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The 2010 discovery that early humans and Neanderthals once interbred was a scientific bombshell: the revelation of a genetic legacy that now plays a role in the lives of modern humans, influencing circadian rhythms, immune system function and the way some people experience pain.
But scientists have found it surprisingly difficult to reconstruct gene flow in the opposite direction: how mixing between the two groups of Neanderthals, who died out about 40,000 years ago, may have shaped their lives. Using new techniques, a new study paints a clearer picture.
The analysis, published July 12 in the journal Science, shows that the two groups exchanged DNA at multiple points over the past 250,000 years, potentially shedding light on how Neanderthals disappeared and potentially rewriting the story of how and when our ancestors, Homo sapiens, left Africa.
“So far, most genetic evidence suggests that modern humans evolved in Africa 250,000 years ago, stayed there for the next 200,000 years, and then decided to leave Africa 50,000 years ago and populate the rest of the world,” said Joshua Akey, a professor at the Lewis-Sigler Institute at Princeton University and lead author of the study.
“But genetics is essentially blind to anything that doesn’t leave ancestry in current populations. What I think is cool about this (paper) is that it provides genetic insights into these out-of-Africa dispersals that we couldn’t see before,” Akey said.
The findings suggest that early human history was complex and that modern humans likely interacted with Neanderthals and other archaic humans, including the enigmatic Denisovans, much more frequently than previously thought since our emergence as a species some 250,000 to 300,000 years ago.
Multiple mating episodes
By comparing DNA sequences in databases, scientists can reconstruct relationships between different populations or species. And because genetic change occurs at a steady rate over the course of a generation, geneticists can calculate the time that elapses between when two groups exchange DNA, like the ticking of a molecular clock.
The study found that humans left Africa, encountered Neanderthals and interbred with them in three waves: the first wave occurred about 200,000 to 250,000 years ago, not long after the very first fossils of Homo sapiens appeared in Africa; the second wave occurred 100,000 years ago, and the final wave occurred about 50,000 to 60,000 years ago.
The most recent episode has been widely recognized, first identified in 2010 when the first Neanderthal genome was sequenced by Nobel Prize-winning geneticist Svante Pääbo. The new research, however, showed that the first two waves were significantly different from that third, a sweeping migration that eventually led to modern humans living in every corner of the world.
The scientists found that the percentage of Homo sapiens DNA in the Neanderthal genome may have been as high as 10% 200,000 years ago and decreased over time. On average, the percentage was between 2.5% and 3.7%.
A similar study published last year identified genetic traces of an encounter between the two groups about 250,000 years ago. However, the contribution of Homo sapiens DNA to Neanderthals about 100,000 years ago is a new discovery, said Laurits Skov, a geneticist and postdoctoral researcher at the University of California, Berkeley, who was not involved in the study.
“What does seem certain is that human and Neanderthal history is much more intertwined than we previously thought,” he said via email.
Genetic research
During the two previous waves of interbreeding, the Neanderthal population adopted human genes and the descendants remained within the Neanderthal groups, the new research finds.
These early mating episodes, the result of small bands of pioneering Homo sapiens migrating out of Africa (but failing to gain a foothold), left little trace in the gene pool of modern human populations but had a major impact on the Neanderthal genome, Akey said.
“I think the simplest explanation is that this reflects changes in population size over time,” he added.
“Initially, (early) modern humans came out of Africa slowly, and the Neanderthal populations were large enough to essentially absorb these initial dispersals of people and their genes into the Neanderthal population,” Akey explains.
When Homo sapiens left Africa about 60,000 years ago and began a long migration around the world, the descendants resulting from the encounters between Homo sapiens and Neanderthals grew up within modern human populations and their genetic signature remained in the human gene pool, which continues to have an impact today, he added.
In the study, the team used machine learning techniques to decode and sequence the genomes of the remains of three Neanderthals, which dated from 50,000 to 80,000 years ago and were found at three different sites: Vindija, Croatia, and Denisova and Chagyrskaya caves in the Altai Mountains. The researchers then compared that data to the genomes of 2,000 modern-day humans.
“We developed a framework to determine whether gene flow from humans to Neanderthals occurred, to estimate how much modern human sequence is in the Neanderthal genome, and to identify the specific sites in the Neanderthal genome that … carry modern human sequences,” Akey said.
Mystery of the Disappearance of the Neanderthals
There are a handful of Homo sapiens fossils that may indicate the species’ early, less successful journeys from Africa to the Middle East and Europe, said Chris Stringer, a research leader in human evolution at the Natural History Museum in London, who was not involved in the study.
These relics include a Homo sapiens fossil found in the Apidima cave in southern Greece that dates back 210,000 years, and remains found at the Israeli sites of Skhūl and Qafzeh. The fossils found in Israel had “primitive features” such as larger eyebrows, flatter skulls and variable chins.
“I have interpreted these features as being inherited from more primitive non-Neanderthal ancestors, but they could also be signs of gene flow from Neanderthals, and perhaps we should now re-examine such features in light of this new work,” Stringer said.
The population dynamics identified in this study could be a key reason why Neanderthals disappeared 40,000 years ago, Akey noted. The researchers’ analysis suggests that the size of the Neanderthal population at that time was 20 percent smaller than previously thought.
“Human populations were larger and, like waves crashing on a beach, eventually eroded the Neanderthals,” with the Neanderthal gene pool likely being absorbed into the human population in the final wave of interbreeding, Akey said.
“Extinction is complicated, so I would hesitate to say it’s the only explanation … but I think the incorporation of Neanderthals into human populations probably explains a significant part of why Neanderthals disappeared,” he added.
Stringer said he agreed that the final phase of interbreeding may have contributed to the Neanderthal extinction, with the Neanderthal population becoming even smaller and less diverse as Neanderthal DNA entered the larger human gene pool.
“I think that’s an important point,” Stringer said. “If you ignore the increase in genetic diversity of Neanderthals from interbreeding with sapiens, their effective population size is also significantly reduced, which provides further evidence that late Neanderthals may already have been an endangered species even without competition from a growing Homo sapiens population.”
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