Modern humans interbred with 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 18th Century, but if this is true he was only the latest in a long line of inhabitants.

In April 2010, a report was published in the journal Nature (Krause, et al., 2010) suggesting that the phalanx had belonged to a hitherto-unknown human species. The small bone was dated by stratigraphic methods and found to be in the region of 30,000 to 48,000 years old. It is believed to have belonged to a child aged between 5 and 7 years old, but other than that no morphological classification could be made. However, due to the cool, dry climate, it proved to be possible to extract DNA from the bone and isolate mtDNA fragments, from which it proved possible to sequence the entire mitochondrial genome. Because we inherit our mtDNA solely from our mothers, this led to the find being dubbed X Woman, despite being from a juvenile of then 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 Homo heidelbergensis appeared no earlier than 600,000 years ago – long after X Woman’s ancestors. On the other hand, the date of one million years was too late for X Woman to be a late-surviving descendant of the first wave of Homo erectus to reach the Far East.

Towards the end of 2010, a second report was released in Nature detailing the sequencing of X Woman’s nuclear genome (Reich, et al., 2010). It turned out that “X-Woman” lacked a Y-chromosome and therefore was indeed female. Also described in the same report was an upper molar tooth. The latter appeared to be from a young adult and also yielded mtDNA, which in turn confirmed that it belonged to a different individual to phalanx. For this reason, the term “X-Woman” was dropped in favour of “Denisovan”.

According to the report, both mitochondrial and nuclear genomes suggest that the Denisovans are more closely related to Neanderthals than they are to modern humans. The nuclear data suggested that the Denisovans diverged from Neanderthals 640,000 years ago and from present-day Africans 804,000 years ago, suggesting that Densovans and Neanderthals were sister groups, sharing a more recent common ancestor than modern humans and Neanderthals. Africans were used for the comparison to avoid the confounding effects of the interbreeding thought to have occurred between archaic humans (previously thought to be Neanderthals) and the first modern humans to leave Africa. It was also found that the archaic component of the modern Eurasian genome has closer affinities to Neanderthals than to Denisovans, confirming that the interbreeding did occur with the former rather than the latter.

The divergence data obtained from the nuclear DNA is rather at odds with that obtained from the mtDNA. The report suggested two possible causes; firstly interbreeding between Denisovans and as yet unknown hominins; secondly, that the Denisovans retained an archaic mitochondrial lineage that has been lost from Neanderthals and modern humans due to the effects of genetic drift. The latter explanation is the more parsimonious, but the report concluded that the two scenarios were equally likely according to the data.

The most remarkable finding was that 4.8 percent of the nuclear genome of present-day Papuans derives from Denisovans, greater than the Neanderthal contribution of 2.5 percent and meaning that uniquely for modern humans, the Papuans are more closely-related to Denisovans than they are to Neanderthals. 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 Papuans interbred with Denisovans, but this did not affect any other non-African populations. The implication is that Denisovans were present in Southeast Asia as well as southern Siberia. This in turn raises the possibility that the archaic humans living in the Far East as recently as 27,000 years ago (Swisher, et al., 1996), conventionally described as late Homo erectus, may in fact be Denisovans.

The Denisova tooth, which is probably a third or possibly second left upper molar, is fairly large, within the size range occupied by Homo erectus and Homo habilis and larger than that typical of Neanderthals and early modern humans. But 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 I) (Trinkaus, Milota, Rodrigo, Mircea, & Moldovan, 2003; Trinkaus, et al., 2003). Size alone probably does not tell us very much. That the tooth shares no derived morphological features with Neanderthals or modern humans further indicates the distinctiveness of the Denisovans; but it also lacks any features in common with the very few third upper molars that have been recovered from other late archaic hominins in the Far East. Thus the tooth fails to support a connection between the Denisovans and known archaic human fossil remains from the Far East.

Clearly there is a very interesting story here, but until further fossil and/or genetic evidence comes to light, there is nothing more definite that can be said at this stage.

References:
Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., et al. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature , 464, 894-897.

Reich, D., Green, R., Kircher, M., Krause, J., Patterson, N., Durand, E., et al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature , 468, 1053-1060.

Swisher, C., Rink, W., Anton, S., Schwarcz, H., Curtis, G., Suprijo, A., et al. (1996). Latest Homo erectus of Java: Potential Contemporaneity with Homo sapiens in Southeast Asia . Science , 274, 1870 – 1874.

Trinkaus, E., Milota, S., Rodrigo, R., Mircea, G., & Moldovan, O. (2003). Early modern human cranial remains from the Pestera cu Oase, Romania. Journal of Human Evolution , 45, 245–253.

Trinkaus, E., Moldovan, O., Milota, Ş., Bîlgăr, A., Sarcina, L., Athreya, S., et al. (2003). An early modern human from Peştera cu Oase, Romania. PNAS , 100 (20), 11231–11236.

© Christopher Seddon 2010

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Author: prehistorian

Prehistorian & author

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