New research shows that recurrent episodes of gene flow, beginning 250,000 to 200,000 years ago, affected the genomes and biology of both modern humans and Neanderthals, and estimates that Neanderthals have 2.5 to 3.7% human ancestry.
Li et al. provide insights into the history of admixture between modern humans and Neanderthals, show that gene flow had substantial impacts on patterns of modern human and Neanderthal genomic variation, and show that accounting for human-introgressed sequences in Neanderthals enables more-accurate inferences of admixture and its consequences in both Neanderthals and modern humans. Image credit: Neanderthal Museum.
“This is the first time that geneticists have identified multiple waves of modern human-Neanderthal admixture,” said Southeast University’s Professor Liming Li.
“We now know that for the vast majority of human history, we’ve had a history of contact between modern humans and Neanderthals,” added Princeton University’s Professor Joshua Akey.
“The hominins who are our most direct ancestors split from the Neanderthal family tree about 600,000 years ago, then evolved our modern physical characteristics about 250,000 years ago.”
“From then until the Neanderthals disappeared — that is, for about 200,000 years — modern humans have been interacting with Neanderthal populations.”
Using genomes from 2,000 living humans as well as three Neanderthals and one Denisovan, the researchers mapped the gene flow between the hominin groups over the past quarter-million years.
They used a genetic tool they designed a few years ago called IBDmix, which uses machine learning techniques to decode the genome.
Scientists previously depended on comparing human genomes against a reference population of modern humans believed to have little or no Neanderthal or Denisovan DNA.
The study authors have established that even those referenced groups, who live thousands of miles south of the Neanderthal caves, have trace amounts of Neanderthal DNA, probably carried south by voyagers (or their descendants).
With IBDmix, they identified a first wave of contact about 200,000-250,000 years ago, another wave 100,000-120,000 years ago, and the largest one about 50,000-60,000 years ago. That contrasts sharply with previous genetic data.
“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,” Professor Akey said.
“Our models show that there wasn’t a long period of stasis, but that shortly after modern humans arose, we’ve been migrating out of Africa and coming back to Africa, too.”
“To me, this story is about dispersal, that modern humans have been moving around and encountering Neanderthals and Denisovans much more than we previously recognized.”
That vision of humanity on the move coincides with the archaeological and paleoanthropological research suggesting cultural and tool exchange between the hominin groups.
The key insight was to look for modern-human DNA in the genomes of the Neanderthals, instead of the other way around.
“The vast majority of genetic work over the last decade has really focused on how mating with Neanderthals impacted modern human phenotypes and our evolutionary history — but these questions are relevant and interesting in the reverse case, too,” Professor Akey said.
They realized that the offspring of those first waves of Neanderthal-modern matings must have stayed with the Neanderthals, therefore leaving no record in living humans.
“Because we can now incorporate the Neanderthal component into our genetic studies, we are seeing these earlier dispersals in ways that we weren’t able to before,” Professor Akey said.
The final piece of the puzzle was discovering that the Neanderthal population was even smaller than previously believed.
Genetic modeling has traditionally used variation — diversity — as a proxy for population size. The more diverse the genes, the larger the population.
But using IBDmix, the team showed that a significant amount of that apparent diversity came from DNA sequences that had been lifted from modern humans, with their much larger population.
As a result, the effective population of Neanderthals was revised down from about 3,400 breeding individuals down to about 2,400.
Put together, the new findings paint a picture of how the Neanderthals vanished from the record, some 30,000 years ago.
“I don’t like to say ‘extinction,’ because I think Neanderthals were largely absorbed,” Professor Akey said.
The idea is that Neanderthal populations slowly shrank until the last survivors were folded into modern human communities.
“This assimilation model was first articulated by Fred Smith, an anthropology professor at Illinois State University, in 1989. Our results provide strong genetic data consistent with Fred’s hypothesis, and I think that’s really interesting,” Professor Akey said.
“Neanderthals were teetering on the edge of extinction, probably for a very long time.”
“If you reduce their numbers by 10 or 20%, which our estimates do, that’s a substantial reduction to an already at-risk population.”
“Modern humans were essentially like waves crashing on a beach, slowly but steadily eroding the beach away.”
“Eventually we just demographically overwhelmed Neanderthals and incorporated them into modern human populations.”
The findings were published in the journal Science.
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Liming Li et al. 2024. Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 385 (6705); doi: 10.1126/science.adi1768
Source : Breaking Science News