Fossil Hominids: The Denisovans

In 2008, a small fossil finger bone was found at the Denisova Cave in the Altai mountains in southern Siberia. Nothing about the bone seemed unusual, and it was assumed to belong to one of the Neandertals living there in that time period, between 30,000 and 48,000 years ago. When the mitochondrial DNA of the bone was sequenced in May 2010 however, it belonged neither to a Neandertal nor to a modern human (Krause et al. 2010). The finger bone was nicknamed the X-Woman, X for 'unknown' and 'woman' because mtDNA is maternally inherited, but in fact it didn't necessarily belong to a female. Males have mtDNA too; they just don't pass it on to their children.

Where Neandertals differ from modern humans by an average of 202 positions in the mtDNA genome, the Denisovan individual differed from modern humans by an average of 385 positions. This means that the most recent common mtDNA ancestor of the Denisovan, Neandertals and modern humans lived an estimated 1,000,000 years ago (with a large error margin), about twice as old as the most recent common mtDNA ancestor of Neandertals and humans. There was speculation that the Denisovan might belong to a previously unknown species, but it was also possible that it belonged to a relic Homo erectus, or to a Neandertal that had retained an archaic mtDNA sequence, or even to a modern human.

In December 2010 another paper was published with details of the nuclear genome of the X-woman (Reich et al. 2010). It remains unclear what species the genome belongs to, but in the absence of good information about their anatomy, they are being called 'Denisovans'.

1) Unlike the mtDNA results, the nuclear DNA results showed that the Denisova individual was more closely related to Neandertals than to modern humans. However, the Denisovan genes do not fall within the range of Neandertal variation. There are a few lines of evidence suggesting that the Denisovan and Neandertal lineages had separate histories once they diverged and did not form a single population. The Neandertal genomes sequenced so far have low genetic diversity, indicating that Neandertals passed through a genetic bottleneck after splitting from the Denisovans. With only one Denisovan genome available as yet, we don't know how diverse they were.

The anomalous Denisovan mtDNA sequence could be an ancient sequence that survived in the Denisovan population but went extinct in the human and Neandertal branches, or it could be that it was introduced into the Denisovan population by interbreeding with yet another population (Homo erectus, for example).

2) Even more spectacular was the finding that the Denisovan genome appears to have made a genetic contribution of about 4.8% (+/- 0.5%) to the genomes of living Melanesians. Interestingly, they did not contribute to the genomes of modern populations such as Han Chinese and Mongolians which live near Denisova now. The Denisovans obviously interbred with the ancestors of modern Melanesians at some point, but it seems unlikely to have happened at Denisova, which suggests that the Denisovans lived over a considerable area of eastern Asia.

This finding recalls another major discovery made earlier in 2010, which was that Neandertals appear to have contributed from 1% to 4% of the genome of all living non-Africans (Green et al. 2010). This was not expected, given that earlier mitochondrial DNA results showed no evidence of any genetic mixing between Neandertals and modern humans (but did not exclude the possibility either). The Reich et al. paper has improved the precision of this estimate; they calculate that Neandertals contributed 2.5% (+/- 0.6%) to the genome of modern non-Africans. That means that the Neandertals and Denisovans together account for an impressive 7.5% of the ancestry of modern Melanesians.

3) A second bone found at Denisova, a second or third upper molar tooth, has also had its mtDNA sequenced. This mtDNA sequence was very similar to that of the finger bone, indicating that both individuals probably belonged to the same population.

4) The molar tooth from Denisova also gives us some intriguing hints about the anatomy of the Denisovans. It is larger than comparable teeth in both early modern humans and Neandertals (and also Homo erectus, if it is a third molar). It also has a number of anatomical differences from Neandertal teeth to which it would be most closely related. Obviously it would be desirable to have more Denisovan fossils and knowledge of more of their anatomy, but the tooth suggests that they are distinctive anatomically as well as genetically from both humans and Neandertals. The 2nd and 3rd molar teeth of other hominids alive at the time such as Homo heidelbergensis and Homo erectus are not well represented in the fossil record, but the little we have also does not seem to closely resemble the Denisovan tooth.

The new analysis, by the way, shows that the 'X-Woman' bone really was female - there are not nearly enough Y-chromosome genetic sequences in it for it to have belonged to a male (the handful of Y-chromosome sequences found would be from contamination).

See also: The Denisova Genome FAQ, by John Hawks

Implications for Creationism

Young-earth creationists such as Answers in Genesis will doubtless claim that this research supports their claims that humans, Neandertals, and other archaic hominids all form one species. However, it's a lot harder to see how all the necessary population events can be squeezed into 10,000 years. Starting from Adam and Eve, humans apparently populated Africa, Asia and Europe, then some of them left Africa, picked up some Neandertal genes from the Middle East, then populated the world again, with some of them picking up more genes from the Denisovans and going on to populate Melanesia. Somehow, this emigrating group was also able to cause all the other humans to become extinct. At some point a flood occurred, killing all but 8 humans and removing most of the genetic variability. It would be tempting to assume the flood took care of removing the Neandertals and Denisovans, but that would leave the problem of explaining how their genetic contributions made it into the modern world. Supposing one person on the ark had Neandertal genes, and another Denisovan genes. The Arkers then had children who would have married each other. How could it happen that Africa ends up with the greatest genetic diversity, and yet none of the Neandertal and Denisovan genes are found there? Meanwhile, the Neandertal genes managed to find their way into all non-Africans, while the Denisovan genes found their way into the Melanesian population, but nowhere else (if 8 people populate the world, how can one of those people account for 5% of the genome of 0.15% of the world's population?). This scenario seems, to put it mildly, hopelessly improbable if not completely impossible.

How could the large amount of genetic diversity between Neandertals, Denisovans and modern humans have arisen in such a short time after Adam and Eve, and why is there so much less genetic diversity now even though far more time has passed in which mutations should have been accumulating? I await with interest a creationist population model to explain all this activity in a young-earth time frame.

Answers in Genesis has in fact commented on the Denisovan genome. However their explanation is just a brief bit of handwaving that doesn't even begin to resolve any of the above problems.

References

Green et al. 2010: A draft sequence of the Neandertal genome. Science, 328:710.

Krause, Good, Viola et al. 2010: The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:894.

Reich, Green, Kircher et al. 2010: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053.

This page is part of the Fossil Hominids FAQ at the talk.origins Archive.