It’s well-established that non-African humans inherit approximately 2 to 3 percent of their DNA from Neanderthal ancestors. Recent research utilizing the most ancient modern human DNA ever examined has linked this genetic contribution to a brief period of interbreeding. This event, occurring between 45,000 and 49,000 years ago, appears to be the primary source of Neanderthal DNA in contemporary non-African populations.

Over tens of thousands of years, Neanderthals (Homo neanderthalensis) and modern humans (Homo sapiens) encountered each other multiple times. Evidence of modern human DNA has been found in Neanderthals who lived over 200,000 years ago, and some human groups continued to interbreed with Neanderthals until the latter went extinct around 39,000 years ago. However, not all of these encounters left a lasting genetic mark on today’s non-African populations. The most significant genetic exchange took place over a few thousand years, involving Neanderthals already settled in Europe and incoming modern humans.

“We estimate that the peak of this interaction occurred around 47,000 years ago, which also helps us approximate the timing of the migration out of Africa,” states Leonardo Iasi, a postdoctoral fellow specializing in evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Iasi is the lead author of one of the studies published in Science and a co-author of a concurrent study in Nature.

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Humans have migrated out of Africa, the cradle of the Homo genus, in multiple waves over millennia, establishing populations in the Near East and Europe. Here, they encountered Neanderthals, who had migrated from Africa much earlier. The last common ancestor of Neanderthals and modern humans is thought to have lived between 650,000 and 500,000 years ago. The exact locations of their interbreeding remain uncertain, but these new studies significantly refine the timeline.

In the Nature study, led by biochemist Johannes Krause and archaeogeneticist Kay Prüfer of the Max Planck Institute, along with doctoral student Arev Sümer, researchers sequenced genomes from six individuals found in Ranis, Germany, and one from the Zlatý kůň site in the Czech Republic. These individuals, who lived between 49,000 and 42,000 years ago, included the oldest known modern human family, according to Sümer. This family group in Ranis consisted of a mother, her young daughter, and another female relative. Intriguingly, the individual from Zlatý kůň was a more distant relative of this family.

This small community, likely numbering around 300 individuals spread across Central Europe, possessed 2.9 percent Neanderthal ancestry. By analyzing the length of Neanderthal DNA segments, the researchers concluded these people were about 80 generations—or between 1,500 and 1,000 years—removed from ancestors who had interbred with Neanderthals.

The Science study examined a broader set of data, including 59 ancient human genomes ranging from 45,000 to 2,200 years ago and 275 modern human genomes. “Our goal was to pinpoint when Neanderthal genes entered the human genome and to determine whether this occurred within a short span or over a prolonged period,” explains Priya Moorjani, a population geneticist at the University of California, Berkeley, and co-senior author of the study. Her team found evidence of a single significant genetic influx from Neanderthals to humans occurring roughly between 50,500 and 43,500 years ago, and noted signs of natural selection shaping these genes.

This genetic shift is significant, according to Princeton University genomicist Joshua Akey, who was not involved in the studies. He notes that it highlights specific areas in the human genome where Neanderthal genes either enhanced survival and reproduction, becoming a permanent part of the human genome, or caused detrimental effects and were lost. “Understanding the genetic nuances that differentiate us from other ancient human forms is inherently intriguing,” Akey says.

Interestingly, the research also suggests that the individuals from Ranis and Zlatý kůň, despite their ties to the broader out-of-Africa migration, left no living descendants. “We’re uncovering multiple lineages that did not contribute to the modern human gene pool,” says Krause, underscoring that the human story includes not only triumphs but also extinctions.

These findings open up new avenues for exploring how modern humans spread and gradually supplanted Neanderthals as the dominant hominid in Europe, notes Isabelle Crevecoeur, a paleoanthropologist at the French National Center for Scientific Research (CNRS) and the University of Bordeaux, who did not participate in the research. “The challenge now is to integrate these genetic insights with archaeological and cultural data to better understand our past,” she concludes.