia. The cave is named for a hermit called Dionisij (Denis) who is supposed to have lived there in eighteenth century, but if this is true he was only the latest in a long line of inhabitants. In April 2010, it was reported that the phalanx had belonged to a hitherto-unknown human species (Krause, et al., 2010).

The small bone was dated by stratigraphic methods and found to be in the region of 30,000 to 48,000 years old. It was believed to have belonged to a child aged between five and seven years old, but other than that no morphological classification could be made. Due to the cool, dry climate, it proved to be possible to extract DNA from the bone, isolate mtDNA fragments, and sequence the entire mitochondrial genome. As we inherit our mtDNA solely from our mothers, this led to the find being dubbed X Woman, despite being a juvenile of unknown gender.

At the time in question, Neanderthals, identified as such by their mtDNA, were living less than 100 km (60 miles) away. The presence of an Upper Palaeolithic industry at Siberian sites such as Kara-Bom and Denisova itself has been taken as evidence for the appearance of modern humans in the Altai before 40,000 years ago. The expectation, therefore, was that the mitochondrial DNA from the bone would match that of either Neanderthals or modern humans, but neither turned out to be the case. Instead, sequencing revealed that X Woman had last shared a common ancestor with Neanderthals and modern humans about a million years ago.

X Woman clearly wasn’t a Neanderthal or a modern human, but what was she (if indeed she was a ‘she’)? One possibility was Homo heidelbergensis, the presumptive common ancestor of the Neanderthals and modern humans, but this species probably appeared no earlier than 600,000 years ago, and was too recent to be associated with X Woman’s ancestors. On the other hand, one million years ago was too recent for X Woman to be a late-surviving descendant of the first wave of Homo erectus to reach Southeast Asia and China.

Towards the end of 2010, it was reported that X Woman’s nuclear genome had been sequenced (Reich, et al., 2010). It turned out that X-Woman lacked a Y-chromosome and therefore was indeed female. The discovery of an upper molar tooth from a young adult was also reported. The sequencing of mtDNA from the tooth confirmed that it belonged to a different individual to the phalanx. For this reason, the term ‘X-Woman’ was dropped in favour of ‘Denisovan’.

The nuclear data allowed more detailed estimates to be made regarding the relatedness of Denisovans, Neanderthals and modern humans. It was found that the Denisovans diverged from Neanderthals 640,000 years ago, and from present-day Africans 804,000 years ago. This meant that the Denisovans were more closely related to the Neanderthals than to modern humans, and may thus be considered a sister group of the former. The most remarkable finding was that 4.8 percent of the nuclear genome of present-day New Guineans derives from Denisovans, greater than the Neanderthal contribution of 2.5 percent (Reich, et al., 2010). The implication was that the Denisovan range had once extended from the deciduous forests of Siberia to the tropics. This is a wider ecological and geographic region than any other hominin with the exception of modern humans (Reich, et al., 2011). Overall, the data was consistent with a scenario in which modern humans, on leaving Africa, interbred with Neanderthals and then, at some subsequent point, the ancestors of present-day New Guineans interbred with Denisovans.

Follow-up studies confirmed the presence of Denisovan genetic material in some other modern populations of island Southeast Asia, and also in Aboriginal Australians, Fijians and Polynesians. Significantly, though, it was absent from mainland populations. The only logical explanation is that the present-day population of Mainland Southeast Asia are descended from a second group of migrants that arrived after the Denisovans had become extinct (Reich, et al., 2011; Skoglund & Jakobsson, 2011; Meyer, et al., 2012).

Interbreeding with Denisovans might have boosted the immune systems of some modern populations. The human leucocyte antigen (HLA) helps the immune system to recognise and combat pathogens. There are three genes known as HLA-A, HLA-B and HLA-C, and it believed that a number of variants of these genes are of Denisovan origin. These variants could have conferred immunity to pathogens to which the incoming modern population had not been previously exposed, and given a survival to those acquiring them from the Denisovans. It is possible that the modern immune system has thus been shaped by ‘importing’ advantageous genes from archaic populations throughout Eurasia (Abi-Rached, et al., 2011).

It has been suggested, on the basis of allele comparison, that the Denisovans were dark-skinned, with brown eyes and hair (Meyer, et al., 2012). Other than that, and beyond their genetic impact on modern populations, we still know very little about them. The Middle Pleistocene fossil record of Southeast and East Asia is very sparse and the Denisova tooth, probably a third or possibly second left upper molar, fails to support a connection with any of the few remains that have been found. The tooth is fairly large, lying within the size range of Homo erectus and Homo habilis. It is above the size range typical for Neanderthals, early modern humans, and the very few third upper molars that have been recovered from other late archaic hominins in the region. The tooth shares no derived morphological features with Neanderthals or modern humans, hinting at the distinctiveness of the Denisovans (Reich, et al., 2010). On the other hand, the report failed to note that some early modern human teeth are also very large, such as those associated with the 35,000-year-old lower jawbone from Peştera cu Oase in Romania (Trinkaus, et al., 2003; Trinkaus, et al., 2003). Size alone probably does not tell us very much (Hawks, 2010).

Recently, it has been suggested that the Denisovans interbred with yet another archaic human species. Given that the Denisovans and Neanderthals diverged from one another after they diverged from modern humans, one would expect the two species to be equally genetically distinct from our own species. However, this is not the case; the Denisovans are more genetically distinct than the Neanderthals. It turns out that scattered fragments amounting to around one percent of their genome is much older than the rest of it. This is best explained by the Denisovans interbreeding with an as yet unidentified human species, possibly Homo heidelbergensis or Homo erectus. We do not yet have genetic material from either species, so this cannot be confirmed (Marshall, 2013).

At all events, it is now clear that the view of modern humans entirely replacing archaic populations is not correct, either in or out of Africa. There is certainly an element of truth to the multiregional model. It is, however, only an element. The range of morphological variation between modern and archaic humans is greater than that in any existing primate species. We should not think of Denisovans and Neanderthals as simply variant forms of Homo sapiens (Stringer, 2012).

References:

Abi-Rached, L. et al., 2011. The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans. Science, 25 August.

Hawks, J., 2010. The Denisova genome FAQ. [Online]
Available at: http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/denisova-nuclear-genome-reich-2010.html
[Accessed 14 November 2011].

Krause, J. et al., 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature, 8 April, Volume 464, pp. 894-897.

Marshall, M., 2013. Mystery human species emerges from Denisovan genome. [Online]
Available at: http://www.newscientist.com/article/dn24603-mystery-human-species-emerges-from-denisovan-genome.html#.Uo5FQMTk-m5
[Accessed 21 November 2013].

Meyer, M. et al., 2012. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science, 30 August.

Reich, D. et al., 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 23/30 December, Volume 468, pp. 1053-1060.

Reich, D. et al., 2011. Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania. The American Journal of Human Genetics, 7 October, Volume 89, pp. 1-13.

Skoglund, P. & Jakobsson, M., 2011. Archaic human ancestry in East Asia. PNAS.

Stringer, C., 2012. What makes a modern human. Nature, 3 May, Volume 485, pp. 33-35.

Trinkaus, E. et al., 2003. Early modern human cranial remains from the Pestera cu Oase, Romania. Journal of Human Evolution, Volume 45, p. 245–253.

Trinkaus, E. et al., 2003. An early modern human from Peştera cu Oase, Romania. PNAS, 30 September, 100(20), p. 11231–11236.

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