The oldest human DNA, dated by scientists at 400,000 years old, is not answering geneticists’ questions about human evolution but actually is baffling them more.

Published in the journal Nature, the study involved hominin fossils, those considered in the tribe that includes the human genus, from caves in northern Spain’s Sierra de Atapuerca. One site specifically, Sima de los Huesos, which translates to “pit of bones,” yielded what the study authors wrote is the “world’s largest assemblage of Middle Pleistocene hominin fossils.”

400,000 Year Old DNA From Thigh Bone Confusing Scientists

The DNA from this reassembled thigh bone’s from a cave in Spain was dated to be 400,000 years old. Scientists studying the DNA were baffled to find a common ancestor linking bone found in Europe to early humans thought to live in East Asia. (Image source: Nature)

The skeletons, according to the research, had characteristics like those found in Homo heidelbergensis and European Neanderthals. Analyzing mitochondrial DNA (DNA located in the organelle that produces energy for a cell) though, the scientists found the sample was related to what the study calls the “eastern Eurasian sister group to Neanderthals,” scientifically identified as Denisovans.

It’s this discrepancy — bones found in Europe with a genetic overlap to samples only found so far in Asia — that’s confusing scientists.

Location of the Middle Pleistocene site

This map shows the distribution of where the fossils were found and where samples from common ancestors linked through DNA analysis have also been found. (Image source: Nature)

“This really raises more questions than it answers really,” senior author Svante Paabo, a biologist at the Max Planck Institute for Evolutionary Anthropology in Germany, said, according to The Los Angeles Times. “It’s a big surprise.”

“No one knows what to make of this,” Ian Tattersall, an anthropologist with the American Museum of Natural History in New York who was not involved in the study, told The Wall Street Journal. “We are lifting the edge of the curtain onto something more complex than any of us had ever thought.”

Here’s how WSJ explained the conundrum the data presented:

Experts offered four tentative theories to account for the puzzling pedigree revealed in the mitochondrial DNA, which is passed from a mother unchanged to all her children: The people at the Sima cave could have been a distinct species that had interbred with Denisovans. They also could have been related to the ancestors of Denisovans; the ancestors of both Denisovans and Neanderthals; or related to an older human species that lived elsewhere in Europe and Asia, such as Homo heidelbergensis. Or all of the above.

[…]

The researchers compared the Sima genetic sequence to the mitochondrial DNA from modern and ancient humans, Neanderthals, Denisovans, chimpanzees and bonobos. The Sima sample overlapped only with Denisovans, according to the researchers.

“We thought they were Neanderthal relatives but the mitochondrial genome told a different story,” said Juan-Luis Arsuaga, director of the Center for Contemporary Human Evolution at the Institute of Health Carlos III in Madrid, who has worked at the Sima site since 1983. “It was unexpected and shocking.”

The researchers hope analysis of DNA from the bone cell’s nucleus could yield more answers.

“It’s possible that we’re simply so far back in the history of these populations that we are close to the population that was ancestral to all these individuals,” Paabo said in a Nature podcast, according the LA Times. “Another alternative is that this ancestral group actually interbred with something much older, something like Homo erectus, and obtained its mitochondrial DNA from them.”

Compared to European Neanderthals, about which scientists know a significant amount based on the number of samples, little is known about the Denisovans.

“What’s fascinating about the Denisovans is we know next to nothing about how they looked,” Paabo said. “We have their genome and we have two teeth, and those teeth are huge. … The only thing we can say is they must have been very big, or at least have big mouths.”

Such genetic analysis, according to the BBC, was made possible by advancement in sequencing technology.

“Years ago, geneticists said they wouldn’t be able to find DNA that was older than 60,000 years old,” study co-author Jose Bermudez de Castro with the National Research Centre for Human Evolution said. “Of course, that wasn’t true. The techniques have advanced hugely.”

“Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old,” Paabo added, according to BBC.