Who We Are: #4 Denisovans

In Chapter 3, Reich talks about the discovery of the Denisovans, a sister archaic group to the Neanderthals that lived in eastern Asia. It all started out with a pinky bone found in a cave in southern Siberia. The DNA in the little bone was very well preserved – they got better info from that one bone than all previous Neanderthal DNA work. It’s an odd situation – we now know a lot about Denisovan genetics, but we don’t have a skeleton and have no idea what they looked like.

The Denisovans were closer to the Neanderthals than they were to AMH, but not by much. Apparently modern humans split with the common ancestors of Denisovans and Neanderthals about 700,000 years ago, while Neanderthals and Denisovans separated not much later. Almost a trichotomy. Something similar happened when AMH spread into Eurasia: quite early, maybe 50,000 years ago, we split into eastern and western branches. Probably it’s all geography.

With a high-quality Denisovan genome to work with, they tested whether any population seemed to be especially close. To their surprise, people from New Guinea were indeed significantly closer: they must have some Denisovan ancestry, somewhat surprising because New Guinea is a long way from Siberia. Although, since the Denisovans had hundreds of thousands of years to differentiate and spread over eastern Eurasia, far more time than we have had, it’s not really that odd.

In a sense, Reich’s team already knew this, although it sounds as if they didn’t know that they knew it. That same year, they had put out their big Neanderthal paper. Deep in the supplements, there was a table that showed genetic distance between a number of populations, including the Bushmen. Since the Bushmen had split off before other modern humans moved out of sub-Saharan Africa and settled the rest of the world, everybody in Eurasia should have been the same distance from Bushmen. And almost all were – except for people from New Guinea, who were noticeably more distant. Which mean that they had extra admixture from some archaic group, probably not Neanderthals, since there’s never been any sign of them that far east. My guess was Denisovan.

Sarah Phillips-Garcia, at the University of New Mexico, saw a sign of archaic admixture in people from New Guinea even earlier: she saw that something had introduced new variation in STRs (short tandem repeats) in New Guinea, variation you didn’t see in the rest of humanity.

Meanwhile Reich’s team were analyzing that Denisovan genome. They found that something like 5% of New Guinea ancestry is Denisovan, on top of the usual Neanderthal ~2% in Eurasians. This Denisovan admixure came from a Denisovan population that was fairly divergent from the genome found in Siberia. Some people in New Guinea have considered taking advantage of this high level of archaic ancestry: when facing potential criticism from the UN Human Rights Commission for some kind of intertribal strife, they were going to argue that it didn’t apply to them, because they weren’t human. I never saw that one coming. Similar amounts of Denisovan admixture are found in Australian Aboriginals, people in the Solomon Islands, and some Philippine Negritos.

You might think that this suggests that this major admixture maybe happened in Southeast Asia or nearby islands, but Reich accepted the argument of Yousuke Kaifu, an anthropologists who pointed to the lack of archaeological artifacts in the region that would support the notion of big-brained hominins in that region. But that’s silly. Bamboo. Probably it did happen in that region, likely in Sundaland. Very recent work suggests that there may have been two separate Denisovan admixture events: the first one contributing to Melanesians, the second to the much smaller amount of Denisovan admixture found in mainland Asia.

Linkage analysis showed that the main Denisovan admixture occurred a bit more recently than Neanderthal admixture, around 50,000 years ago. The possible second admixture seems to have happened more recently.

Reich talks briefly about some of the advantageous genes we picked up from Neanderthals and Denisovans. It was predictable [ John Hawks and I predicted it] that at least some of their gene variants would be useful – after all, they’d lived in Eurasia for hundreds of thousands of years and ought to be well-adapted to local conditions. Reich mentions the high frequency of Neanderthal-origin keratin gene variants in Eurasians, variants that affect hair and skin. He also mentions a particular Denisovan variant of the EPAS1 gene that has become common in Tibetans and helps them deal with life at high altitude. Since Tibetan adaptations to high altitude are considerably more effective than those of Andean Indians, more like those of species that had spent a long time at high altitude, there was an obvious possibility that Tibetans had picked up variants from archaic populations that had spent hundreds of of thousands of years in that environment. And lo, it was so.

The oldest-found human DNA is from ancient fossils at the Sima de Los Huesos caves in Spain, more than 400,000 years old. These skeletons looks like ancestors of Neanderthals, but they carry mtDNA that is much closer to that found in the Denisovan sample. There is an idea that Neanderthals may have mixed a bit with the ancestors of modern humans, say a quarter of a million years ago, and picked up a new form of mtDNA. Which they may have needed: Neanderthal population was small enough to potentially cause trouble in the long run ( because of inefficient selection) but that’s even more true for mtDNA, whose effective population size is four times smaller.

It also looks as if the Denisovans may have mixed with an unknown but very archaic population in East Asia, possibly descendants of homo erectus, which goes back 2 million years in Eeurasia.

One growing suspicion, originating from ancient DNA work and recent fossil finds, is that anatomically modern humans may not necessarily have originated in sub-Saharan Africa. The oldest probably-modern skeleton we have was recently found in Morocco. There is evidence that African populations, too, mixed with unknown archaic hominids (evidence for Pygmies, Bushmen, and also more typical West Africans such as the Yoruba, which implies that at least some parts of sub-Saharan Africa were occupied relatively recently by non-AMH populations. Homo Naledi, a small-brained homonin identified from recently discovered fossils in South Africa, appears to have hung around way later that you’d expect (up to 200,000 years ago, maybe later) than would be the case if modern humans had occupied that area back then. To be blunt, we would have eaten them.

Deep prehistory was always complicated: we just didn’t know much about it before. Ancient DNA analysis is the path forward.