People of European and Asian descent today retain Neanderthal DNA that may affect their hair, skin, fertility, predisposition to certain diseases and possibly other characteristics, a new study in the journal Nature suggests.

The genetic material inherited from Neanderthals combined with that of humans when the two species interbred 40,000 to 80,000 years ago, the study holds. The research further supports that indigenous Africans possess little or no Neanderthal DNA because their ancestors did not breed with Neanderthals, which lived in Europe and Asia.

It now appears that mating between the two species was much more prevalent than was previously suspected.

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Some genetic mutations introduced by Neanderthals were not beneficial to humans. Neanderthals' contribution to modern DNA was partially removed by natural selection over time.

“Given the large amount of Neanderthal alleles (gene variants) that were swept away by selection, we think that there was a larger fraction of Neanderthal ancestry initially,” lead author Sriram Sankararaman explained to Discovery News, adding that “we think that this ancestry was reduced by a third.”

Sankararaman, a post-doctoral researcher at Harvard Medical School’s Department of Genetics, co-authored the paper with leading evolutionary geneticists, such as Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology and Harvard’s David Reich.

The researchers analyzed genetic variants in 846 people of non-African heritage, 176 people from sub-Saharan Africa and a 50,000-year-old Neanderthal.

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The clearest indicator that a gene variant came from a Neanderthal was if the variant appeared in some non-Africans and the Neanderthal, but not in the sub-Saharan Africans.

Levels of Neanderthal ancestry differ in European and Asian groups, according to the study. Han Chinese people in Beijing, for example, have the most such ancestry while Puerto Ricans have the least.

A replica of a Neanderthal is dressed in modern clothes at the Neanderthal Museum in Mettmann, Germany. Federico Gambarini/Corbis

All Europeans and Asians, however, retain Neanderthal genes affecting keratin, which is a fibrous protein in skin and hair. Reich explained that keratin makes skin, hair and nails tougher and better able to withstand cold temperatures. 

“It’s tempting to think that Neanderthals were already adapted to the non-African environment and provided this genetic benefit to humans,” Reich said.

It's possible that the lighter skin and hair of many Europeans was also influenced by Neanderthal ancestry, but Sankararaman indicated that further research is needed to fully make that connection.

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The study additionally found that genetic variants passed down from Neanderthals also affect an individual’s disposition toward type 2 diabetes, Crohn’s disease, lupus, a liver condition known as biliary cirrhosis and even whether a person is likely to smoke.

X chromosome-related genetic mutations from Neanderthals, along with DNA associated with male sexual organs, were more likely to have been incompatible with the human genome. These were less easily exchanged between the two species. People who still retain such Neanderthal DNA, like East Asians, experience reduced fertility as a probable result.

“This suggests that when ancient humans met and mixed with Neanderthals, the two species were at the edge of biological incompatibility,” Reich said.

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Daven Presgraves, an associate professor in the University of Rochester’s Department of Biology said the Nature paper implies humans migrating out of Africa were able to “borrow” genes associated with skin, hair and nails from Neanderthals “perhaps accelerating adaptation to a Eurasian environment that was new to them.”

The findings also strongly support the theory that Neanderthals were simply absorbed into the human gene pool. They are now, in essence, a part of many people.