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Which Denisovan gene allows some people today to be healthy at high altitudes?

A Denisovan, cousin of the Neanderthals, with a superathlete gene for staying healthy at very high elevations, gave Tibetans a gene that gives today's Tibetans an advantage at those high elevations, says a new study, "Altitude adaptation in Tibet caused by introgression of Denisovan-like DNA," published online July 2, 2014 in the journal Nature in advance of the print version. Tibetans don't get altitude sickness from living at high elevations because this Denisovan gene helped Tibetans adapt to low oxygen levels at high altitudes. This variant allowed them to survive despite low oxygen levels at elevations of 15,000 feet or more, whereas most people develop thick blood at high altitudes, leading to cardiovascular problems.

Extinct human cousin gave Tibetans advantage at high elevation.
Photo credit: Beijing Genomics Institute (BGI-Shenzhen) photo. A Chinese researcher collects a blood sample from an ethnic Tibetan man participating in the DNA study. Extinct human cousin gave Tibetans advantage at high elevation.

About 87 percent of Tibetans now have the high-altitude version, compared to only 9 percent of Han Chinese, who have the same common ancestor as Tibetans. The gene has been referred to as the superathlete gene because at low elevations, some variants of it help athletes quickly boost hemoglobin and thus the oxygen-carrying capacity of their blood, upping endurance. Several thousand years ago, the common ancestors of Han Chinese and Tibetans moved onto the Tibetan plateau, a low-oxygen environment that probably proved fatal to many because of early heart disease and high infant mortality.

A healthy gene variant for hemoglobin regulation spread through the Tibetan population

A specific variant of a gene for hemoglobin regulation, picked up from earlier interbreeding with a mysterious human-like species, Denisovans, gradually spread through the Tibetan population, allowing them to live longer and healthier and avoid cardiovascular problems. You also may wish to see the July 1, 2010 news release, "Tibetans adapted to high altitude in less than 3,000 years."

Tibetans were able to adapt to high altitudes thanks to a gene picked up when their ancestors mated with a species of human they helped push to extinction, according to a new report by University of California - Berkeley, scientists.

An unusual variant of a gene involved in regulating the body's production of hemoglobin – the molecule that carries oxygen in the blood – became widespread in Tibetans after they moved onto the high-altitude plateau several thousand years ago

"We have very clear evidence that this version of the gene came from Denisovans," a mysterious human relative that went extinct 40,000-50,000 years ago, around the same time as the more well-known Neanderthals, under pressure from modern humans, says principal author Rasmus Nielsen, according to the July 2, 2014 news release, "Extinct human cousin gave Tibetans advantage at high elevation." Nielsen is a UC Berkeley professor of integrative biology.

"This shows very clearly and directly that humans evolved and adapted to new environments by getting their genes from another species." This is the first time a gene from another species of human has been shown unequivocally to have helped modern humans adapt to their environment, Nielsen explains, according to the news release. You also may wish to view Rasmus Nielsen’s group web site.

Nielsen and his colleagues at BGI-Shenzhen in China reported their findings online July 2, 2014 in advance of publication in the journal Nature

The gene, called EPAS1, is activated when oxygen levels in the blood drop, triggering production of more hemoglobin. At high altitude, however, the common variants of the gene boost hemoglobin and its carrier, red blood cells, too much, increasing the thickness of the blood and leading to hypertension and heart attacks as well as low-birth-weight babies and increased infant mortality.

The variant or allele found in Tibetans raises hemoglobin and red blood cell levels only slightly at high elevation, avoiding the side-effects seen in most people who relocate to elevations above 13,000 feet. "We found part of the EPAS1 gene in Tibetans is almost identical to the gene in Denisovans and very different from all other humans," Nielsen says, according to the news release. "We can do a statistical analysis to show that this must have come from Denisovans. There is no other way of explaining the data."

Harsh conditions on Tibetan plateau

The researchers first reported the prevalence of a high-altitude version of EPAS1 in Tibetans in 2010, based on sequencing of the genomes of numerous Han Chinese and Tibetans. Nielsen and his colleagues argue that this was the result of natural selection to adapt to about 40 percent lower oxygen levels on the Tibetan plateau. People without the variant died before reproducing at a much higher rate than those with it.

Nielsen and his colleagues subsequently sequenced the EPAS1 gene in an additional 40 Tibetans and 40 Han Chinese. The data revealed that the high-altitude variant of EPAS1 is so unusual that it could only have come from Denisovans.

Aside from its low frequency in Han Chinese, it occurs in no other known humans, not even Melanesians, whose genomes are nearly 5 percent Denisovan. A high quality sequence of the Denisovan genome was published in 2012.

Nielsen sketched out a possible scenario leading to this result: modern humans coming out of Africa interbred with Denisovan populations in Eurasia as they passed through that area into China, and their descendants still retain a small percentage – perhaps 0.1 percent – Denisovan DNA. The group that invaded China eventually split, with one population moving into Tibet and the other, now known as Han Chinese, dominating the lower elevations.

He and his colleagues are analyzing other genomes to pin down the time of Denisovan interbreeding, which probably happened over a rather short period of time

"There might be many other species from which we also got DNA, but we don't know because we don't have the genomes," Nielsen says, according to the press release. "The only reason we can say that this bit of DNA is Denisovan is because of this lucky accident of sequencing DNA from a little bone found in a cave in Siberia. We found the Denisovan species at the DNA level, but how many other species are out there that we haven't sequenced?"

Nielsen's coauthors include former UC Berkeley postdoctoral fellow Emilia Huerta-Sánchez, now at UC Merced; postdocs Benjamin Peter and Nicolas Vinckenbosch of UC Berkeley's Department of Integrative Biology; and colleagues in China, Hong Kong, Denmark, Saudi Arabia and Turkey.

The research was funded by the State Key Development Program for Basic Research of China, 973 Program, China National GeneBank-Shenzhen, the Shenzhen Key Laboratory of Transomics Biotechnologies and grants from the U.S. National Institutes of Health (R01HG003229 and R01HG003229-08S2). You also may wish to see the website of the National Institutes of Health, State Key Development Program for Basic Research of China. Or you may wish to check out the abstract of another study, "Study on the Hemoglobin levels among the Tibetan pregnant women in rural Lhasa."

Other noteworthy studies are, "Searching for signatures of cold adaptations in modern and archaic humans: hints from the brown adipose tissue genes" and "Reconstructing the DNA methylation maps of the Neandertal and the Denisovan."

Other noteworthy studies on prehistoric peoples of the world

And still other noteworthy studies include, "Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European " and "The Lengths of Admixture Tracts." In the study, "Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European," on the 7,000 year-old European from Spain, Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet.

What the researchers found, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome.

Skin color genes varied throughout Europe 7,000 years ago

Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes.

This finding suggests, according to the researchers, that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, the study's abstract explains that the research provides evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer. The main point is that some genes from long ago are still with us and may influence our health in various living conditions.

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