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Neandertal hot spots highlighted in modern humans’ DNA

Stone Age people’s mating with now-extinct species had genetic pros and cons

1:19pm, January 29, 2014
Magazine issue: Vol. 185, March 8, 2014
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Humans appear to have inherited some traits related to skin, hair and some autoimmune diseases from Neandertal ancestors.

Two independent investigations identify for the first time the specific parts of the human genome that appear to have been most affected by Stone Age interbreeding with Neandertals. They locate part of Neandertals’ legacy in sections of present-day Europeans’ and East Asians’ DNA that are stocked with genes influencing the production of keratin, a key substance in skin, hair and nails. By occasionally mating with Neandertals after leaving Africa around 70,000 years ago, Stone Age humans inherited and retained keratin-related genes that must have aided survival outside Africa, propose computational geneticist Sriram Sankararaman of Harvard Medical School in Boston and his colleagues in the Jan. 30 Nature.

Neandertals lived in Europe and Asia between around 200,000 and 30,000 years ago. Previous studies estimated that 1 to 3 percent of non-Africans’ DNA today comes from Neandertals, while present-day Africans have little or no Neandertal ancestry.

Neandertals’ DNA contributions to modern humans also encompass genes related to several medical conditions, including lupus and Crohn’s disease, Sankararaman’s group says.

About 20 percent of the Neandertal genome shows up at various places in the DNA of current Europeans and East Asians, geneticists Benjamin Vernot and Joshua Akey of the University of Washington in Seattle conclude January 30 in Science.

These new reports represent “the first steps toward getting a genomic picture of the actual Neandertal individuals that mixed with modern humans,” remarks paleogeneticist Mattias Jakobsson of Uppsala University in Sweden.

The genome of a Neandertal woman who lived about 50,000 years ago has already been sequenced. The two research teams compared it with modern-day humans’ DNA, using different statistical techniques. Future work will be able to use genomes from additional Neandertals to home in on genes that modern humans inherited through particular instances of Stone Age interbreeding.

Sankararaman’s team developed a method for calculating the probability that modern human gene variants and DNA segments containing multiple genes came from Neandertals. The researchers compared the Neandertal woman’s genome with the DNA of 1,004 modern-day humans living in different parts of the world.

If, for instance, a non-African person carried a gene variant found in Neandertals but not in present-day West Africans, whose ancestors do not appear to have interbred with Neandertals, the researchers concluded that that gene variant probably originated in Neandertals.

In an analysis of DNA from 379 Europeans and 286 East Asians, Vernot and Akey identified unusually long chains of gene variants that people probably inherited via Stone Age interbreeding, presumably from Neandertals. These Neandertal hot spots did not appear in the DNA of 13 West Africans.

Comparisons with the Neandertal woman’s DNA enabled the researchers to narrow down their list of modern human DNA segments inherited from the extinct Stone Age species.

Sankararaman’s group found that far fewer signs of Neandertal ancestry appeared on the X chromosome and along a stretch of DNA containing genes that affect the testicles than in other parts of modern humans’ genomes. Genes that reduce male fertility tend to accumulate on the X chromosome when closely related species of modern animals interbreed, suggesting that such genes initially passed from Neandertals to humans before disappearing due to natural selection. Neandertal genes that compromised how the testicles work may have met the same fate.

Patterns of surviving Neandertal DNA suggest that ancient interbreeding occurred many times across Europe and Asia, Vernot and Akey say.

Still, large swaths of Europeans’ and East Asians’ genomes contain unexpectedly little Neandertal DNA, Akey says. “These regions potentially are a roadmap to finding genes that make us human.”

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