The mystery only deepened in 2013. Another team of researchers retrieved mitochondrial DNA from a Neanderthal-like fossil at Sima de los Huesos, dating back 430,000 years.
The researchers had expected the DNA to resemble that of later Neanderthals in Europe. Instead, the mitochondrial DNA looked like it belonged to Denisovans — even though the Denisova cave was 4,000 miles away in Siberia.
Last year, the researchers announced they had gathered a small fraction of the nuclear DNA from the same Sima de los Huesos fossil. That genetic material looked like it belonged to a Neanderthal, not a Denisovan.
Dr. Krause and his colleagues have now discovered new Neanderthal DNA that they believe can solve the mystery of this genetic mismatch.
In 2013, one of Dr. Krause’s graduate students, Cosimo Posth, examined a Neanderthal fossil from a German cave called Hohlenstein-Stadel. He was able to reconstruct all of its mitochondrial DNA.
Dr. Posth estimated that the Neanderthal fossil was 120,000 years old and, more important, that it belonged to a branch of the Neanderthal family tree with a long history. He and his colleagues determined that all known Neanderthals inherited their mitochondrial DNA from an ancestor who lived 270,000 years ago.
All the data pointed to a sequence of events that could solve the puzzle that had bedeviled Dr. Krause for so long.
The common ancestors of Neanderthals and Denisovans spread across Europe and Asia over half a million years ago. Gradually the eastern and western populations parted ways, genetically speaking.
In the east, they became Denisovans. In the west, they became Neanderthals. The 430,000-year-old fossils at Sima de los Huesos — Neanderthals with Denisovanlike genes — capture the early stage of that split.
At some point before 270,000 years ago, African humans closely related to us moved into Europe and interbred with Neanderthals. Their DNA entered the Neanderthal gene pool.
More Reporting on Human Origins
Over many generations, most of that new DNA disappeared. But the mitochondrial DNA survived, passed down from mothers to their children. In fact, eventually all the Neanderthals inherited it, for some reason discarding the mitochondrial DNA that the species once had.
Dr. Posth said it was possible that early members of our own species moved from North Africa into Europe. Supporting this idea was the discovery reported last month of fossils of Homo sapiens in Morocco dating back 300,000 years.
But Dr. Posth said it was too soon to rule out another possibility: that these migrants belonged to another species in Africa closely related to us that scientists have yet to document.
“I feel uncomfortable to give a name to these humans,” Dr. Posth said.
Adam C. Siepel, a geneticist at Cold Spring Harbor Laboratory on Long Island who was not involved in the new study, said the hypothesis fit the evidence. “I think that’s absolutely possible,” he said.
The new study raises a host of tantalizing implications about human history.
It is not possible to know just how many times these early Africans interbred with Neanderthals. But somewhere in prehistory, at least one female human from Africa must have carried the child of a male Neanderthal.
“Now you have this hybrid child, which is probably pretty unusual-looking,” Dr. Siepel said. “One way or another, this hybrid individual was absorbed into Neanderthal society.”
Dr. Siepel warned that the hypothesis hinges on the new DNA found in the Hohlenstein-Stadel fossil. Dr. Krause and his colleagues are now trying to retrieve nuclear DNA from the fossil.
The research at Sima de los Huesos shows just how far back in time scientists can now search for genes. The most revealing DNA might come from the mountains of Morocco.
There, scientists may be able to find genes from the earliest Homo sapiens, which they can then compare to Neanderthals’.
“These are things that I never thought possible five years ago,” Dr. Krause said.
In Neanderthal DNA, Signs of a Mysterious Human Migration – New York Times