In 2012, Dr. Paabo and his colleagues took samples from the bone to search for DNA. To their surprise, it held a number of genetic fragments.

“This is an amazing and shocking and unique sample,” said David Reich, a geneticist at Harvard Medical School and co-author of the new study.

The researchers used the DNA fragments to recreate a high-resolution copy of the man’s complete genome. A Y chromosome revealed that the thighbone belonged to a man.

The scientists then compared the genome of the so-called Ust’-Ishim man to those of ancient and living people.

They found that his DNA was more like that of non-Africans than that of Africans. But the Ust’-Ishim man was no more closely related to ancient Europeans than he was to East Asians.

He was part of an earlier lineage, the scientists concluded — a group that eventually gave rise to all non-African humans.

Homo sapiens, our own species, appeared in Africa around 200,000 years ago. Previous studies — both on genes and fossils — have suggested that they then expanded through the Near East to the rest of the Old World.

The Ust’-Ishim man’s genome suggests he belonged to a group of people who lived after the African exodus, but before the split between Europeans and Asians.

Dr. Paabo and his colleagues also found that the Ust’-Ishim man had pieces of Neanderthal DNA in his genome, just as living non-Africans do. But his Neanderthal DNA has some important differences.

Fossils indicate that Neanderthals spread across Europe and Asia before becoming extinct an estimated 40,000 years ago. Today, the Neanderthal DNA in each living non-African human is broken up into short segments sprinkled throughout the genome.

Dr. Paabo and his colleagues have hypothesized that this arrangement is the result of how cells divide.

During the development of eggs and sperm, each pair of chromosomes swaps pieces of their DNA. Over the generations, long stretches of DNA get broken into smaller ones, like a deck of cards repeatedly shuffled.

Over thousands of generations, the Neanderthal DNA became more fragmented. Dr. Paabo and his colleagues predicted, however, that Neanderthal DNA in the Ust’-Ishim man’s genome would form longer stretches.

And that’s exactly what they found. “It was very satisfying to see that,” Dr. Paabo said.

By comparing the Ust’-Ishim man’s long stretches of Neanderthal DNA to shorter stretches in living humans, Dr. Paabo and his colleagues estimated the rate at which they fragmented. They used that information to determine how long ago Neanderthals and humans interbred.

Previous studies — based on only living humans — had yielded an estimate between 37,000 and 86,000 years. Dr. Paabo and his colleagues have now narrowed down that estimate dramatically: Humans and Neanderthals interbred between 50,000 and 60,000 years ago, according to the new data.