New research provides an updated timeline of human-Neanderthal interactions, revealing patterns in the genetic legacy of this ancient exchange.
Tens of thousands of years ago, as modern humans migrated out of Africa and into unfamiliar territories, they encountered Neanderthals-a now-extinct group of ancient humans who lived in Eurasia. These interactions left a lasting mark on our DNA; today, nearly all non-African humans carry traces of Neanderthal DNA, a genetic inheritance that provides important insights into human migration and survival.
Despite years of research, however, questions remain regarding the timing, extent, and impact of the genetic exchange between Neanderthals and modern humans.
In two groundbreaking new studies published in Science and Nature, researchers from the University of Rochester-along with colleagues at the Max Planck Institute for Evolutionary Anthropology, the University of California, Berkeley, and others-traced how ancient interactions with Neanderthals shaped modern human evolution. By examining patterns of Neanderthal DNA in both modern and ancient human genomes, they reconstructed a timeline of interbreeding and its evolutionary impacts. Their findings reveal when and where these exchanges occurred-and highlight how Neanderthal genes helped humans adapt to new environments.
"Our study provides the most detailed insights yet into how Neanderthal gene flow impacted human genomes," says Benjamin Peter, an assistant professor in the University's Department of Biology. "It helps us understand when Neanderthals and humans interacted, which Neanderthal genes were beneficial for our ancestors, and the forces that influenced genetic diversity and shaped the course of human evolution."
Human-Neanderthal divergence and gene flow
About 500,000 years ago, Neanderthals and modern humans diverged from a common ancestor. Following this split, one lineage evolved into Neanderthals in Eurasia, while the other evolved into modern humans in Africa. Both groups had complex behaviors, including tool use and social structures, but Neanderthals developed unique physical traits, such as a stockier build and larger brow ridges, reflecting adaptations to their environment.
Sometime around 40,000 to 60,000 years ago, modern humans left Africa, encountering Neanderthals and interbreeding. The gene flow between Neanderthals and modern humans resulted in most non-Africans carrying one to two percent Neanderthal DNA.
However, the exact timing of the gene flow event has remained elusive.
A single period of gene flow
To uncover a more precise timeline, the researchers used genome sequencing techniques to analyze more than 300 genomes from ancient and modern humans spanning the last 50,000 years. They examined Neanderthal DNA segments in the individual genomes across different time periods and geographic regions, identifying patterns to determine when interbreeding occurred and how natural selection influenced which Neanderthal genes were passed on.
They found that most Neanderthal DNA in modern humans can be traced to a single major period of gene flow, which occurred about 47,000 years ago and lasted approximately 7,000 years. This suggests there was one extended period of interaction between the two groups, rather than multiple separate events, as some researchers had previously believed.
The findings provide tighter constraints for when humans migrated out of Africa-known as the "Out-of-Africa event"-helping to more precisely pinpoint when migration and interbreeding occurred.
"Our results suggest that all Neanderthal ancestry in living people traces back to the same event shortly after the Out-of-Africa event," Peter says.
Ancient traits stand the test of time
So, what Neanderthal genes are in humans? The researchers found that Neanderthal DNA is not evenly spread throughout the genome. In fact, some regions lack Neanderthal DNA entirely, suggesting that Neanderthal ancestry in those areas wasn't beneficial for survival. Other regions-particularly those linked to traits such as skin pigmentation, metabolism, and immune function-have higher concentrations of Neanderthal DNA. The researchers discovered that this uneven distribution existed in human genomes more than 40,000 years ago, indicating that some Neanderthal genes provided immediate benefits, such as helping humans adapt to new climates as they migrated out of Africa.
"This shows that natural selection on Neanderthal genetic variants, both beneficial and harmful, acted very rapidly and was likely quite strong," Peter says.
The patterns in the DNA also suggest that interbreeding may not have been entirely random. Instead, factors such as geography or culture may have influenced which groups of humans were more likely to interact with Neanderthals, leading to different amounts of Neanderthal DNA in different populations.
Ancient encounters and future discoveries
Uncovering when and how certain Neanderthal genes were passed down reveals how these ancient encounters shaped human adaptation and diversity.
These latest findings not only show the lasting influence of Neanderthal genes on human evolution, but they also pave the way for future research. Gathering more genetic data from areas of the world where early human-Neanderthal interactions remain a mystery could deepen the understanding of this key moment in human history.
"A major limitation of our study is that we do not have genetic data from early modern humans in several key areas of the world, such as the Middle East, South Asia, and Oceania," Peter says. "Direct data from there would likely allow more insights on where exactly Neanderthals and humans met."
