Four-hundred-thousand-year-old human remains found deep in the Pit of Bones — a cave 43 feet under the ground in northern Spain — could hold the secrets of our origin. For now, however, the first analysis of ancient human genetic material has created more questions than answers.

"Right now, we've basically generated a big question mark," study researcher Matthias Meyer, of the Max Planck Institute for Evolutionary Anthropology in Germany, told The New York Times.

Skeleton of a Homo heidelbergensis from Sima de los Huesos, a unique cave site in Northern Spain. Javier Trueba, MADRID SCIENTIFIC FILMS

The Pit of Bones was discovered in the 1970s and scientists have been studying it and the bones it contains ever since. So far they've found the bones of 28 ancient humans, tentatively classified as Homo heidelbergensis, dating back hundreds of thousands of years.

The 400,000-year-old bones were originally thought to belong to ancient relatives of Neanderthals, a species of ancient hominin on a different branch of the evolutionary tree than our ancestors, based on their size and shape.

But the new genetic information published Dec. 4 in the journal Nature has thrown that assumption into question.

The researchers used a completely new technique to isolate the DNA from a thigh bone, which they say wouldn't even have been possible a year ago.

Previously, the oldest human DNA ever sequenced was a paltry 100,000 years old.

The genetic material they sequenced is not the DNA we traditionally think of but the specialized DNA that runs our cell's energy-making machine (the mitochondria) and is passed down only from the mother.

This mitochondrial DNA indicated that these ancient humans, though they looked like Neanderthals, were more genetically related (or, at least their mitochondria were) to another ancient human species, the Denisovians.

The Denisovians are a completely different, also dead, branch of the human evolutionary tree. They are known to have lived about 80,000 years ago in East Asia. The bones from those Denisovians don't look like Neanderthals or like the 400,000-year-old bones that researchers have found in the pit.

The thigh bone of a 400,000-year-old hominin from Sima de los Huesos, Spain, was excavated by Arsuaga and his team. Javier Trueba, MADRID SCIENTIFIC FILMS Finding their DNA thousands of miles and hundreds of thousands of years away from where we thought Denisovians evolved throws everything we know about ancient humans and how they spread out around the globe and evolved into distinct species into question.

"It's extremely hard to make sense of," Meyer told The NYT. "We still are a bit lost here."

The DNA isolated from these ancient bones suggests that there could have been many more species of ancient humans than we thought.

Another possibility is that these mysterious people found in the Pit of Bones were the evolutionary ancestors of both the Neanderthals and Denisovians. The mitochondrial DNA might have disappeared from the Neanderthals at some point but remained with the Denisovians, the researchers said.

This builds upon other findings, presented Nov. 18 at a meeting on ancient DNA at the Royal Society and reported by Nature News, that indicated that ancient humans interbred with not just Neanderthals and Denisovians, but also another mystery relative. The researchers on that study suggest that it could have been the ancient human species Homo erectus, which came along a few million years ago, then disappeared from the fossil record right before modern humans.

Ben Shapiro, an ancient DNA researcher from the University of California, Santa Cruz, suggested to The New York Times that Homo erectus could be the species in the Pit of Bones as well.

The only way to find answers is to sequence more of the ancient DNA in the pit and from other ancient human fossils.