Thursday, 9 December 2021

Evolution News - How Denisovans Helped Han Chinese Live the High-Life

The Tibetan Plateau where the research took place.

Photo credit: Peiqi Zhang/UC Davis
Denisovans or Homo Sapiens: Who Were the First to Settle (Permanently) on the Tibetan Plateau? | UC Davis

The story from human evolution of how the inhabitants of the Tibetan plateau acquired the ability to live permanently at such a high altitude just got a lot more interesting.

Once it was thought to be an example of very rapid evolution under intense selection pressure as a band of Han Chinese migrated to the Tibetan Plateau where the low oxygen pressure over a prolonged period would make them sick, and reduce their fertility with a very high rate of foetal death. Today, Han Chines living in Tibet have an infant mortality rate three times that of Tibetans. This intense selection pressure was believed to have favoured the evolution of the Endothelial Pas1 (EPAS1) gene which, in living populations, is known to improve oxygen transport in the blood. Most modern Tibetans carry a high frequency of the EPAS1 gene.

Tibetan woman
It also favoured the evolution of genes which reduce the tendency of the body to react to a low oxygen pressure by making more red blood cell, so making the blood thicker and causing blood pressure to increase - the cause of altitude sickness. This is normally the result of the kidneys being deprived of oxygen so secreting the hormone, haemopoietin, which stimulates red blood cell production (after severe blood loss, for example). The presence of the EPAS1 gene means that no such increase in red blood cells is necessary because it increases the oxygen-carrying capacity of haemoglobin.

But that rapid evolution hypothesis, delicious though it was, was before the DNA, extracted from a finger bone found in a the Denisova cave in Siberia was sequenced and found to contain the same gene. Their gene and that of the Tibetans are so similar that almost identical genes evolving twice in two different hominins is highly improbable. There was little doubt that the Han Chinese who migrated to Tibet had acquired the gene from Denisovans.

It was also believed that this migration had been very recent in geological terms. The question then became, how did these migrants acquire this Denisovan gene, which is absent in the Han who stayed put? It was thought unlikely that they acquired it directly from Denisovans since interbreeding was believed to pre-date the split from the Han. It was proposed that they acquired it from South Asian people such as the Nepalese. South Asian people carry a large proportion of Denisovan DNA, acquired by earlier periods of interbreeding.

Based on archaeological evidence, we know that there are gaps between these occupation periods, but the archaeological work on the Tibetan Plateau is very limited. There’s still a possibility of continuous human occupation since the late ice age, but we haven’t found enough data to confirm it.

Peiqi Zhang, co-lead author
Department of Anthropology
University of California, Davis, CA, USA
Now this latest piece of research by researchers from University of California, Davis, UCLA, the Chinese Academy of Sciences in Beijing and Brown University in Providence, Rhode Island, USA, shows that they could indeed have acquired the gene directly from Denisovans because the two species, Homo sapiens and Denisovans are believed to have co-existed on the Tibetan Plateau and Han Chinese had been present there much earlier than was once thought. Combining genetic and archaeological evidence, the researchers, led by Peiqi Zhang, a UC Davis doctoral student, and Xinjun Zhang (unrelated), a postdoctoral researcher at UCLA, have come up with the hypothesis that there were four successive major periods of occupation, beginning with Denisovans about 160,000 years ago and followed by three periods of humans who arrived starting around 40,000 years ago, 16,000 years ago and 8,000 years ago.

It could mean that the interbreeding happened somewhere in Asia in the ancestral Asians before the further subdivision of local populations that we see today. From the genetic studies, we can detect that all East Asians, including the Tibetans, interbred with two distinct Denisovan groups, with one of such events unique to East Asians (and the other shared with other South Asians)

Since all East Asians show the same patterns, we have reason to believe that this interbreeding event (the one that’s unique to East Asians) happened somewhere in the lowland instead of on the plateau.

Xinjun Zhang, co-lead author
Department of Ecology and Evolutionary Biology
University of California, Los Angeles, CA, USA
The UC, Davis news release explains:
Denisovans were first identified in 2010, based on DNA extracted from a girl’s finger bone found in a cave in the Altai Mountains in Siberia. Her DNA carried the haplotype highly similar to the Endothelial Pas1 (EPAS1) gene, which in living populations is known to improve oxygen transport in the blood. Most modern Tibetans carry a high frequency of the EPAS1 gene.

In 2019, a jawbone from a cave on the Tibetan Plateau was tentatively identified as Denisovan, but it could not be determined if the mandible carried the same gene. “We don’t know whether the Denisovans are adaptive to the hypoxia of the Tibetan Plateau at this point,” Peiqi Zhang said.

Little is known about the biology and behavior of the Denisovans on the plateau. Genetic studies show that Asians and Oceanians (people of Australia, New Zealand, Melanesia, Micronesia and Polynesia) inherited different amounts of Denisovan DNA, Xinjun Zhang said.

[…]

Zhang and Zhang propose two models of human occupation of the Tibetan Plateau as a framework for scholars that can be tested by future discoveries:
  • Intermittent visits before settling there year-round about the end of the ice age, about 9,000 years ago.
  • Continuous occupation beginning 30,000 to 40,000 years ago.

The main question is whether they’re staying there all year-round, which would mean that they were adapted biologically to hypoxia, or did they just end up there by accident, and then retreated back to the lowlands or just disappeared?

Professor Nicolas Zwyns, Supervising author
Associate professor of anthropology
Department of Anthropology
University of California, Davis, CA, USA
In either model, Denisovans could have passed the EPAS1 haplotype to modern humans about 46,000 to 48,000 years ago.

[…]

It’s unclear when Denisovans went extinct, but some studies suggest it may have been as late as 20,000 years ago. “Although we don't know if they were adapted to the high altitude, the transmission of some of their genes to us will be the game changer thousands of years later for our species to get adapted to hypoxia,” [Nicolas Zwyns, a UC Davis associate professor of anthropology and the paper’s supervising author] said. “That to me is a fantastic story.”
The interesting thing about this paper is that is shows how science doesn't settle for easy answers but constantly checks and reassesses and changes its mind in the light of new or improved data. In the course of less than ten years we have moved from believing that Tibetans quickly evolved their adaptation to high altitude living, to thinking they acquired this adaptation from Denisovans by some circuitous route, to now thinking they acquired it directly from them by interbreeding only a few tens of thousands of years ago and that the Tibetan Plateau has been occupied by both modern humans and Denisovans for considerably longer than we thought.

It also explain how Denisovans acquired this evolutionary adaptation, probably by natural selection as they experienced the same physiological effects of altitude as H. sapiens and so were subject to the same intense selection pressures that we once thought the Han Chinese migrants had been subjected to - indicating a much wider distribution of Denisovans in different habitats than the findings from a single Altaian cave would suggest.

And the whole thing illustrates yet again that for most of our evolution we behaved like a ring species - able to interbreed with varying degrees of success with closely related species where and when we came into contact with them as we spread out of Africa and met the descendants of an earlier migration by an archaic African hominin, recently renamed H. bodoensis

The reality is very far from the biblical notion of a founding couple as there was not even a founding species. Most non-African people are the result of hybridizations between at least three species and our ancient relatives still live on in the form of chunks of DNA that we inherrited from them.

Sadly, the published paper in Trends in Ecology & Evolution is behind an expensive paywall. However, the abstract can be read here.


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