Neanderthals and early humans may have interbred over a vast area

Homo sapiens and Neanderthals were probably interbreeding over a huge area stretching from western Europe into Asia.

We have long known that early humans (Homo sapiens) and Neanderthals (Homo neanderthalensis) interbred, which is why most non-African people today have some Neanderthal DNA, typically about 2 per cent of their genome. The interbreeding also saw the Neanderthal Y chromosome lineages replaced by lineages from H. sapiens.

But where this interbreeding happened and on what kind of scale has long been a mystery, even if we are now starting to get a handle on when it occurred. The ancestors of Neanderthals left Africa about 600,000 years ago, heading into Europe and western Asia. And the earliest evidence of H. sapiens migrating out of Africa is skeletal remains from sites in modern day Israel and Greece, dating back around 200,000 years.

There are signs that H. sapiens contributed genetically to Neanderthal populations from the Altai mountains in what is now Siberia roughly 100,000 years ago, but the main pulse of their migration out of Africa came after about 60,000 years ago. Two studies from 2024 based on ancient genomes implied that the most gene flow between H. sapiens and Neanderthals happened in a sustained period of between around 4000 and 7000 years, starting about 50,000 years ago.

It was thought that this probably happened in the eastern Mediterranean region, but the location is hard to pin down.

To investigate, Mathias Currat at the University of Geneva in Switzerland and his colleagues have used data from 4147 ancient genetic samples, the oldest being about 44,000 years old, which come from more than 1200 locations. They assessed the proportion of genetic variants from Neanderthal DNA – called introgressed alleles – that have been repeatedly transferred by hybridisation.

“The idea was to see whether it is possible using the patterns of Neanderthal DNA integration in past human genomes to see where integration took place,” says Currat.

The results show a gradual increase in the proportion of transferred DNA the further you go from the eastern Mediterranean region, which plateaus after about 3900 kilometres both westwards towards Europe and eastwards into Asia.

“We were quite surprised to see a nice increasing pattern of introgression proportion in human genomes resulting from what we guess is the out-of-Africa human expansion,” says Currat. “It’s increasing toward Europe, it’s increasing toward East Asia, and so it allows us to estimate the boundary of this hybrid zone.”

The researcher’s computer simulations indicate a hybrid zone that covered most of Europe and the eastern Mediterranean and went into western Asia.

“What we see seems to be a single continuous pulse – a continuous series of interbreeding events in space and time,” says Currat. “However, we don’t know when hybridisation took place in the zone.”

The hybrid zone includes almost all known sites associated with Neanderthal fossils, spanning western Eurasia, except those from the Altai region.

“The finding that the inferred hybrid zone extends broadly into western Eurasia is intriguing and suggests that interactions between populations may have been geographically widespread,” says Leonardo Iasi at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

However, the Atlantic fringe, including western France and most of the Iberian peninsula, isn’t in the hybrid zone, despite the well-documented Neanderthal presence there. It could be that there was no hybridisation in this region, says Currat, or that any interbreeding occurring here isn’t represented in the 4147 genetic samples.

“Overall, the study paints a picture of repeated interactions between modern humans and Neanderthals across a broad geographic range and over extended periods of time,” says Iasi, adding that the hybrid zone might extend further, but limited ancient DNA sampling in regions such as the Arabian peninsula makes it difficult to assess how far it went in that direction.

“This is an important paper that challenges the view that there was only one region, probably western Asia, and one Neanderthal population (not represented in the current Neanderthal genetic samples) that hybridised with the Homo sapiens population dispersing from Africa,” says Chris Stringer at the Natural History Museum in London. “As early sapiens spread out in ever-growing numbers and over an ever-expanding range, it seems they mopped up small Neanderthal populations they encountered along the way, across virtually the whole known Neanderthal range.”