When Matthias Meyer began studying the ancient DNA in the 400,000 year old fossils he found in the Sima de los Huesos, or Pit of Bones cave, deep beneath the Atapuerca mountains in Spain, he was pretty sure he knew what he’d find. The bones looked like they belonged to an ancestor of the Neanderthals, who roamed Europe from at least 250,000 to 30,000 years ago. Right place, right time, right bones ought to mean right genetic material too.
But as he examined the genome he and his collaborators had painstakingly put together, Meyer couldn’t find the matches he expected with the Neanderthal genome. This was another pre-human group altogether—the Denisovans, who were around until about 41,000 years ago. There was just one problem with that: the Denisovans, as far we know, were never near Spain. The only traces we have of them place them some 6,000 miles (9,700 km) away, in Siberia, not a distance easily traversed in the Pleistocene.
The story of whose ancestor is in the Pit of Bones and how the remains got there could shed new light on the evolutionary relationships among early humans. And the techniques used to probe the question, detailed in this week’s Nature, could open up new vistas in the exploration of human ancestry.
The DNA used in the study is some of the oldest ever to be sequenced. Meyer, a molecular geneticist at the Max Planck Institute of Evolutionary Biology, and colleagues, including paleogeneticist Svante Paabo, are experts at this kind of genetic sleuthing, part of the group that released a draft Neanderthal genome in 2010, as well as a Denisovan genome in 2012. But working with DNA this ancient was a new challenge. The Neanderthal and Denisovan fossils used for sequencing are all less than 100,000 years old. The DNA from the Pit of Bones is four times as ancient—and that’s a problem.
DNA falls apart as it ages, disintegrating into fragments like a rusty tin can. The older it is, the tinier the pieces that are left, and the tinier the pieces, the harder to get a sequence. Heat makes DNA fall apart faster. Meyer says that previous ancient sequencing studies were made easier because the DNA was deposited during a cold period.
“But if you go back then a few hundred thousand years further,” he says, “some of these times you had warmer temperatures than now.” Some DNA from that era has been sequenced from rare samples preserved in permafrost. But the fossils in the Pit of Bones had been exposed to warmer temperatures.
To make their study work, the team thus focused on sequencing DNA from the mitochondria of the cell, rather than DNA from the nucleus of the cell. While each cell has just one set of nuclear DNA, it has at least several hundred copies of the mitochondrial version, so there would be more of it left after all this time. Also, while nuclear DNA has many repetitive sections that make it difficult to sequence from small fragments—you can never tell if what you have is the next piece in the puzzle or just a duplicate lying around—mitochondrial DNA does not.
The researchers next sieved out DNA fragments from two grams of fossil femur, collecting fragments that tended to consist of clumps of single-stranded DNA, rather than the long double strands that sequencing usually works best for. Still, with some creative tweaking, Meyer and his colleagues were able to get the sequencer to detect the samples. Along the way, they also had to deal with contamination from modern human DNA—from excavators and even the researchers themselves, despite their efforts to keep their work field sterile—a problem that plagues every study of ancient genetic material. Even with all that meticulous processing, in the end, Meyer estimates, “there’s less than a 10th of the DNA of an ancient cell inside two grams of material.”
But it was enough to get a reading—to reveal that what seemed to be the wrong bones were in the wrong place. So how did they get there? The researchers lay out several possible explanations, none of them particularly tidy or airtight. The fossil could come from an ancestor of the Denisovans—but that would imply that the Denisovans and Neanderthals lived in the same areas, at least for a while, while remaining genetically distinct. It could be from a group, separate from the other two, that gave the Denisovans their mitochondrial DNA—but the bones look a little too Neanderthal-like to be totally distinct. Narrowing down these and other possibilities will require a sequence of nuclear DNA, a task that will require further refinements of sample-production technique and a much larger amount of fossil bone.
Still, the fact that a mitochondrial genome could be reconstructed in this way has important ramifications, says Beth Shapiro, a professor of ecology and evolutionary biology at University of California, Santa Cruz, who specializes in paleogenomics. “It means that there are likely to be many more samples out there that contain recoverable amounts of DNA — samples that we otherwise might have glossed over or given up on, thinking they were too old, or from a climate that was too warm, for DNA to be preserved,” she wrote in an email.
One thing at least is clear: We have hardly written the last chapter on either genetic science or our human ancestry. As either one advances it will carry the other along with it—a nice case of cooperative evolution if ever there was one.