The geneticists reached this conclusion, reported on Thursday in the journal Cell, after decoding the entire genome of three isolated hunter-gatherer peoples in Africa, hoping to cast light on the origins of modern human evolution. But the finding is regarded skeptically by some paleoanthropologists because of the absence in the fossil record of anything that would support the geneticists’ statistical calculations.
Two of the hunter-gatherers in the study, the Hadza and Sandawe of Tanzania, speak click languages and carry ancient DNA lineages that trace to the earliest branchings of the human family tree. The third group is that of the forest-dwelling pygmies of Cameroon, who also have ancient lineages and unusual blood types.
The geneticists, led by Joseph Lachance and Sarah A. Tishkoff of the University of Pennsylvania, decoded the entire genomes of five men from each of these groups. The costs of whole-genome sequencing have fallen so much that the technique can now be applied to populations for the first time, said Dr. Tishkoff, who paid the company Complete Genomics around $10,000 for each of the 15 genomes.
Among the DNA sequences special to pygmies, Dr. Tishkoff and colleagues found a variant of the usual gene that controls development of the pituitary gland, the source of the hormones that control reproduction and growth. This could be the cause of the pygmies’ short stature and early age of reproduction, the researchers say.
The genomes of the pygmies and the Hadza and Sandawe click-speakers contained many short stretches of DNA with highly unusual sequences. Through mutation, the genomes of species that once had a common ancestor grow increasingly unlike one another. Dr. Tishkoff’s team interprets these divergent DNA sequences as genetic remnants of an interbreeding with an archaic species of human. Genetic calculations suggest the interbreeding took place between 20,000 and 80,000 years ago.
From calculations of the amount of divergence in the DNA, the geneticists estimate that the archaic species split from the ancestors of modern humans about 1.2 million years ago, about the same time as did the ancestors of the Neanderthals, who dominated Europe during the end of the last ice age.
But the archaic species has a different DNA sequence from that of Neanderthals, whose genome has been reconstructed from DNA surviving in ancient bones, and so may be a sister species, the geneticists say.
Inquiries into human origins are on strong ground when genetic data and fossil evidence point in the same direction, but at present geneticists and paleoanthropologists have somewhat different stories to tell. All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. Another team of geneticists reported in 2010 the finding that Neanderthals had interbred 100,000 years ago with Europeans and Asians, but not Africans. This, too, conflicted with the fossil evidence in implying that modern humans left Africa 100,000 years ago, some 55,000 years before the earliest known fossil evidence of this exodus.
In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.
These three claims of interbreeding have opened up a serious discordance between geneticists and paleoanthropologists. For digesting the geneticists’ claims, “sup with a long spoon,” advised Bernard Wood, a paleoanthropologist at George Washington University.
Richard Klein, a paleoanthropologist at Stanford University, said the new claim of archaic and modern human interbreeding “is a further example of the tendency for geneticists to ignore fossil and archaeological evidence, perhaps because they think it can always be molded to fit the genetics after the fact.”
Dr. Klein said the claims of interbreeding could be “a methodological artifact” in the statistical assumptions on which the geneticists’ calculations are based. The flaw may come to light when enough inconsistent claims are published. “Meanwhile, I think it’s important to regard such claims skeptically when they are so clearly at odds with the fossil and archaeological records,” he said.
Dr. Tishkoff said that she agreed on the need for caution in making statistical inferences, and that there are other events besides interbreeding, like a piece of DNA getting flipped around the wrong way, that can make a single DNA sequence look ancient. “But when you see it at a genomewide level, it’s harder to explain away,” she said.
A co-author, Joshua M. Akey of the University of Washington in Seattle, said he was “reasonably confident that what we are seeing in Africa does represent archaic introgression.” The archaic sequences make up only 2.5 percent of the genomes of the living hunter-gatherers, and there is no evidence that they are being favored by natural selection. They may, therefore, have no effect on a person’s physical form, which could explain why the fossils show little sign of them, Dr. Akey said.
Although all known African fossils are of modern humans, a 13,000-year-old skull from the Iwo Eleru site in Nigeria has certain primitive features. “This might have indicated interbreeding with archaics,” said Chris Stringer, a paleoanthropologist at the Natural History Museum in London. “For half of Africa we really have no fossil record to speak of, so I think it’s quite likely there were surviving archaic forms living alongside modern humans.”
Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.