Neandertal genome yields evidence of interbreeding with humans

Some people don’t just have a caveman mentality; they may actually carry a little relic of the Stone Age in their DNA.

A new study of the Neandertal genome shows that humans and Neandertals interbred. The discovery comes as a big surprise to researchers who have been searching for genetic evidence of human-Neandertal interbreeding for years and finding none.

About 1 percent to 4 percent of DNA in modern people from Europe and Asia was inherited from Neandertals, researchers report in the May 7 Science. “It’s a small, but very real proportion of our ancestry,” says study coauthor David Reich of the Broad Institute of MIT and Harvard in Cambridge, Mass. Comparisons of the human and Neandertal genomes are also revealing how humans evolved to become the sole living hominid species on the planet.

Neandertals lived in Europe, the Middle East and western Asia until they disappeared about 30,000 years ago. The new data indicate that humans may not have replaced Neandertals, but assimilated them into the human gene pool.

“Neandertals are not totally extinct; they live on in some of us,” says Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and leader of the Neandertal genome project.

He and other geneticists involved in the effort to compile the complete genetic instruction book of Neandertals didn’t expect to find that Neandertals had left a genetic legacy. Earlier analyses that looked at only a small part of the genome had contradicted the notion that humans and Neandertals intermixed (SN Online: 8/7/08).

“We as a consortium came into this with a very, very strong bias against gene flow,” Reich says. In fact, when he and his colleagues announced the completion of a rough draft of the Neandertal genome a year ago, the researchers said such genetic exchange was unlikely (SN: 3/14/09, p. 5).

But several independent lines of evidence now convince the researchers that humans and Neandertals did interbreed. “The breakthrough here is to show that it could happen and it did happen,” Pääbo says.

The result came as no surprise to some scientists, however. Archaeologists have described ancient skeletons from Europe that had characteristics of both early modern humans and Neandertals; evidence, the researchers say, of interbreeding between the two groups. But until the cataloging of the entire Neanderthal genome, genetic studies could find no evidence to support the idea.

“After all these years the geneticists are coming to the same conclusions that some of us in the field of archaeology and human paleontology have had for a long time,” says João Zilhão, an archaeologist and paleoanthropologist at the University of Bristol in England. “What can I say? If the geneticists come to this same conclusion, that’s to be expected.”

Researchers re-created the Neandertal’s genetic blueprints using DNA extracted from three bone fragments — each from a different Neandertal woman — found in a cave in Croatia.

Comparing the resulting blueprints of the female Neandertals, who lived about 40,000 years ago, with those of five present-day humans from China, France, Papua New Guinea and southern and western Africa, revealed that people outside of Africa carry Neandertal DNA.

Scientists were surprised to find that people from China and Papua New Guinea (places where Neandertals never lived) have just as much Neandertal ancestry as people from France. The group did not find traces of Neandertal heritage in the two African people studied. The result probably means that interbreeding between Neandertals and humans took place about 50,000 to 80,000 years ago in the Middle East as humans began migrating out of Africa to colonize the rest of the world, Reich says.

It is not clear how extensive interbreeding was; the data are consistent with either a short period with a great deal of interbreeding or with a long period of little interbreeding, says Richard E. (Ed) Green, a genome biologist now at the University of California Santa Cruz and a coauthor of the new study.

Comparison of the Neandertal genome to human and chimpanzee genetic sequences have led to some clues about recent human evolution. Neandertals “were not genetically very distinct from us,” says Pääbo. For example, the researchers were able to find only 78 proteins in which humans carry a different amino acid than is found in Neandertals and chimpanzees. That means that few changes in proteins have taken place in the past few hundred thousand years of human evolution. Researchers don’t know yet whether the changes in the proteins alter their function or give humans some survival advantage.

But some parts of the human genome clearly do produce an evolutionary advantage, the researchers say. Again, the team compared the human genome to those of Neandertals and chimpanzees and identified places where humans differ. If nothing of importance had happened in human evolution since humans and Neandertals diverged, such changes would be spread evenly across the genome, Green says. Instead, the researchers found large swaths of the genome where humans have distinct changes not found in Neandertals or chimpanzees. The team identified 212 such regions where “selective sweeps” were likely to have happened, many of which include genes involved in brain function. The researchers don’t yet know what the changes are or how they produce a selective advantage.

“These data are really a goldmine for understanding recent human evolution,” Green says.

Since humans and Neandertals could interbreed, some people question whether the two groups are different hominid species. The question doesn’t hold interest for John Hawks, an anthropologist at the University of Wisconsin–Madison. Genealogically, he says, the new study shows that many humans had a Neandertal great-great-great-great … grandfather.  “It’s impossible to talk about them as ‘them’ anymore,” he says. “Neandertals are us.”

______________________________________________________________________

Back Story | Fossil clues to intermingling

Some archaeologists have long argued that fossil evidence suggests interbreeding between Homo sapiens and Neandertals.

1. Lagar Velho child
Uncovered in the late 1990s in Portugal, this child’s skeleton dates to 24,500 years ago and displays a mix of H. sapiens and Neandertal characteristics. Human traits include a well-formed chin and small lower arms, while Neandertal characteristics include a huge jaw, large front teeth, short legs and a broad chest (SN: 5/8/99, p. 295).
Credit: José Paulo Ruas

2. Châtelperronian artifacts
Bone and stone tools blending Neandertal and human techniques have been found in a French cave and date to roughly 40,000 and 35,000 years ago. Though not evidence for interbreeding, the artifacts suggest that humans and Neandertals lived side by side for at least a millennium and that there wasn’t necessarily a mental gulf between the species.
Credit: Gravina et al./Nature 2005

3. Oase fossils
A 40,000-year-old skull found in a Romanian cave defies traditional anatomical categorization. Though the skull has the proportions of a modern human cranium, it has a retreating forehead and large upper molars (palate shown), among other features typical of Neandertals (SN: 3/24/07, p. 186). A similar jaw had previously been found at the site.
Credit: Rougier et al./PNAS 2007