New tests on human bones hidden in a Spanish cave for some 400,000 years set a new record for the oldest human DNA sequence ever decoded—and may scramble the scientific picture of our early relatives.

Analysis of the bones challenges conventional thinking about the geographical spread of our ancient cousins, the early human species called Neanderthals and Denisovans. Until now, these sister families of early humans were thought to have resided in prehistoric Europe and Siberia, respectively. (See also: "The New Age of Exploration.")

But paleontologists write in a new study that the bones of what they thought were European Neanderthals appear genetically closer to the Siberian Denisovans, as shown by maternally inherited "mitochondrial" DNA found in a fossil thighbone uncovered at Spain's Sima de los Huesos cave.

"The fact that they show a mitochondrial genome sequence similar to that of Denisovans is irritating," says Matthias Meyer of Germany's Max Planck Institute for Evolutionary Anthropology in Leipzig, lead author of the study, published Wednesday in Nature.

"Our results suggest that the evolutionary history of Neanderthals and Denisovans may be very complicated and possibly involved mixing between different archaic human groups," he said.

Neanderthals and Denisovans arose hundreds of thousands of years before modern-looking humans spread worldwide from Africa more than 60,000 years ago. The small traces of their genes now found in modern humans are signs of interbreeding among ancient human groups.

Previously, the oldest human DNA sequenced came from bones that were less than 120,000 years old.

Meyer said stable temperatures in the cave helped preserve the mitochondrial DNA, and credited recent advances in gene-sequencing technology for establishing the basis for the new milestone.

Mixed Up or Mixing It Up?

For humanity's tangled past, the new mitochondrial DNA results raise an unexpected question: How does a Spanish early human species end up with Siberian DNA?

The authors propose several possible scenarios. For instance, Sima hominins could simply be close relatives of the Denisovans. But that would mean they lived right alongside Neanderthals without having close genetic ties to them.

The Sima hominins could also be a completely independent group that mingled with Denisovans, passing on their mitochondrial DNA, but it would be hard to explain why they also have Neanderthal features.

Another possibility, suggested by anthropologist Chris Stringer of the Natural History Museum in London, is that mitochondrial DNA from the Sima people reached the Denisovans thanks to interspecies sexual adventures among early humans, which introduced the DNA to both the Sima and Denisovans.

In the end, the identity of these ancient people remains a mystery, and further work is needed to clarify their identity. "The current genetic data [mitochondrial DNA] is too limited to conclude much about their population history," Meyer says.