A discovery in 2010 that early humans and Neanderthals interbred it was a scientific bombshell—the revelation of a genetic legacy that has since played a huge role in the lives of modern people, influencing biological rhythms, immune system function, and even the way some people feel pain.
Scientists, however, have discovered that it is surprisingly difficult to piece together gene flow in the opposite direction: how the mixture between the two groups may have influenced Neanderthals, which became extinct around 40,000 years ago. With the help of new techniques, a new study is shedding light on this question.
The analysis, published on July 12 in Science magazineshowed that the two groups exchanged DNA at various points over the last 250,000 years, shedding light on how Neanderthals disappeared and potentially rewriting the story of how and when our Homo sapiens ancestors left Africa.
“To date, most genetic data suggests that modern humans evolved in Africa 250,000 years ago, remained there for the next 200,000 years, and then decided to disperse out of Africa 50,000 years ago and settled throughout the rest of the world,” he said. Joshua Akey, a professor at Princeton University’s Lewis-Sigler Institute and senior author of the study.
“But genetics is essentially blind to anything that doesn’t leave ancestry for current populations. What I think is kind of cool about this one [artigo] is that it provides genetic insights into these out-of-Africa dispersals that we couldn’t see before,” Akey said.
The discoveries suggest that early human history was complex, and modern humans likely interbred with Neanderthals — and with other types of archaic humans, including the enigmatic Denisovans — much more frequently than previously known since our emergence as a species, around 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 changes occur at a constant rate over a generation, geneticists can calculate the time elapsed between the time when two groups exchanged DNA — like the ticking of a molecular clock.
The study found that humans left Africa, encountered and interbred with Neanderthals in three waves: one about 200,000 to 250,000 years ago, not long after the first Homo sapiens fossils appeared in Africa; another 100,000 years ago; and the last about 50,000 or 60,000 years ago.
The most recent episode is widely recognized and was first identified in 2010, when the first Neanderthal genome was sequenced by Nobel Prize-winning geneticist Svante Pääbo. However, new research has shown that the first two waves differed significantly from the third — a sweeping migration that ultimately led to modern humans residing in every corner of the globe.
Scientists have discovered that the percentage of Homo sapiens DNA in the Neanderthal genome may have reached 10% more than 200,000 years ago and decreased over time; on average, it was 2.5% to 3.7%.
A similar study published last year identified genetic traces of an encounter between the two groups about 250,000 years ago, but 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 seems certain, however, is that human and Neanderthal history are much more intertwined than we previously thought,” he said in an email.
Genetic detective
During the previous two waves of interbreeding, the Neanderthal population absorbed human genes and descendants remained within Neanderthal groups, according to the new study.
These early mating episodes, the result of small groups of pioneering Homo sapiens migrating—but not establishing a solid foothold—out of Africa, left little record in the genetics of modern human populations, but had a major impact on the Neanderthal genome, Akey explained.
“I think the simplest explanation is that it reflects changes in population size over time,” he added.
“In the beginning, (early) modern humans were moving out of Africa, and the Neanderthal populations were large enough that they could essentially absorb these early dispersals of humans and their genes into the Neanderthal population,” Akey explained.
However, when Homo sapiens left Africa about 60,000 years ago on a long-lasting migration around the world, the descendants resulting from encounters between Homo sapiens and Neanderthals grew up within modern human populations and their genetic signature remained in human genes, influencing our lives to this day, he added.
In the study, the team used machine learning techniques to decode and sequence genomes from the remains of three Neanderthals, which dated to 50,000 to 80,000 years ago and were found in three different locations: Vindija, Croatia, and the Denisova and Chagyrskaya caves in Altai Mountains.
The researchers then compared this data with the genomes of 2,000 current humans.
“We developed a framework to determine whether gene flow from humans to Neanderthals occurred, estimate how much modern human sequence there is in Neanderthal genomes, and identify the specific places in the Neanderthal genome that carry…modern human sequences,” Akey said.
Mystery of the disappearance of Neanderthals
There are a handful of Homo sapiens fossils that may reflect the species’ earliest and least successful journeys from Africa to the Middle East and Europe, said Chris Stringer, leader of human evolution research at London’s Natural History Museum, who doesn’t. was involved in the study.
These relics include a Homo sapiens fossil found in the Apidima Cave in southern Greece, dated to 210,000 years ago, and remains found at the Israeli sites of Skhūl and Qafzeh. Homo sapiens fossils found in Israel had “primitive features” such as larger eyebrows, flatter skulls and variable chins.
“I interpreted these features as retained from more primitive non-Neanderthal ancestors, but they could be signs of Neanderthal gene flow, and perhaps such features should be looked at again now in light of this new work,” Stringer said.
A Population dynamics identified in this research may be one of the main reasons why Neanderthals disappeared 40,000 years ago, noted Akey. The researchers’ analysis suggests that the size of the Neanderthal population at the time was 20% smaller than previously thought.
“Human populations were larger and, like waves crashing on the beach, they eventually eroded the Neanderthals,” with Neanderthal genetics 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 this is the only explanation… but I think the absorption of Neanderthals into human populations probably explains a significant portion of why Neanderthals disappeared,” he added.
Stringer said he agreed that the last phase of interbreeding may have contributed to the extinction of the Neanderthals, with the Neanderthal population becoming even smaller and less diverse as Neanderthal DNA became part of the human gene pool.
“I think that’s an important point,” Stringer said. “Factoring the increase in Neanderthal genetic diversity from interbreeding with Sapiens also significantly reduces their effective population size, adding further evidence that the last Neanderthals may have already been a threatened species even without competition from an expanding Homo sapiens population. .”
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