Humans and Neanderthals are far more connected than once thought

The discovery of ancient human cousins has long stirred wonder and debate. Early Neanderthal remains offered a glimpse into our distant past, prompting questions about how they lived and whether they mingled—or clashed—with early humans. The plot thickened with the later discovery of Denisovans, another mysterious branch of the human family tree. Each new finding deepened the mystery of who we are and where we came from.

Now, a new study is adding rich detail to that ancient story. A team of geneticists and artificial intelligence experts has found that early humans and Neanderthals were far more connected than once thought. Led by Joshua Akey from Princeton’s Lewis-Sigler Institute for Integrative Genomics, the team’s work points to a history filled with repeated contact and genetic exchange.

“This is the first time geneticists have identified multiple waves of modern human–Neanderthal admixture,” said Liming Li, a professor at Southeast University in Nanjing, China. Li conducted this research while working in Akey’s lab, helping to decode the patterns hidden in ancient DNA.

According to Akey, our ancestors branched off from Neanderthals roughly 600,000 years ago. Around 250,000 years ago, early humans began to show signs of the traits we now consider modern. From that moment on, humans and Neanderthals didn’t just coexist—they interacted, sometimes mixing their genes.

“For about 200,000 years, modern humans interacted with Neanderthal populations,” Akey said. These repeated encounters left lasting genetic footprints in our DNA. The findings show that our ancestors had ongoing relationships with Neanderthals rather than brief or isolated contact.

Published in Science, the research challenges old ideas about Neanderthals as crude or unsophisticated. Evidence now shows they were skilled at crafting tools, hunted with precision, and even treated injuries with methods far ahead of their time. They survived the harsh climates of Ice Age Europe through innovation and resilience.

To unravel this complex history, Akey’s team examined DNA from 2,000 present-day humans, three Neanderthals, and one Denisovan. The goal was to trace how genes moved between these groups over the last 250,000 years. The scale of this data allowed the researchers to detect moments of contact that earlier studies missed.

Central to their success was a new tool called IBDmix. It uses machine learning to detect segments of DNA shared between species, allowing scientists to identify when and where gene flow occurred. Unlike older genetic methods, IBDmix can reveal hidden patterns, painting a more detailed picture of how humans and their ancient cousins came together across time.

Previously, researchers compared human genomes against a reference population thought to have little Neanderthal or Denisovan DNA. Akey’s team found even those reference groups had trace amounts of Neanderthal DNA, likely brought by travelers.

With IBDmix, the team identified three waves of contact: 200-250,000 years ago, 100-120,000 years ago, and the largest around 50-60,000 years ago. This challenges previous genetic data suggesting modern humans stayed in Africa for 200,000 years before dispersing 50,000 years ago.

“Our models show that shortly after modern humans arose, they migrated out of and back into Africa,” said Akey. “This story is about dispersal, showing that humans moved around and encountered Neanderthals and Denisovans more than previously recognized.”

This view aligns with archaeological evidence of cultural and tool exchange between these groups.

DNA Insights Li and Akey’s key insight was to search for modern-human DNA in Neanderthals, instead of vice versa. “Most genetic work has focused on how mating with Neanderthals impacted modern human evolution, but these questions are also interesting in reverse,” said Akey.

They realized that the offspring of early Neanderthal-modern human matings likely stayed with Neanderthals, leaving no trace in modern humans. “Incorporating the Neanderthal component into genetic studies reveals these earlier dispersals in ways we couldn’t see before,” Akey noted.

The team also discovered that the Neanderthal population was smaller than previously believed. Genetic modeling usually uses gene diversity as a proxy for population size. However, using IBDmix, the team showed that much of the apparent diversity in Neanderthals came from modern human DNA. Consequently, the estimated Neanderthal population size was revised down from about 3,400 to 2,400 breeding individuals.

The Disappearance of Neanderthals These findings suggest how Neanderthals disappeared around 30,000 years ago. “I don’t like to say ‘extinction,’ because I think Neanderthals were largely absorbed,” said Akey. He believes Neanderthal populations shrank until the last survivors were integrated into modern human communities.

This “assimilation model” was first proposed by Fred Smith, an anthropology professor at Illinois State University, in 1989. “Our results provide strong genetic data supporting Fred’s hypothesis, which is very interesting,” Akey commented.

“Neanderthals were likely on the brink of extinction for a long time,” he said. “If you reduce their numbers by 10 or 20%, that’s a substantial reduction for an already at-risk population.”

“Modern humans were like waves eroding a beach, steadily overwhelming Neanderthals and incorporating them into our populations,” Akey concluded.

This research adds significant depth to our understanding of human evolution, highlighting a complex history of migration and interaction that shaped our species.

The primary evolutionary differences between Homo sapiens (modern humans) and Neanderthals (Homo neanderthalensis) stem from genetic, anatomical, and behavioral adaptations that influenced their survival, development, and interaction with the environment.

These differences highlight how both species adapted to their environments, with modern humans ultimately outlasting Neanderthals due to a combination of genetic advantages, cultural innovation, and environmental flexibility.

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