Studies find Neanderthal genes in modern humans

Correction: An earlier version of this article incorrectly said that scientists had sequenced the genome of a 130,000-year-old Neanderthal toe bone. The bone was about 50,000 years old. This version has been corrected.


Researchers compared the data collected from a 50,000-year-old toe bone with 1,004 genomes of present-day humans. (Bence Viola/Max Planck Institute for Evolutionary Biology)
January 29

Neanderthal genes lurk among us. Small traces of Neanderthal DNA have been confirmed in the areas of the genome that affect skin and hair of modern humans, according to two new studies that also give clues as to which Neanderthal traits may have been helpful — or harmful — to the survival of our species.

The studies, published online Wednesday in the journals Nature and Science, came to similar conclusions despite using vastly different methods of genomic analysis.

For East Asian and European populations, genes that provide the physical characteristics of skin and hair have a high incidence of Neanderthal DNA — possibly lending toughness and insulation to weather the cold as early man emerged from Africa, the studies conclude. Neanderthals were thought to have already been adapted to a chillier, more northern environment.

Perhaps most notably, Neanderthal DNA was not found in genes that influence testicles or the X chromosome, according to the Nature study, hinting that when the Neanderthal ventured outside his species for sex, the introduction of his DNA may have reduced male fertility in early humans. As a result, evolution wiped away the Neanderthal DNA that negatively affected procreation.

“There’s strong evidence that when the two met and mixed, they were at the edge of biological compatibility,” said Nature study author and Harvard University geneticist David Reich. “The people who eventually survived and thrived had quite a bit of hurdles to overcome.”


Scientist found the bones of a Neanderthal female in a Siberian cave. (Bence Viola/Max Planck Institute for Evolutionary Biology)

This is consistent with what is seen in nature: When two species mate that are sufficiently far away biologically, the resulting hybrids tend to have lowered fertility. Early humans and Neanderthals interbred about 40,000 to 80,000 years ago around the Middle East, during man’s migration out of Africa.

And the last Neanderthals died off some 30,000 years ago.

Reich’s team used an ancient genome his lab had sequenced last year — as high-quality as any modern DNA data set — from a 50,000-year-old female Neanderthal’s toe bone found in a Siberian cave. They compared her data with 1,004 genomes of present-day humans, including those of sub-Saharan Africans. The Science study, led by University of Washington geneticist Joshua Akey, used only East Asian and European sequences, because indigenous Africans possess little or no traces of Neanderthal.

Because Neanderthals occupied Europe and Asia, African ancestors did not have the opportunity to interbreed with them. Reich and his colleagues used the African sequences as a sort of negative control; if parts of the ancient genome were found in East Asians and Europeans, but not in Africans, then those parts may have carried over from Neanderthals. They also found some Neanderthal DNA in genes associated with diseases such as lupus, Crohn’s disease and Type 2 diabetes.

“Because they contributed part of our genome, they contributed part of our risk for disease,” Reich said. But he cautions that such data shouldn’t be over-interpreted, especially because the genes passed down compose such a small fraction of our genetic blueprint. Non-African humans inherit about 1 to 3 percent of their genomes from Neanderthal ancestors, with East Asians tending to have a slightly larger proportion than Europeans.

“Although it’s true that each individual has only a small percentage of Neanderthal DNA, the small sequence that I carry might be different than the amount that you carry,” Akey said.

In total, he found that all the sequence bits among his analysis population of 379 European and 286 East Asian subjects spanned about 20 percent of the Neanderthal genome. As opposed to Reich, Akey scanned the modern genomes without comparing against the ancient DNA, finding regions that were likely to be contributed by a certain era’s ancestors. Only later did he compare those parts with the Neanderthal reference genome.

Geneticist Edward Rubin of the Lawrence Berkeley National Laboratory, who was not involved in the studies but has sequenced sections of the Neanderthal genome, found the results plausible and interesting.

“I was stunned by the public interest in Neanderthals,” he said. “Everybody wanted to know two things: whether we had sex with them, and we did, and what happened to them.”

Their DNA has confirmed interbreeding, but scientists don’t know why these hominids failed to survive. Theories abound; some suggest a violent genocide at the hands of Homo sapiens, others say they fell short and died off.

“They kind of disappear from the archeological record, and it’s tempting to think that they were out-competed for resources,” Reich said. “But we know they got incorporated into modern humans, and they live on in us today.”

Kim is a freelance science journalist based in Philadelphia.

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