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 an international team of scientists who have pieced together the genetic code of humanity’s closest relatives.

Traces of that ancient DNA live on in most human beings today, the researchers report in today’s edition of the journal Science.

The finding, which was made by analyzing DNA from Neanderthal bones and comparing it with 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, an evolutionary geneticist at the University of Wisconsin who was not involved in the study. “They’re not ‘them’ anymore — they’re ‘us.'”

Svante Paabo, the geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who spearheaded the study, said he now sees his ancestors in a new light. His initial research on a different type of DNA that contains far less information had concluded — incorrectly, it turns out — 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 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 is now at the University of California at Santa Cruz. “It’s understanding us.”

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

The researchers constructed the Neanderthal genome from three bone fragments found in Croatia’s Vindija Cave. Using a dentistry drill, the scientists removed 400 milligrams of bone powder — an amount equivalent to the size of an aspirin.