A new landmark study has revealed the oldest known human DNA ever to be found, dating back approximately 400,000 years – substantially older than the previous earliest human DNA from a 100,000-year-old Neanderthal. Initial analysis on the DNA reveals a complex and confusing interbreeding of species which took place in our ancient past, and scientists are still scratching their heads over exactly what kind of species the DNA belonged to.

The genetic material came from the bone of a hominin found in Sima de los Huesos, the “bone pit”, which is a cave site in Northern Spain that has yielded the world’s largest assembly of hominin fossils from the Middle Pleistocene, consisting of at last 28 skeletons.

Until now, it has not been possible to study the DNA of these unique hominins, however, scientists from the Max Planck Institute for Evolutionary Anthropology were able to use novel techniques to extract the DNA and have determined an almost complete mitochondrial genome sequence of a 400,000-year-old representative of the Homo genus.

The researchers then compared the DNA with Neanderthals, Denisovans, present-day humans and apes, and found that the individual shared a common ancestor with the Denisovans, a relatively newfound relative of humans who are thought to have lived in the vast expanse from Siberia to Southeast Asia. This was unexpected since the skeletal remains carry Neanderthal-derived features. In addition, this fossil was uncovered in Europe and not eastern Asia where it was believed the Denisovans lived.

"This opens up completely new possibilities in our understanding of the evolution of modern humans, Neanderthals and Denisovans," said study lead author Matthias Meyer, a molecular biologist.

The researchers suggest a number of possible explanations for these findings. First, this specimen may have been a close relative of the Denisovans. However, this seems unlikely because it would mean they lived alongside Neanderthals without having close genetic ties to them.

Second, the Sima de los Huesos humans may be related to the ancestors of both Neanderthals and Denisovans, but they would then have to explain how two very different DNA lineages stemmed from one group, one leading to Denisovans, the other to Neanderthals.

Third, the humans found at the Sima de los Huesos may be a lineage distinct from both Neanderthals and Denisovans that later perhaps contributed DNA to Denisovans. However, this suggests the group was distinct from Neanderthals but also independently evolved several Neanderthal-like features.

Fourth, the investigators suggest a currently unknown species brought Denisovan-like DNA into the Pit of Bones region, and possibly also to the Denisovans in Asia. This is the second study this month which has found evidence of a species currently unknown to science which bred with ancient human ancestors.

"The story of human evolution is not as simple as we would have liked to think," Meyer said. "This result is a big question mark. In some sense, we know less about the origins of Neanderthals and Denisovans than we knew before."

The scientists detailed their findings in the Dec. 5 issue of the journal Nature.

By April Holloway