Perhaps Neanderthals did not actually go extinct, but instead were absorbed into the modern human population. That’s one conclusion of a new study that found that modern human DNA may make up 2.5% to 3.7% of the Neanderthal genome.

“This study really highlights that what we thought was a separate Neanderthal lineage was actually more closely related to our ancestors,” Fernando Villanea, a population geneticist at the University of Colorado Boulder who was not involved in the research, told Live Science. “Both modern humans and Neanderthals “shared a long history of personality variation.”

Neanderthals were among the closest extinct relatives of modern humans, with our lineages diverging around 500,000 years ago. More than a decade ago, scientists discovered that Neanderthals had interbred with the ancestors of modern humans who had left Africa. Today, the genomes of modern humans outside Africa contain about 1–2% Neanderthal DNA.

But researchers know less about how modern human DNA might have entered the Neanderthal genome. This is largely because there are only three surviving high-quality samples of a complete Neanderthal genome: samples from Vindija Cave in Croatia, which date to 50,000–65,000 years ago, and samples from Chagyr and Denisova Caves in Russia, which date to 80,000 and 50,000 years ago, respectively.

For comparison: Scientists sequenced the genomes of hundreds of thousands of modern humans after the Human Genome project was completed in 2003.

“There has been a significant amount of research focused on how interbreeding between Neanderthals and modern humans influenced our DNA and evolutionary history,” senior study author Joshua Aki, a population geneticist at Princeton University in New Jersey, told Live Science. “But we know much less about how these encounters influenced Neanderthal genomes.”

In the new study, the scientists relied on the fact that both modern humans and Neanderthals tend to have two versions of each gene, one inherited from the father and one from the mother. Because the two groups differed more from other groups of their species, interbreeding between Neanderthals and humans may have resulted in offspring with a higher chance of having two different versions of each gene (a condition known as heterozygosity) than would have been the result of such a crossover.

Researchers compared the genomes of three Neanderthals to those of 2,000 modern humans. They found that the Neanderthal genome may consist of 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 team’s analysis suggested that modern human DNA entered the Neanderthal genome during at least two separate periods of interbreeding, one around 200,000 to 250,000 years ago and another around 100,000 to 120,000 years ago. Interbreeding may have occurred at other times, but such events may not have left visible traces in the Neanderthal genome, Aki said.

A new study, not yet peer-reviewed, suggests that most of the Neanderthal DNA found in the modern human genome is the result of a single major interbreeding period that lasted about 6,800 years, starting around 47,000 years ago. Like the earlier events that affected the Neanderthal genome, interbreeding that occurred at a different time likely left no visible trace in our genome.

The skulls, found in the Shul and Qafzeh caves in Israel, date to about 100,000 years ago, roughly the same time as one of the most significant interbreeding events identified in the study. The fossils appear to be modern human remains, but they still have relatively primitive features, such as larger eyebrows, which could be “signs of gene flow from Neanderthals,” said Chris Stringer, a paleoanthropologist at the Natural History Museum in London, who was not involved in the study. Live Science reports on the new study.

The new study, which analyzed the level of genetic diversity among three Neanderthal genomes, also found that the long-term population average of Neanderthals was about 20% smaller than previously thought. “It doesn’t seem like a big difference, but it’s an important idea that it was even smaller, given that Neanderthals already had a fairly small population,” Aki said.

These new lower estimates of Neanderthal population size suggest that Neanderthals may have disappeared because they were “swallowed up by the modern human population,” Aki said. “Repeated waves of migration of modern humans out of Africa eventually overwhelmed the ability of Neanderthals to persist as a distinct population, and they were eventually assimilated into the modern human gene pool.”

Aki said future research could examine the biological effects, good or bad, of modern human DNA on Neanderthals. The scientists detailed their findings Thursday in the journal Science.