Neanderthals may not have actually gone extinct, but they may have been absorbed into modern human populations. That’s one implication of a new study, which shows that modern human DNA may make up 2.5% to 3.7% of the Neanderthal genome.
“This research underscores that what we consider a distinct Neanderthal lineage was actually more closely linked to our ancestors,” Fernando Villaneaa population geneticist at the University of Colorado Boulder who was not involved in the study, told Live Science. Both modern human and Neanderthal populations “shared a long history of exchanging individuals.”
Neanderthals were among the closest extinct relatives of modern humans, with our lineages diverging about 500,000 years ago. More than a decade ago, scientists revealed that Neanderthals interbred with ancestors of modern humans that traveled out of Africa. Today, the genomes of modern human groups outside of Africa contain about 1% to 2% of Neanderthal DNA.
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However, researchers know less about how modern human DNA entered the Neanderthal genome. That’s largely because there are currently only three known high-quality examples of a complete Neanderthal genome that have survived — from specimens excavated in Vindija cave in Croatiadating from 50,000 to 65,000 years ago, and Chagyrskaja And Deniseva caves in Russia, which are about 80,000 and 50,000 years old respectively.
For comparison, scientists have analyzed the genomes of hundreds of thousands of modern people since the completion of the Human Genome Project in 2003.
“There has been a lot of research into how mating between Neanderthals and modern humans has influenced our DNA and our evolutionary history,” said the study’s lead author. Joshua Akeya population geneticist at Princeton University in New Jersey, told Live Science. “However, we know much less about how these encounters affected the genomes of Neanderthals.”
In the new study, scientists based their findings on the fact that both modern humans and Neanderthals generally have two versions of each gene, one inherited from their father and the other from their mother. Because the two groups were more different from each other than they were from others of their own species, interbreeding between Neanderthals and humans would have resulted in offspring that were more likely to have two different versions of each gene — a condition known as heterozygosity — than children who weren’t the result of such interbreeding.
The researchers compared the genomes of the three Neanderthals with those of 2,000 modern humans. They found that the Neanderthal genome may contain between 2.5% and 3.7% modern human DNA. That’s comparable to 1 in 30 modern human parents in the ancestral Neanderthal population.
The research team’s analysis suggested that modern human DNA entered the Neanderthal genome during at least two different interbreeding episodes: one about 200,000 to 250,000 years ago, and the other about 100,000 to 120,000 years ago. Interbreeding may have occurred at other times, but such events may not have left detectable traces in the Neanderthal genome, Akey said.
a recent, not yet peer-reviewed study suggests that most of the Neanderthal DNA seen in the modern human genome is the result of a single major period of interbreeding about 47,000 years ago that lasted about 6,800 years. Interbreeding that occurred at other times, such as the earlier events that affected the Neanderthal genome, likely left no detectable trace in our genome.
Skulls found in the Skhul and Qafzeh Caves in Israel date to about 100,000 years ago — about the same time as one of the major interbreeding events identified in the study. Those fossils appear to be modern human remains, but they still have relatively primitive features like larger eyebrows, which could be “signs of gene flow from Neanderthals” Chris Strijkera paleoanthropologist at the Natural History Museum in London who was not involved in the new study, told Live Science.
By analyzing the level of genetic variation seen across the three Neanderthal genomes, the new study also suggested that the average Neanderthal population was about 20 percent smaller over the long term than previously estimated. “This doesn’t sound like a big difference, but given that Neanderthals were already estimated to have a fairly small population size, the fact that it was even smaller is an important insight,” Akey said.
These new smaller estimates of Neanderthal population size suggest that Neanderthals may have disappeared because “they were simply absorbed into the modern human population,” Akey said. “Returning waves of modern human migrations out of Africa eventually overwhelmed the ability of Neanderthals to remain a distinct population, and they were eventually simply absorbed into the modern human gene pool.”
According to Akey, future research could reveal what biological effects, good or bad, modern human DNA had on Neanderthals.
The scientists published their findings online Thursday (July 11) in the journal Science.