DNA from a man who lived 40,000 years ago in Romania reveals that up to 11 percent of his genome came from Neanderthals.

Because large segments of the individual’s chromosomes are of Neanderthal origin, a Neanderthal was among the man’s ancestors as recently as four generations back in his family tree, reports a study published in the latest issue of the journal Nature.

The finding reveals that some of the first members of our species who came to Europe interbred with the local Neanderthals.

Photos: Faces of Our Ancestors

To this day, individuals of European and Asian heritage retain Neanderthal DNA in their genomes, but whether or not Neanderthals went extinct or simply were absorbed into the modern human population remains a matter of definition, senior author Svante Pääbo told Discovery News.

“Some Neanderthals clearly became incorporated in modern human societies,” said Pääbo, director of the Department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology. “It is still unclear exactly how much of the complete Neanderthal genome exists today in people, but it seems to approach something like 40 percent.”

“But, of course, the Neanderthals are clearly extinct in the sense that they do not exist as an independent, separate group since some 30,000 or 40,000 years.”

David Reich from Harvard Medical School coordinated the population genetic analysis of the study, which was an international effort. At the center of the research were the remains of the man, named “Oase 1,” unearthed at a cave system called Peștera cu Oase in Romania.

The researchers believe that the man derived from the same expansion out of Africa as other modern people, but was likely to have been part of an early “pioneer foray into Europe,” ahead of other migrations that were to come later.

Photos: Are You Related to Neanderthals?

Under what conditions his relatives, and those of other early Neanderthal-human hybrids, interbred is a big question.

Chris Stringer, an expert on early humans at the Natural History Museum in London, posed some intriguing questions about the matings.

“Were these peaceful exchanges of partners, raids which stole women or girls, or even the adoption of orphaned babies?” he asked, adding that the answer remains a mystery.

What is clear is that the interbreeding took place at different times and locations. This particular individual, Oase 1, did not contribute much, if at all, to later modern human populations, however. Pääbo explained that whatever population he represented seems to have “disappeared,” leaving behind no known tools or other artifacts.

Jaw and teeth of Oase 1, an early modern human and Neanderthal hybrid. MPI f. Evolutionary Anthropology/ Paabo

The man’s DNA does share many alleles (alternative forms of genes) with present day East Asians and Native Americans.

“There are several studies now that show East Asians and Native Americans have about 20 percent more Neanderthal contribution (in their genomes) and that this could be due to extra inbreeding in the ancestors of East Asians,” Pääbo explained.

Other studies also conclude that there was likely a natural selection against a Neanderthal contribution to the Homo sapiens genome, such that even if interbreeding were very common, the evidence for that would not fully reveal itself in the genomes of modern humans of European and Asian heritage.

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“In the case of the Neanderthal gene flow into modern humans, it is clear that much of that DNA has been lost or selected away since, but there are some examples where it may have been retained because it was advantageous to the modern groups receiving it,” Stringer said, adding that he was surprised that interbreeding between Neanderthals and Homo sapiens “was still happening long after 55,000 years ago.”

Milford Wolpoff, a professor in the Department of Anthropology at the University of Michigan, told Discovery News that he is one of the few paleoanthropologists who was not surprised by the new findings about Oase 1. He said the discovery is “exciting, because it fits well into the framework that is emerging to understand Neolithic Europe.”

Wolpoff added that as modern humans spread into Europe from Western Asia, they interbred with the native Europeans, but because the migrating group was “quite numerous, the descendants of the earliest modern Europeans were largely swamped out.”