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Feature Story: Our Tangled Family Ties

Homo Neanderthalensis

Our Tangled Family Ties

Scientists call it "gene flow." The rest of us call it "sex." And apparently, our ancestors had it with Neanderthals, Denisovans, and who knows who else.

 

If you’ve ever been pressed to declare your loyalty as a “Beatles person” or a “Stones person” – no points for saying “both” – you know how paleoanthropologists felt back in 1988. That was the year Chris Stringer and Peter Andrews divided their field in two with a Science paper that laid out opposing models for how Homo sapiens came to be. In the first model, dubbed “multiregionalism,” people around the world gradually evolved from archaic forms such as Homo erectus and Neanderthals into what we are today. In the second, “out-of-Africa,” the modern human species arose on that continent, migrated out in one swoop some 65,000 years ago, and displaced (but did not mate with) all the other hominids on the planet.

The models laid out in the paper were irreconcilable. Either ancient hominids outside Africa had contributed to our DNA by breeding with our ancestors, or they hadn’t; either modern humans arose as a new species in Africa, or they didn’t. Neither model necessarily represented what Stringer and Andrews actually believed. They had written their arguments in black and white because that enabled them to make diverging predictions about future fossil discoveries, “which might help bring some resolution to what had been a very long and difficult debate” already, says Steven Churchill, a biological anthropologist at Duke University. Some paleoanthropologists, including Churchill, looked at the models and decided truth must lie somewhere in the middle.

Genetic evidence collected since 1988 was spurring a “growing realization of just how complex [the rise of modern humans] probably was.” And was it ever!

a caveBut others took sides. Milford Wolpoff of the University of Michigan, became the chief defender of multiregionalism, noting that early modern European fossils had some Neanderthal-like features. Stringer championed the 'out-of-Africa' model, which was supported by the limited genetic data available at the time. Within a few years, textbooks had been rewritten to reflect the divide. One book from 1998 even featured opposing photos of Wolpoff and Stringer (under the heading “Competing Hypotheses”) looking as if, at any minute, they might get into a fistfight. Yet the textbook acknowledged that real life is rarely as clear-cut as dichotomous models make it out to be, and that genetic evidence collected since 1988 was spurring a “growing realization of just how complex [the rise of modern humans] probably was.”

And was it ever! It’s probably time to rewrite the textbooks again, because genomics has now shown that the answer to “which model” is in fact “both.” Yes, the human species arose recently in Africa and migrated out. And yes, ancient hominids contributed to our DNA by interbreeding. “The rival interpretations may tell us a lot about the evolutionary process,” says Rick Potts, director of the Smithsonian Institution’s Human Origins Program. “They’re competing ideas only if you live in a simple universe. And evolution isn’t simple.”

the Denisovans, an even more ancient group of Asian hominids who were cousins of the Neanderthals. They also appear to have contributed genes to our species (so, yes, we had sex with them too)

The first genomic finding that shook up the debate came in 2010 with the sequencing of the Neanderthal genome. It showed that 1 to 4 percent of the DNA of non-Africans living today comes from Neanderthals. In other words, at some point, probably between 47,000 and 65,000 years ago, Neanderthals or a group of hominids with very similar genes got together with anatomically modern humans and had kids.

Before 2010 was out, another finding had upended the field again: the unveiling of the Denisovans, an even more ancient group of Asian hominids who were cousins of the Neanderthals. They also appear to have contributed genes to our species (so, yes, we had sex with them too), based on an analysis of DNA taken from a broken finger bone and a wisdom tooth. The genomes of Australian Aborigines and people who live in New Guinea today are almost 5 percent Denisovan. In May of this year, researchers revealed a fuller analysis of Denisovan DNA. Apparently, the Denisovans were quite the swingers: The new data showed that they mated with not only us, but also two other hominids. Seventeen percent of the Denisovan genome comes from a familiar source – the Neanderthals, their cousins. Another 4 percent comes from a different, archaic species about which almost nothing is known.

​And the modern human populations who continued to live in Africa while their counterparts expanded throughout the rest of the world? There is mounting evidence that they, too, interbred with previously unknown archaic humans. Last year, scientists sequenced 15 full genomes from three African hunter-gatherer groups and found a number of unusual genetic features that could be explained by interbreeding with an archaic African species less than 80,000 years ago. In March of this year, another group published a paper describing an astonishingly ancient Y chromosome that had been passed down intact for 338,000 years – well before the first anatomically modern human fossils appeared around 200,000 years ago. The chromosome, which had shown up by chance in a consumer genetic database, belonged to an African American man; scientists also tracked it down in a handful of Cameroonian villagers who might be that man’s very distant relatives. It is possible that an ancestor of these people interbred sometime in the last 200,000 years with an archaic African human who carried the very old Y. There is even a hunch (if only a hunch) as to where that could have happened: the site of Iwo Eleru, relatively near the Cameroonian village, but across the Nigerian border, contains fossils that date to between about 12 and 16 thousand years ago with an unusual mix of ancient and modern traits.

an astonishingly ancient Y chromosome that had been passed down intact for 338,000 years – well before the first anatomically modern human fossils appeared

What does all this genomic data mean for the Wolpoff-Stringer showdown? That depends on whom you ask. Wolpoff himself views it as validation for his model, which was built on the idea that we all carry ancient DNA. “We multiregionalism folks are absolutely thrilled,” he says. “I’m 70 years old, and I’m so happy to have lived to see this.” Then again, Stringer has embraced the data too. He writes about it at length in a new book, pointing out that we don’t know how often interbreeding occurred – but also emphasizing that he never thought it was impossible and highlighting evidence he finds especially interesting, such as the Nigerian fossil site.

scientist drilling into boneBut other paleoanthropologists have not greeted some genomic evidence of interbreeding with open arms. The African hunter-gatherer study in particular has irked some, because there is relatively little fossil evidence of archaic species from that continent – and no ancient DNA. Even if good archaic African fossils did exist, they might not yield much genomic material, as it degrades quickly in humid, tropical climates. So the debate may continue indefinitely.

But perhaps not, says Potts, since scientists are working on ways to extract more and more information from smaller samples of DNA. “If techniques were developed that let us get DNA and amplify it out of tropical fossils,” he says, “a vast expansion in both our confusion and our clarity would emerge.” Confusion, then clarity, then more confusion – in this field, that’s just how it goes.

Mary Carmichael is a science writer in Boston, Massachusetts. According to 23andMe, her genome is 2.6 percent Neanderthal.

Photo Credits

Stone tools photos courtesy of Curtis Marean, Ph.D.

Resources

(1) Revolutionizing the Out-of-Africa Story. Genetic Engineering & Biotechnology News.

(2) Out of Africa: Startling New Genetics of Human Origins. Scientific American.

(3) Palming Homo Erectus. Weblog.

(4) Liujiang Homo Sapiens Fossil Skull. The Bradshaw Foundation.