Scientists using DNA testing discovered that modern human beings interbred with Neanderthals tens of thousands of years ago.

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LOS ANGELES — The first modern humans to leave Africa 80,000 years ago encountered Neanderthal settlements in the Middle East and — on at least some occasions — chose to make love instead of war, according to scientists who pieced together the genetic code of humanity’s closest relatives.

Traces of the ancient DNA from the much-caricatured, beetle-browed caveman live on in most human beings today, the researchers report in Friday’s edition of the journal Science.

The finding, made by analyzing DNA from Neanderthal bones and comparing it to that of five living humans, appears to resolve a long-standing mystery about the relationship between Neanderthals and Homo sapiens, who coexisted in Europe and western Asia for more than 10,000 years until Neanderthals disappeared about 30,000 years ago.

“We can now say with absolute certainty that we’ve got these Neanderthal genes,” said John Hawks, a University of Wisconsin evolutionary geneticist who was not involved in the study. “They’re not ‘them’ anymore; they’re ‘us.’ “

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Svante Paabo, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who spearheaded the study, said he sees his ancestors in a new light. His initial research on a different type of DNA that contains far less information had concluded — incorrectly — that Neanderthals have no genetic connection to people alive today.

Now, Paabo said, “I would more see them as a form of humans that were a bit more different than people are from each other today.”

Most important, scientists said, knowing the precise structure of the Neanderthal genome will help answer the fundamental biological question: What makes us human?

Neanderthal DNA is 99.7 percent identical to that of people, according to the analysis, which involved an international team of dozens of researchers. Something in the remaining 0.3 percent must make us unique.

“It’s not about understanding Neanderthals,” said genome biologist Ed Green, who led the study as a research fellow in Paabo’s lab and now is at the University of California, Santa Cruz. “It’s understanding us.”

By lining up the Neanderthal genome with DNA from humans and chimpanzees, Green and colleagues identified small changes unique to humans. Some were in genes involved in energy metabolism, skeletal structure and brain development, including four believed to contribute to conditions such as autism, Down syndrome and schizophrenia.

Researchers constructed the Neanderthal genome from three bone fragments found in Croatia’s Vindija Cave. One fragment is 38,000 years old, another 44,000 years old and one undated. They appear to be shin bones, and all are from females. They also seem to have been broken intentionally, possibly to get at the marrow to eat. Using a sterile dentistry drill, the scientists removed 400 milligrams of bone powder, an amount equivalent to the size of an aspirin.

Extracting DNA from ancient bones was a dicey proposition.

For starters, 95 to 99 percent of the DNA the team found came from microbes that colonized the bones after the Neanderthals died more than 38,000 years ago. To address that problem, the scientists discarded DNA fragments with letter combinations that were especially common in microbes.

In addition, the Neanderthal DNA was degraded, which caused sequencing machines to misread some chemical letters in the sequence. The researchers developed a computer program to correct those mistakes.

The researchers took special precautions to keep their personal DNA out of the Neanderthal samples. Workers wore full-body suits, including masks and gloves. The air pressure inside the lab was kept high so that nothing could blow in accidentally, and the room was irradiated after the researchers went home, Green said.

After four years of work, the team identified 4 billion fragments of Neanderthal DNA and organized them into a draft genome. The sequence is 60 percent complete.

“It is a very poor quality for a human genome, but it is outstanding for a 30,000-year-old extinct hominid,” said Eddy Rubin, who has sequenced samples of Neanderthal DNA at Lawrence Berkeley National Laboratory but was not involved in the Science study.

To look for evidence of gene flow between humans and Neanderthals, the researchers sequenced the DNA of five people who live in southern Africa, western Africa, France, China and Papua New Guinea.

Because they didn’t think Neanderthal genes had passed to humans, they expected to find the same degree of difference between the Neanderthal genome and all five people.

Instead, they discovered that the Neanderthal DNA was slightly more similar to the three people living outside Africa. Even more surprising, the relationship was just as strong for the individuals from China and Papua New Guinea as for the person from France, who lives in the Neanderthals’ old stomping grounds.

The simplest explanation is that a small group of humans met the Neanderthals 50,000 to 80,000 years ago after they left Africa but before they had spread throughout Europe, Asia and beyond. The logical meeting place was the Middle East, which connects northeast Africa to the Eurasian continent.

“The contact must have happened early for the Neanderthals genes to have spread so widely and uniformly,” said Henry Harpending, a University of Utah anthropologist who was not involved in the study.

The amount of mixing was small: 1 to 4 percent of the DNA in non-African humans originated in Neanderthals, according to the study. The researchers said none of that DNA is functional; in fact, the particular 1 to 4 percent is different in every individual.

Interbreeding may have continued in Europe, but that would be harder to detect because both populations there were large and any small Neanderthal contribution would be too dilute to see, Paabo said.

Todd Disotell, an anthropologist at New York University, suggested more Africans should be sampled.

“My guess is, as we sample more Africans, we’re going to find some of these old lineages in Africa,” said Disotell, who was not part of the research team. He noted that the researchers looked at the genomes of a West African and a southern African, but not someone from northeast Africa, where he said the mixture would be more likely to have occurred.

Erik Trinkaus, an anthropologist at Washington University in St. Louis, who long has argued that Neanderthals contributed to the human genome, said researchers now “can get on to other things than who was having sex with who in the Pleistocene (epoch).”

Information from The Associated Press and The Washington Post is included in this report.

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