An international team of researchers led by Josh Akey of Princeton University and Li-Ming Li of Southeast University reports that modern humans have been interbreeding with Neanderthals for over 200,000 years. Akey and Li identify the first wave of contact around 200,000-250,000 years ago, the next wave of contact 100,000-120,000 years ago, and the largest wave of contact around 50,000-60,000 years ago. They used a genetic tool called IBDmix, which uses AI instead of a modern human reference population, to analyze 2,000 modern humans, three Neanderthals, and one Denisovan. Photo by Matilda Luk, Princeton University
Geneticist Joshua Akey says that modern humans and Neanderthals interacted for 200,000 years.
New genetic research reveals extensive interbreeding and long-term interaction between Neanderthals, Denisovans and modern humans, suggesting a more integrated history than previously thought and supporting the theory that Neanderthals assimilated into modern human populations.
Since the first Neanderthal bones were discovered in 1856, curiosity about this ancient human species has grown. How were they different from us? How similar were they? Did our ancestors live in harmony with them? Did they fight with them? Did they love them? The recent discovery of a Neanderthal-like group that lived in Asia and South Asia, the Denisovans, raises new questions.
Now, an international team of geneticists and AI experts is writing a new chapter in our shared human story, under the direction of Professor Joshua Akey. Lewis Sigler Institute for Integrative Genomics, Princeton UniversityThe researchers found a history of genetic intermingling and exchange, suggesting that these early human populations were much closer connected than previously thought.
“This is the first time that geneticists have identified multiple waves of interbreeding between modern people and Neanderthals,” said Li-ming Li, a professor in the Department of Medical Genetics and Developmental Biology at Southeast University in Nanjing, China, who conducted the study as an associate investigator in Akey’s lab.
“We know that there was a history of contact between modern humans and Neanderthals for most of human history,” Akey says. Our most direct ancestors, hominins, split off from the Neanderthal family tree about 600,000 years ago and then evolved modern physical characteristics about 250,000 years ago.
Continuous exchanges over thousands of years
“Modern humans continued to interact with the Neanderthals for about 200,000 years until their extinction,” he said.
Their findings appear in the latest issue of the journal. Science.
Once thought to be slow and stupid, Neanderthals are now thought to have been skilled hunters and tool-makers who had sophisticated techniques for treating one another’s wounds and who thrived in Europe’s cold climate.
(Note: All of these hominin groups are human, but to avoid using the terms “Neanderthals,” “Denisovans,” and “ancient versions of our species,” most archaeologists and anthropologists use the abbreviations Neanderthals, Denisovans, and modern humans.)
Akey and his team used the genomes of 2,000 modern humans, three Neanderthals, and one Denisovan to map gene flow between hominin groups over the past 250,000 years. The researchers used genetic tools they designed. A few years Previous studies have used a machine learning technique called IBDmix to sequence genomes, but researchers have previously relied on comparing the human genome to “reference populations” of modern humans thought to have few or no Neanderthal or Denisovan genes. DNA.
Akey’s team found that even the populations mentioned, living thousands of miles south of the Neanderthal caves, carry traces of Neanderthal DNA that was likely carried south by voyagers (or their descendants). Using IBDmix, Akey’s team identified a first wave of contact about 200,000-250,000 years ago, a second wave 100,000-120,000 years ago, and a maximum wave of contact about 50,000-60,000 years ago.
Rethinking human migration models
This is in stark contrast to the genetic data to date, which suggests that modern humans evolved in Africa 250,000 years ago and remained there for another 200,000 years. after that “They dispersed out of Africa 50,000 years ago and decided to spread to other people all over the world,” Akey said.
“Our model shows that rather than a long period of stagnation, modern humans emerged shortly after and then migrated out of Africa and back again,” he said. “To me, the story is one of diffusion, and modern humans moved around a lot more than we’ve realized, encountering Neanderthals and Denisovans.”
This vision of migrating humans is consistent with archaeological and paleoanthropological studies that suggest exchanges of culture and tools between human groups.
Lee and Akey’s key insight was not to look for modern human DNA in the Neanderthal genome, but the other way around. “Much of the genetic research in the past decade has focused on how interbreeding with Neanderthals influenced modern human phenotype and evolutionary history, but these questions are also relevant and intriguing in the opposite direction,” Akey said.
The researchers realized that the descendants of this first wave of interbreeding between Neanderthals and modern humans must have lived alongside Neanderthals and left no trace among modern humans. “Because we can now incorporate the Neanderthal component into our genetic studies, we can look at these early spreads in ways we couldn’t before,” Akey said. The final piece of the puzzle was the discovery that the Neanderthal population was even smaller than previously thought.
Genetic modelling has traditionally used variation, or diversity, as a proxy for population size: the more genetic diversity, the larger the population. But using IBDmix, Akey’s team showed that a significant portion of that apparent diversity came from DNA sequences taken from modern humans, which are much more populous.
As a result, the effective Neanderthal population dropped from about 3,400 breeding individuals to about 2,400.
Taken together, the new findings paint a picture of how Neanderthals disappeared from the record about 30,000 years ago.
“I don’t like to use the word ‘extinction’ because I think the Neanderthals were largely absorbed,” Akey said, suggesting that Neanderthal populations gradually declined and the last survivors were absorbed into modern human communities.
This “assimilation model” was first proposed by Fred Smith, a professor of anthropology at Illinois State University, in 1989. “Our findings provide strong genetic data that is consistent with Fred’s hypothesis, which I think is really exciting,” Akey said.
“Neanderthals have probably been on the brink of extinction for a very long time,” he says. “If their numbers have declined by 10 to 20 percent, as we estimate, that would be a major setback for an already-threatened population.”
“Modern humans were essentially like waves crashing on a beach, slowly but surely eroding the beach. Eventually, we demographically overwhelmed the Neanderthals and incorporated them into the modern human population.”
Reference: “Repeated gene flow between Neanderthals and modern humans over the past 200,000 years” by Li-Min Li, Troy J. Komi, Rob F. Bierman, and Joshua M. Akey, July 12, 2024, Science.
DOI: 10.1126/science.adi1768
This study National Institutes of Health (Grant R01GM110068 to JMA).
