Neanderthal man interbred with the first anatomically modern humans to migrate out of Africa, according to a pioneering study showing that there was a flow of genetic material between early Homo sapiens and our extinct cousins.
Scientists had dismissed the idea that Neanderthalers could have had children with our early ancestors, but a study of the Neanderthal genome, derived from analysing 40,000-year-old fossilised bones, has produced the most convincing evidence to date of limited interbreeding.
The findings suggest that although there was "gene flow" from Neanderthalers to H. sapiens, there was no evidence of any genetic exchange in the opposite direction – suggesting that the resulting children were raised by modern humans. Interbreeding was more likely between Neanderthalers and H. sapiens women.
Although it is known that the territories of the Neanderthalers, which extended across Europe and central Asia, overlapped with those of modern humans, there was little evidence that they interacted with one another, despite living cheek by jowl for thousands of years.
Scientists said they were surprised at their analysis of the draft Neanderthal genome, which comprises some three billion "letters" of the genetic code and was painstakingly built up from small fragments of DNA extracted from the bones of various Neanderthal specimens excavated in Croatia, Spain, Russia and Germany.
When they compared the Neanderthal genome to that of five modern-day humans, the scientists found small fragments of Neanderthal sequences in all non-Africans, even in a person from Papua New Guinea, where Neanderthalers had never lived. This suggests the interbreeding occurred soon after the initial migration of H. sapiens out of Africa between 50,000 and 80,000 years ago.
"We can now say that, in all probability, there was gene flow from Neanderthals to modern humans," said Dr Ed Green of the University of California, Santa Cruz, the lead author of the study, which was published in the journal Science.
"The scenario is not what most people had envisaged. We found the genetic signal of Neanderthals in all the non-African genomes, meaning the admixture occurred early on, probably in the Middle East, and is shared with all descendants of the early humans who migrated out of Africa," Dr Green said.
Dr David Reich of Harvard Medical School in Boston, Massachusetts said that other possible explanations for the results have been largely dismissed and that they appear to resolve the controversy over whether there was any interbreeding between the two species of humans.
"The main finding is that there was gene flow from Neanderthals into the ancestors of all modern non-Africans. We do not find any evidence at all of gene flow into sub-Saharan Africans. We also do not find any evidence of gene flow in the reverse direction into Neanderthals," Dr Reich said.
"The proportion of Neanderthal ancestry in non-Africans today is between 1 and 4 per cent so it's a small but very real proportion of ancestry in non-Africans today," he added.
Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany had previously dismissed the idea of interbreeding when he analysed Neanderthal mitochondrial DNA, which is maternally inherited from mothers to offspring.
He said the findings on the nuclear DNA of Neanderthalers had surprised him because he was biased into believing that interbreeding did not occur. However, the work on mitochondrial DNA hints at the idea that the interbreeding was between Neanderthalers and H. sapiens women, he said.