Neanderthals may not have truly gone extinct, but instead may have been absorbed into the modern human population. That’s one of the conclusions of a new study that finds modern human DNA may have made up 2.5% to 3.7% of Neanderthal genome.
“This study really highlights that what we think of as a separate Neanderthal lineage was really more interconnected with our ancestors,” Fernando Villanea, a population geneticist at the University of Colorado Boulder who was not involved in the study, told Live Science. Both modern human and Neanderthal populations “share a long history of exchange of 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 the ancestors of modern humans who 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 may have entered the Neanderthal genome. This is largely due to the fact that there are currently only three known high-quality examples of a complete Neanderthal genome that have survived—from specimens found in Vindija Cave in Croatiawhich date from 50,000 to 65,000 years ago, and Chagarskaya and Denisova caves in Russia that date from about 80,000 and 50,000 years ago, respectively.
For comparison, scientists have sequenced the genomes of hundreds of thousands of modern humans following the completion of the Human Genome Project in 2003.
“There is a significant amount of research focused on how interbreeding between Neanderthals and modern humans affected our DNA and evolutionary history,” the study’s senior author Joshua Aki, a population geneticist at Princeton University in New Jersey, told Live Science. “However, we know much less about how these encounters affected Neanderthal genomes.”
In the new study, the scientists rely on the fact that both modern humans and Neanderthals typically possess two versions of each gene, one inherited from the father, the other from the mother. Because the two groups were more different from each other than from others of their own species, interbreeding between Neanderthals and humans would have resulted in offspring that had a greater chance of having two different versions of each gene—a situation known as heterozygosity – than children not resulting from such interbreeding.
The researchers compared the genomes of the three Neanderthals to those of 2,000 modern humans. They found that the Neanderthal genome may comprise 2.5% to 3.7% of modern human DNA. This is similar to 1 in 30 modern human parents in the ancestral Neanderthal population.
The research team’s analysis suggests that modern human DNA entered the Neanderthal genome during at least two distinct epochs of interbreeding — 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 any detectable traces in the Neanderthal genome, Aki said.
A a recent, as yet unverified study suggests that most of the Neanderthal DNA seen in the modern human genome is the result of one major interbreeding period 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, probably left no discernible trace in our genome.
Skulls found in Skhul and Qafzeh Caves in Israel date back to around 100,000 years ago – around the same time as one of the main interbreeding events identified in the study. These fossils look like modern human remains, but still have relatively primitive features like larger eyebrows that may be “signs of gene flow from Neanderthals,” Chris Stringerpaleoanthropologist 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 between the three Neanderthal genomes, the new study also suggests that the long-term average Neanderthal population was about 20% smaller than previously estimated. “That doesn’t sound like a big difference, but given that Neanderthals were already estimated to be a relatively small population, the fact that it was even smaller is an important insight,” Aki said.
These new smaller estimates of Neanderthal population size suggest that Neanderthals may have gone extinct because “they were simply swallowed up by the modern human population,” Aki said. “Repeated waves of modern human migrations out of Africa eventually overwhelmed Neanderthals’ ability to remain a distinct population, and eventually they were simply assimilated into the modern human gene pool.”
Future research could examine the biological effects, good or bad, that modern human DNA may have had in Neanderthals, Aki said.
The scientists described their findings online Thursday (July 11) in the journal Science.
