Ancient DNA, new mystery

  • Article by: CARL ZIMMER , New York Times
  • Updated: December 4, 2013 - 9:10 PM

Human DNA found in a thigh bone in the Spanish cave Sima de los Huesos (“the pit of bones”) dates back 400,000 years, the oldest discovery yet. But it’s not Neanderthal.

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what they looked like: An artist’s rendering showed the humans of Sima de los Huesos, who are estimated to have lived about 400,000 years ago during the Middle Pleistocene. So far, their discovery has provided more questions than answers.

Photo: Photos by Madrid Scientific Films,

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Scientists have found the oldest DNA evidence yet of humans’ biological history. But instead of neatly clarifying human evolution, the finding is adding mysteries.

In a paper in the journal Nature, scientists reported Wednesday that they had retrieved ancient human DNA from a fossil dating back about 400,000 years, shattering the previous record of 100,000 years.

The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story.

It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, they were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found.

The mismatch between the anatomical and genetic evidence surprised the scientists, who are now rethinking human evolution over the past few hundred thousand years.

It is possible, for example, that there are many extinct human populations that scientists have yet to discover. They might have interbred, swapping DNA. Scientists hope that further studies of extremely ancient human DNA will clarify the mystery.

“Right now, we’ve basically generated a big question mark,” said Matthias Meyer, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and a co-author of the new study.

Hints at new hidden complexities in the human story came from a 400,000-year-old femur found in a cave in Spain called Sima de los Huesos (“the pit of bones” in Spanish). The scientific team used new methods to extract the ancient DNA from the fossil.

“This would not have been possible even a year ago,” said Juan Luis Arsuaga, a paleoanthropologist at Universidad Complutense de Madrid and a co-author of the paper.

But the DNA did not match that of Neanderthals. Meyer then compared it with the DNA of the Denisovans, the ancient human lineage he and his colleagues had discovered in Siberia in 2010. He was shocked to find that it was similar.

The new finding is hard to reconcile with the picture of human evolution that has been emerging based on fossils and ancient DNA. Denisovans were believed to be limited to East Asia, and they were not thought to look so Neanderthal-like.

One alternative explanation is that the humans of Sima de los Huesos were not true Neanderthals but belonged to the ancestors of both Denisovans and Neanderthals.

It is also possible the newly discovered DNA was passed to both Neanderthals and Denisovans but eventually disappeared from Neanderthals, replaced by other variants.

“It got lost in one lineage but made its way in the other,” suggested Jean-Jacques Hublin, a Max Planck paleoanthropologist who was not involved in the research.

Beth Shapiro, an expert on ancient DNA at the University of California, Santa Cruz, favors an even more radical possibility: that the humans of Sima de los Huesos belong to yet another branch of humans. They might have been a species called Homo erectus, which originated about 1.8 million years ago and became extinct within the past few hundred thousand years.

Piecing together the puzzle

When an organism dies, its DNA breaks down into smaller and smaller fragments, while also becoming contaminated with the DNA of other species such as soil bacteria.

In 1997, Svante Paabo of the Max Planck Institute and his colleagues, who had pioneered the techniques for retrieving DNA fragments, published a snippet of DNA from a Neanderthal fossil dating back about 40,000 years. They and other scientists then built on this success by searching for bits of DNA from other Neanderthals.

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  • This undated photo provided by Madrid Scientific Films in December 2013 shows the thigh bone of a hominin estimated to be about 400,000-years-old, excavated from Sima de los Huesos, Spain. Scientists have reached farther back than ever into the ancestry of humans to recover and analyze DNA, with a sample from this bone. So far, the achievement has provided more questions than answers about the human family tree. Results were presented online Wednesday, Dec. 4, 2013 in the journal Nature by Matthias Meyer and colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, with co-authors in Spain...

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