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Mystery Human Ancestor Found in African Genes

We are not alone. An unknown group of archaic humans interbred with our more modern species in Africa thousands of years ago, contributing DNA that is still with us, according to a new scientific paper. These ghosts within our genome are revising the history of Homo sapiens, which once was thought to have crushed any humanlike competitors on its way to inheriting the earth. In reality, we had sex and had kids with these extinct groups.

In fact, this is the third population of archaic humans—groups slightly different from the modern mold—that we consorted with. Within the last two years, scientists have pulled ancient DNA from Neanderthal bones and learned that it matches some of ours. And a finger bone from a cave in Siberia, belonging to a 30,000-year-old group called the Denisovans, has yielded a different set of DNA that we carry as well. Now comes evidence of these unknown Africans. But this time the hints of an ancient dalliance don’t stem from fossils but from DNA alone.

Hadza archers in Tanzania

They are small stretches of genetic material that turned up in three hunter-gatherer groups: Pygmies in western Cameroon, and the Hadza and the Sandawe in Tanzania. The material doesn’t look as if it originated with those groups, but because it is common to all three, it seems to have been introduced prior to 40,000 years ago, when the groups split apart. (If the DNA entered three populations after the split, it would be unlikely to be so similar in all three of them.)

“That’s pretty cool,” said John Hawks, an anthropologist at the University of Wisconsin at Madison who works with Neanderthal and Denisovan DNA. “Anthropologists have historically looked at fossils and tried to draw lines connecting them. But that’s a poor approach because fossils are really hard to find.” DNA, on the other hand, tells its story within every human cell, and new technology is making those tales ever easier to read.

Indeed, the paper, published today in the journal Cell, is the first to sequence the entire genomes of those African groups, some of the oldest lineages in the world; previous analyses have focused on Europeans. And it shows an extraordinary diversity that has been missed in the Eurocentric effort. “The total number of known human DNA variants is about 40 million,” said Sarah Tishkoff, the geneticist at the University of Pennsylvania who led the research. “We found another three million just from sequencing five people from each group. That’s a huge percentage increase from just 15 individuals.”

Another key finding is that most of the new variants are not genes—stretches of DNA that code for proteins that run a cell’s machinery—but regulatory regions that sit next to genes, turning them on or off, or increasing their protein production rate the way a radio volume knob increases sound. “Just because a stretch of DNA doesn’t have any genes doesn’t mean it can’t be functionally important,” noted Joseph Lachance, a postdoctoral researcher at Pennsylvania who is first author on the paper. To the contrary, he said, because those regions persisted and most genes didn’t, it shows that things like on-off switches are important evolutionary adaptations.

The genetic revelations about a previously unknown ancestral group don’t completely shock anthropologists who have studied stones and bones, because they have been painfully aware of the gaps in the fossil record that Mr. Hawks mentioned. “This is no surprise to me!,” wrote Christopher Stringer, an anthropologist at the Natural History Museum in London, in an e-mail. Last year he cited a human skull from Nigeria that had primitive features but was only 13,000 years old. Since more modern-looking humans had lived in that area for 100,000 years, the skull indicated a long overlap between the two groups and raised the possibility of interbreeding.

Henry Harpending, an anthropologist at the University of Utah, added in an e-mail that “there are funny findings in African archaeology that no one understands very well,” tools that can’t be easily linked to groups that anthropologists know about. He singled out “some beautiful stone harpoon points …, at about 110,000 years ago from the Congo basin. They are unlike anything for another 70,000 years.” These oddities point to archaic human populations that so far have escaped scrutiny.

Now the evidence is mounting that not only did they exist, they interbred with the branch of humanity leading directly to us. For decades, scientists argued that the only interactions modern humans had with Neanderthals was to kill them, since the heavy-browed, barrel-chested group disappeared about 30,000 years ago and our branch showed no traces of their distinctive skeletons in our shapes. And after all, we were modern and thus somehow superior. But the discovery that Europeans got about 4 percent of their genes from Neanderthals—specifically, immune-system genes—knocked the legs from under that argument.

In Africa, without well-preserved bones to pull ancient DNA from, Tishkoff, Lachance, and their colleagues relied upon the modern DNA that they sequenced and a model of the population that produced it. Essentially, a small group—the Hadza, for instance, have about 1,000 members—should have a limited amount of DNA diversity. But if they have an unusually large number of DNA variants in a particular stretch of their genome, it indicates an influx of genes from elsewhere. And if those variants are not found in other typical modern genomes, it indicates the source was another archaic group.

“We have evidence of Neanderthals, Denisovans, and ‘hobbits’ [short skeletons found in Indonesia, formally called Homo floriensis] all living sometime in the relatively recent past before either dying out,” Lachance said. “It’s certainly possible there were several more.” A paper published last year in the journal Evolution used a mathematical model to estimate there were eight archaic lineages, and perhaps as many as 27.

But it’s not just that they existed but how they existed that intrigues anthropologists. “Now we can begin to talk about the genetic adaptations of a group of people for whom we don’t have fossils,” said Wisconsin’s Hawks. Like Lachance, he is particularly interested in the non-genes, the regulatory, non-protein-coding regions that predominate in this DNA. “There was something about the coding regions that didn’t work, so they weren’t picked up in future generations,” he said. “Non-coding regions are clearly adaptive.”

Genes are crucial too, Tishkoff hastened to add. In the three hunter-gatherer groups, her team found variants in genes that influence taste and smell. Such variation could be adaptive in groups that live in different environments and hunt and gather different food: the Pygmies inhabit the forest, for instance, while the Hadza and Sandawe live in more open lands.

In her previous work among Pygmies, she found an abundant presence of a gene that influences the immune response, useful in a region rife with parasites and viruses. But it also hampered the production of growth hormone, and could explain why Pygmies are short. The new research, however, used more-complete sequences, and it revealed a surprise in the Pygmies: another gene called HESX1. “We’d completely overlooked this the first time, and the gene is a known cause of short stature. It regulates the pituitary gland, which produces growth hormone. That really excites me,” she said.

These new genetic approaches to anthropology are exciting the entire field, as detailed walks through the genome are starting to unravel the mysteries of both the living and the dead.

(Photo courtesy Woodhouse, Creative Commons license)

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