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“To date, most genetic data suggests that modern humans evolved in Africa 250,000 years ago, stayed put for the next 200,000 years, and then decided to disperse out of Africa 50,000 years ago and go on to people the rest of the world,” said Joshua Akey, a professor at the Lewis-Sigler Institute at Princeton University and senior author of the study.

“But genetics is essentially blind to anything that doesn’t leave ancestry to present day populations. What I think (is) kind of cool about this (paper) is that it provides genetic insights into these dispersals out of Africa that we previously weren’t able to see,” Akey said.

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By comparing DNA sequences in databases, scientists can reconstruct relationships between different populations, or species, and because genetic changes take place at a steady rate over the course of a generation, geneticists can calculate the time elapsed between when two groups exchanged DNA — like ticks on a molecular clock.

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“What seems certain though is that human and Neanderthal history is much more interwoven than we had previously thought,” he said via email.

During the two earlier waves of interbreeding, the Neanderthal population absorbed human genes and the offspring stayed within Neanderthal groups, according to the new study.

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“I think the simplest explanation is this reflects changes in population sizes over time,” he added.

“At first, (early) modern humans were trickling out of Africa, and Neanderthal populations were large enough that they were able to essentially absorb these initial dispersals of humans and their genes into the Neanderthal population,” Akey explained.

However, when Homo sapiens left Africa around 60,000 years ago in a lasting migration around the world, the offspring resulting from Homo sapiens-Neanderthal encounters grew up within modern human populations and their genetic signature remained within the human gene pool, influencing our lives today, he added.

In the study, the team used machine learning techniques to decode and sequence genomes from the remains of three Neanderthals, which dated from 50,000 to 80,000 years ago and were found in three different locations: Vindija, Croatia, and Denisova and Chagyrskaya caves in the Altai Mountains. The researchers then compared that data with the genomes of 2,000 present-day humans.

“We developed a framework to determine if human to Neanderthal gene flow occurred, estimate how much modern human sequence are in Neanderthal genomes, and identify the specific places in the Neanderthal genome that are carrying …modern human sequences,” Akey said.

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“I’ve interpreted (these) traits (as) retained from more primitive non-Neanderthal ancestors, but they could alternatively be signs of gene flow from Neanderthals, and perhaps such characteristics should be looked at again now, in the light of this new work,” Stringer said.

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“Human populations were larger, and like waves crashing on the beach, eventually eroded the Neanderthals,” with the Neanderthal gene pool likely absorbed into the human population in the last wave of interbreeding, Akey said.

“Extinction is complicated, so I think I would be hesitant to say it’s the only explanation … but I think the absorption of Neanderthals in human populations likely explains a significant amount of why the Neanderthals disappeared,” he added.

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“I think that is an important point,” Stringer said. “Factoring out the increase in Neanderthal genetic diversity from interbreeding with sapiens also significantly reduces their effective population size, adding further evidence that the late Neanderthals might already have been an endangered species even without competition from an expanding Homo sapiens population.”

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