Gene profiles suggest people interbred with a now-extinct species on the continent not that long ago

By Tina Hesman Saey

Web edition: July 31, 2012
Print edition: September 8, 2012; Vol.182 #5 (p. 9)

Expeditions to Africa may have brought back evidence of a hitherto unknown branch in the human family tree. But this time the evidence wasn’t unearthed by digging in the dirt. It was found in the DNA of hunter-gatherer people living in Cameroon and Tanzania.

Buried in the genetic blueprints of 15 people, researchers found the genetic signature of a sister species that branched off the human family tree at about the same time that Neandertals did. This lineage probably remained isolated from the one that produced modern humans for a long time, but its DNA jumped into the Homo sapiens gene pool through interbreeding with modern humans during the same era that other modern humans and Neandertals were mixing in the Middle East, researchers report in the August 3 Cell.

The evidence for ancient interbreeding is surprisingly convincing, says Richard “Ed” Green, a genome biologist at the University of California, Santa Cruz. “There is a signal that demands explanation, and archaic admixture seems to be the most reasonable one at this point,” he says.

Scientists have discovered that some people with ancestry outside Africa have DNA inherited from Neandertals or Denisovans, a mysterious group known only through DNA derived from a fossil finger bone found in a Siberian cave (SN: 6/5/10, p. 5; SN: 1/15/11, p.10).

But those researchers had DNA from fossils to guide their research. This time, researchers led by Sarah Tishkoff at the University of Pennsylvania in Philadelphia didn’t have fossil DNA, or even fossils.

Tishkoff’s group took DNA donated by 15 African hunter-gatherers — five Pygmies from Cameroon and five Hadza and five Sandawe from Tanzania— and compiled complete genetic blueprints for each person. Population geneticist Joshua Akey of the University of Washington and his colleagues helped analyze the data. Using a statistical analysis, the team determined that about 2 percent of the DNA from the hunter-gatherers came from an unknown species of hominid that split from modern human ancestors about 1.1 million years ago. These long-lost human cousins must have then interbred with modern humans sometime before the common ancestral lineage of the three hunter-gatherer groups separated about 30,000 to 70,000 years ago, Akey says.

A separate study posted online July 23 on arXiv.org examined patterns of single DNA unit changes, known as SNPs, in 22 African groups. That study, by Joseph Pickrell of Harvard Medical School and colleagues, also presents evidence that some African groups, including the Hadza, may harbor DNA from unknown extinct hominids.

Other researchers aren’t convinced that the DNA remnants identified are the genetic remains of a new species of human cousin. The DNA could have come from a genetically distinct group of modern humans that has since died out due to changes in their environment, diseases or confrontations with rival groups of humans, says Jean-Jacques Hublin, a paleoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

Relatively recent interbreeding isn’t the only explanation for the presence of this newly discovered DNA, says anthropological geneticist Paul Verdu of Stanford University. He thinks the DNA may be the genetic stamp left by a common ancestor of modern humans and another species. The DNA may have morphed so much in non-African groups, just by chance, that it is now unrecognizable.