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Only a small fraction of our DNA is exclusively human

Genetic adjustments that make humans human can only appear in small plots interspersed with DNA inherited from extinct ancestors and cousins.

Researchers report on July 16 in Science Advances that only 1.5 to 7 percent of the collective human genetic instruction book or genome contains human DNA exclusively.

Human-only DNA, spread throughout the genome, tends to contain genes involved in brain development and function, suggesting that the evolution of the brain was important in making humans human. But researchers still don’t know exactly what genes do and how unique human adjustments to DNA near these genes can affect brain evolution.

“I don’t know if we will ever be able to say what makes us human exclusively,” says Emilia Huerta-Sanchez, a population geneticist at Brown University in Providence, R.I., who did not participate in the study. "We don't know if that makes us think in a specific way or if we have specific behaviors." And Neanderthals and Denisovans, both extinct human cousins, may have thought the way humans do (SN: 22/02/18).

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The results do not mean that people are primarily Neanderthals or Denisovans, or some other mixture of ancient hominids. The researchers found (SN: 4/7/21) that, on average, people in sub-Saharan Africa inherited between 0.096 and 0.46 percent of their DNA from ancient interbreeding between their human and Neanderthal ancestors. Non-Africans inherited more DNA from Neanderthals: 0.73 to 1.3%. And some people have also inherited a fraction of their denisovans DNA.

Using a new computational method, researchers at the University of California, Santa Cruz examined all DNA spots in the genomes of 279 people. The team compiled the results of those individual genomes into a collective image of the human genome. For each point, the team determined whether the DNA came from Denisovans, Neanderthals, or inherited from a common ancestor of humans and those lost relatives.

Although each person can carry about 1 percent Neanderthal DNA, "if you look at a couple of hundred people, most won't have their piece of Neanderthal DNA in the same place," says Kelley Harris, a population geneticist at the University of Washington in Seattle who did not participate in the work. "So if you add up all the regions where someone has a little Neanderthal DNA, they'll soon cover most of the genome."

In this case, about 50 percent of the collective genome contains regions where one or more people inherited DNA from Neanderthals or Denisovans, the researchers found. Most of the rest of the genome has been passed down from the most recent common ancestor of humans and their extinct cousins. After removing the old inherited DNA, the team looked for regions where all people have specific settings for DNA that no other species has. This meant that the estimate of human DNA exclusively was between 1.5 and 7 percent of the genome.

The finding underscores the amount of crossbreeding with other hominid species that has affected the human genome, says co-author Nathan Schaefer, a computational biologist at the University of California, San Francisco. The researchers confirmed previous findings from other groups that humans raised with Neanderthals and Denisovans, but also with other unknown hominids (SN: 2/12/20). It is not known whether these mysterious ancestors are the groups that included "Dragon Man" or Nesher Ramla Homo, who may be closer relatives of humans than Neanderthals (SN: 25/06/21; SN: 24/06/21). And mixing and blending probably occurred several times between different groups of humans and hominids, Schaefer and colleagues found.

The adjustments that make human DNA distinctive have emerged in a couple of evolutionary explosions, probably about 600,000 years ago and about 200,000 years ago, the team found. About 600,000 years ago it was the time when humans and Neanderthals formed their own branches of the hominid family tree.

Estimating the amount of human DNA exclusively does not take into account the places where humans gained DNA by duplication or other means or lost it, says James Sikela, a genome scientist at Anschutz Medical Campus at the University of Colorado at Aurora, who was not He did not participate in the study (SN: 8/6/15). Such extra or missing DNA may allow humans to evolve new traits, including some involved in brain evolution (SN: 3/9/11; SN: 26/02/15).

Ancient DNA was usually degraded into small fragments and the researchers put together only portions of the genome of the extinct hominids. Fragmented genomes make it difficult to know where large chunks of DNA have been lost or gained. For that reason, the researchers studied only small adjustments to DNA that include one or more DNA bases: the parts of the molecule that carry information. Given that humans and Neanderthals followed their evolutionary pathways separately relatively recently, it is not surprising that only 7 percent or less of the genome has evolved exclusively human adjustments, Sikela says. "I don't get that number." Considering the DNA that humans have only added to their genomes can result in a higher estimate of exclusively human DNA, he said.

Or it could go the other way. As more genomes are deciphered from Neanderthals, Denisovans, and other extinct hominids, researchers may find that some of what now look like human DNA exclusively were also carried by those extinct relatives, Harris says. "This estimate of the number of human regions exclusively will only go down."

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