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In 2010, the discovery that early humans and Neanderthals interbred was groundbreaking, revealing a genetic legacy affecting modern humans‘ circadian rhythms, immune systems, and pain perception. However, understanding the gene flow in the opposite direction has been challenging. A new study published in the journal Science on July 12 has shed light on how this intermingling shaped Neanderthals, suggesting multiple episodes of DNA exchange over 250,000 years, thus rethinking the story of Homo sapiens‘ migration out of Africa, reported CNN.
Most genetic data indicates that modern humans evolved in Africa 250,000 years ago, remained there for 200,000 years, and then dispersed globally around 50,000 years ago. “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 the study’s senior author.
“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 added.
The findings indicate that early human interactions with Neanderthals and other archaic humans, including Denisovans, were more frequent than previously believed since the emergence of Homo sapiens about 250,000 to 300,000 years ago. By comparing DNA sequences in databases, scientists can reconstruct relationships between populations or species and calculate the time since DNA exchanges occurred.
The study found that humans left Africa and interbred with Neanderthals in three waves: the first between 200,000 to 250,000 years ago, shortly after the first Homo sapiens fossils appeared in Africa; the second around 100,000 years ago; and the third between 50,000 to 60,000 years ago. The most recent episode from 50,000 years ago is already widely acknowledged and was first identified in 2010 after sequencing the first Neanderthal genome.
The research revealed that the DNA contribution of Homo sapiens to Neanderthals was significant in earlier waves, making up as much as 10% of the Neanderthal genome over 200,000 years ago and decreasing over time to an average of 2.5% to 3.7%. Laurits Skov, a geneticist and postdoctoral researcher at the University of California Berkeley who wasn’t involved in the study, noted that a similar study last year identified a genetic exchange around 250,000 years ago. However, the contribution around 100,000 years ago was a new finding.
“What seems certain though is that human and Neanderthal history is much more interwoven than we had previously thought,” Skov said via email.
During the earlier waves of interbreeding, Neanderthals incorporated human genes, and their offspring remained within Neanderthal groups. These early mating episodes resulted from small groups of pioneering Homo sapiens migrating out of Africa but not establishing strong populations outside African territories. Consequently, their genetic impact is not significant in modern human populations but did influence the Neanderthal genome considerably.
Akey noted that population size differences could explain why early Homo sapiens did not leave a large genetic record in Neanderthals initially. “I think the simplest explanation is this reflects changes in population sizes over time,” Akey stated. “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.”
When Homo sapiens left Africa around 60,000 years ago in a more substantial migration, the offspring of Homo sapiens-Neanderthal encounters remained within modern human populations, thus influencing our gene pool today. Using machine learning, the research team decoded and sequenced genomes from three Neanderthals dating back 50,000 to 80,000 years, found in Croatia and the Altai Mountains. They compared this 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 explained.
Researchers believe the population dynamics discovered could explain why Neanderthals disappeared 40,000 years ago. The analysis suggests Neanderthal population size was 20% smaller than previously thought. Akey added, “Human populations were larger, and like waves crashing on the beach, eventually eroded the Neanderthals,” implying Neanderthal genes were likely absorbed into the human population during the last wave of interbreeding.
“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 noted.
Chris Stringer, research lead in human evolution at the Natural History Museum in London, agreed. He stated that Neanderthal extinction might have been influenced by the last phase of interbreeding, which reduced Neanderthal diversity as their DNA entered the larger human gene pool. Stringer emphasized, “I think that is an important point. 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.”
There are some Homo sapiens fossils, like those found in Greece and Israel, that may reflect these early, less successful migrations out of Africa. These fossils often show traits considered primitive, such as larger brows and variable chins, possibly due to gene flow from Neanderthals.
“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.
Most genetic data indicates that modern humans evolved in Africa 250,000 years ago, remained there for 200,000 years, and then dispersed globally around 50,000 years ago. “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 the study’s senior author.
“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 added.
The findings indicate that early human interactions with Neanderthals and other archaic humans, including Denisovans, were more frequent than previously believed since the emergence of Homo sapiens about 250,000 to 300,000 years ago. By comparing DNA sequences in databases, scientists can reconstruct relationships between populations or species and calculate the time since DNA exchanges occurred.
The study found that humans left Africa and interbred with Neanderthals in three waves: the first between 200,000 to 250,000 years ago, shortly after the first Homo sapiens fossils appeared in Africa; the second around 100,000 years ago; and the third between 50,000 to 60,000 years ago. The most recent episode from 50,000 years ago is already widely acknowledged and was first identified in 2010 after sequencing the first Neanderthal genome.
The research revealed that the DNA contribution of Homo sapiens to Neanderthals was significant in earlier waves, making up as much as 10% of the Neanderthal genome over 200,000 years ago and decreasing over time to an average of 2.5% to 3.7%. Laurits Skov, a geneticist and postdoctoral researcher at the University of California Berkeley who wasn’t involved in the study, noted that a similar study last year identified a genetic exchange around 250,000 years ago. However, the contribution around 100,000 years ago was a new finding.
“What seems certain though is that human and Neanderthal history is much more interwoven than we had previously thought,” Skov said via email.
During the earlier waves of interbreeding, Neanderthals incorporated human genes, and their offspring remained within Neanderthal groups. These early mating episodes resulted from small groups of pioneering Homo sapiens migrating out of Africa but not establishing strong populations outside African territories. Consequently, their genetic impact is not significant in modern human populations but did influence the Neanderthal genome considerably.
Akey noted that population size differences could explain why early Homo sapiens did not leave a large genetic record in Neanderthals initially. “I think the simplest explanation is this reflects changes in population sizes over time,” Akey stated. “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.”
When Homo sapiens left Africa around 60,000 years ago in a more substantial migration, the offspring of Homo sapiens-Neanderthal encounters remained within modern human populations, thus influencing our gene pool today. Using machine learning, the research team decoded and sequenced genomes from three Neanderthals dating back 50,000 to 80,000 years, found in Croatia and the Altai Mountains. They compared this 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 explained.
Researchers believe the population dynamics discovered could explain why Neanderthals disappeared 40,000 years ago. The analysis suggests Neanderthal population size was 20% smaller than previously thought. Akey added, “Human populations were larger, and like waves crashing on the beach, eventually eroded the Neanderthals,” implying Neanderthal genes were likely absorbed into the human population during the last wave of interbreeding.
“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 noted.
Chris Stringer, research lead in human evolution at the Natural History Museum in London, agreed. He stated that Neanderthal extinction might have been influenced by the last phase of interbreeding, which reduced Neanderthal diversity as their DNA entered the larger human gene pool. Stringer emphasized, “I think that is an important point. 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.”
There are some Homo sapiens fossils, like those found in Greece and Israel, that may reflect these early, less successful migrations out of Africa. These fossils often show traits considered primitive, such as larger brows and variable chins, possibly due to gene flow from Neanderthals.
“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.
