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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 has since been discovered to play a role in the lives of modern people, influencing circadian rhythms, immune system function and the way some feel pain.
Scientists, however, have found it surprisingly difficult to piece together gene flow in the opposite direction: how mixing between the two groups may have shaped the Neanderthals, which went extinct about 40,000 years ago. With the help of new techniques, a new study is painting a clearer picture.
The analysis, published on July 12 in the journal Scienceshowed 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, stayed where they were for the next 200,000 years, and then decided to disperse from Africa 50,000 years ago and move on to populate 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 other than ancestry in current populations. What I think is cool about this (paper) is that it provides genetic information about these out-of-Africa dispersals that we weren’t able to see previously,” Akey said.
The findings suggest that very early human history was complex and that modern humans likely interacted with Neanderthals – and other types of archaic humans, including enigmatic Denisovans – much more frequently than previously recognized 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 when two groups exchanged DNA – like ticks. in 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 thousand years ago; and the last about 50,000 to 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 eventually led modern humans to reside 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, geneticist and postdoctoral researcher at the University. of California Berkeley, who was not involved in the study.
“What seems certain is that human and Neanderthal history are much more intertwined than we previously thought,” he said in an email.
Genetic detective work
During the first two waves of interbreeding, the Neanderthal population absorbed human genes and offspring remained within Neanderthal groups, according to the new study.
These first mating episodes, the result of the migration of small groups of pioneering Homo sapiens – but without establishing a solid base – out of Africa, left few records in the gene pool of modern human populations, but had a great impact on the Neanderthal genome. , Akey said.
“I think the simplest explanation is that this reflects changes in population size over time,” he added.
“In the beginning, the (first) modern humans were moving out of Africa, and the Neanderthal populations were large enough to be able to essentially absorb these initial dispersals of humans and their genes into the Neanderthal population,” Akey explained.
However, when Homo sapiens left Africa about 60,000 years ago in a long-lasting migration around the world, the descendants resulting from encounters between Homo sapiens and Neanderthals grew into 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 to 50,000 to 80,000 years ago and were found in three different locations: Vindija, Croatia, and 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 human-to-Neanderthal gene flow occurred, estimate the amount of modern human sequences in Neanderthal genomes, and identify the specific locations 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’ early and less successful journeys out of Africa toward the Middle East and Europe, said Chris Stringer, human evolution research leader at the Natural History Museum of London, who was involved in the study.
These relics include a Homo sapiens fossil found in Apidima Cave in southern Greece dated to 210,000 years ago and remains found at Israeli sites Skhul It is Qafzeh. 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 alternatively be signs of Neanderthal gene flow, and perhaps such features should be looked at again now in light of this new work,” Stringer said. .
The population dynamics identified in this research could be one of the main reasons why Neanderthals disappeared 40,000 years ago, Akey noted. 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 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 hesitate to say it’s the only explanation… but I think the absorption of Neanderthals into human populations probably explains a significant part 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 entered the larger human gene pool.
“I think that’s an important point,” Stringer said. “Factoring the increased genetic diversity of Neanderthals due to interbreeding with Sapiens also significantly reduces their effective population size, adding further evidence that the last Neanderthals may have already been an endangered species even without competition from a population of Expanding homo sapiens.”
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