Ancient Interactions: Homo sapiens and Neanderthals' 200,000-Year Relationship Uncovered

New research reveals recurring gene flow and cultural exchanges between modern humans and Neanderthals, significantly impacting both groups' genomes and biology.

A groundbreaking study¹ has revealed that modern humans and Neanderthals engaged in repeated episodes of interbreeding over a span of 200,000 years. This discovery, spearheaded by researchers from Southeast University and Princeton University, sheds new light on the complex history of human evolution and interaction.

Unveiling a History of Interaction

Professor Liming Li of Southeast University stated,

"This is the first time that geneticists have identified multiple waves of modern human-Neanderthal admixture."

The research underscores the long-standing history of contact between these two hominin groups.

Professor Joshua Akey from Princeton University added,

"For the vast majority of human history, we’ve had a history of contact between modern humans and Neanderthals."

The study highlights that our direct ancestors diverged from the Neanderthal lineage approximately 600,000 years ago, developing modern human characteristics around 250,000 years ago. From this point until the Neanderthals' disappearance, modern humans and Neanderthals interacted frequently.

Mapping Gene Flow Over Millennia

Utilizing genomes from 2,000 contemporary humans, three Neanderthals, and one Denisovan, researchers mapped the gene flow between these hominin groups over the last 250,000 years. They employed a genetic tool known as IBDmix, which uses machine learning to decode genomes, identifying three significant waves of contact: around 200,000-250,000 years ago, 100,000-120,000 years ago, and 50,000-60,000 years ago.

Professor Akey noted,

"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."

This challenges previous models that suggested a single, late dispersal out of Africa by modern humans.

Detecting modern human–to-Neanderthal gene flow (H→N) and its consequences. Modern human–to-Neanderthal admixture causes a local increase in heterozygosity in the Neanderthal genome, a characteristic that enabled approaches to quantify and detect introgressed sequences. We leveraged modern human–introgressed sequences in the Neanderthal genome to refine estimates of Neanderthal ancestry in contemporary humans by decomposing IBDmix-detected segments into those attributable to human-to-Neanderthal (H→N) versus Neanderthal-to-human (N→H) gene flow in 2000 modern human individuals. We also used modern human–introgressed sequences to discover that Neanderthals had a smaller effective population size (N_e) than previously estimated and that a second wave of modern human–to-Neanderthal gene flow occurred ~100 to 120 thousand years ago (ka). bps, base pairs.

Evidence of Cultural Exchange

The research aligns with archaeological findings that indicate cultural and tool exchanges between modern humans and Neanderthals. Akey emphasized the importance of examining Neanderthal genomes for modern-human DNA, revealing early interactions previously undetectable. Akey explained,

"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.”

Revising Neanderthal Population Estimates

The study also revised the estimated population size of Neanderthals, reducing it from about 3,400 to around 2,400 breeding individuals. This adjustment reflects the significant genetic input from modern humans, which had previously inflated apparent genetic diversity in Neanderthals.

The Gradual Absorption of Neanderthals

Akey proposed that Neanderthals were not simply extinct but were absorbed into modern human populations.

"I don’t like to say ‘extinction,’ because I think Neanderthals were largely absorbed."

… he remarked. This model, first suggested by Fred Smith in 1989, posits that Neanderthal populations dwindled and were eventually assimilated into expanding modern human communities.

"Modern humans were essentially like waves crashing on a beach, slowly but steadily eroding the beach away."

…Akey said. Over time, the demographic pressure from modern humans overwhelmed Neanderthal populations, leading to their integration rather than outright extinction.

Conclusion

These findings, published in the journal Science, provide a nuanced understanding of human-Neanderthal interactions and their lasting impact on our genetic heritage. The study highlights the complexity of human evolution and the intricate web of relationships that shaped our ancestors' journey.

Understanding this long history of interaction not only enriches our knowledge of human evolution but also underscores the dynamic nature of our species' past, marked by movement, contact, and exchange across millennia.

1. Li, L., Comi, T. J., Bierman, R. F., & Akey, J. M. (2024). Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science (New York, N.Y.), 385(6705). https://doi.org/10.1126/science.adi1768