An early wave of modern human ancestors interbred with Neanderthals between 470,000 and 220,000 years ago, a new DNA discovery from an ancient Neanderthal thigh bone suggests. That’s much earlier than experts had thought, and it could help explain why human DNA seems to be appearing in Neanderthal genomes much earlier than it should.

There are conflicting answers in ancient DNA

It’s not entirely clear when humans and Neanderthals split — and there are conflicting answers in ancient DNA. The 124,000-year-old leg bone offers scientists a peek at the DNA animals get primarily from their mothers, tucked away in the cells’ energy generators. It looked a lot more human-like than it should, according to scientists led by Cosimo Posth at the Max Planck Institute for the Science of Human History.

We knew already that human ancestors interbred with Neanderthals. Even today, we can see signs of the inter-species hookups in the genomes of people with European ancestry. We also know that genes flowed in the opposite direction: DNA from a 130,000-year-old Siberian Neanderthal included chunks that looked human.

But that’s weird: humans didn’t engage in mass migration from Africa, their home turf, to Europe, Neanderthal territory, until 75,000 years ago. Early human-like DNA suggests that a female ancestor of modern humans gave birth to a Neanderthal several hundred thousand years before humans and Neanderthals were first thought to meet. Does that mean a small group of archaic humans left Africa early, and interbred before the big migration? Today’s findings, in the journal Nature Communications, suggest that it could.

It’s an interesting and provocative explanation, says Joshua Schraiber, a population geneticist at Temple University who was not involved in the research. And both he and Posth are eager to see if further genetic analyses back it up.

The reason scientists have trouble figuring out when Neanderthals split with humans has to do with the two different kinds of DNA in human cells: that contained in the cell’s nucleus, and the separate DNA inherited exclusively from one’s mother that build the cell’s energy generators, the mitochondria. Nuclear DNA says humans and Neanderthals split 765,000 to 550,000 years ago. Mitochondrial DNA, on the other hand, suggests the split was 365,000 years later, just 400,000 years ago.

But if a small party of human ancestors made its way into Europe, interbred with the Neanderthals, and left behind genetic traces in the mitochondria, that discrepancy might make sense. That’s why Posth and his colleagues extracted and sequenced the mitochondrial DNA from an ancient Neanderthal thigh bone discovered 80 years ago in Germany.

They added this new sequence to population models to recreate the genetic relationships between Neanderthals, their close cousins the Denisovans, and ancient humans. To do this, they pick chunks of DNA to compare between specimens. The more similar the sequences are, the more closely related the specimens. These family trees suggest that Neanderthals and an early wave of ancient human relatives may have interbred between 470,000 and 220,000 years ago. If the population of Neanderthals was small enough, this could have left the mark that Posth and his colleagues detected.

“It’s hard for genes to move when they don’t have cars and airplanes.”

There’s a hitch. Neanderthal populations, even if they were small, were probably spread out from Spain to Siberia — so Schraiber’s not certain how these genes could have spread across such a big area. “It’s hard for genes to move when they don’t have cars and airplanes,” he says.

Mitochondrial DNA is also a small piece of the larger genetic puzzle; to confirm their analyses, the researchers will need nuclear DNA. Right now, there isn’t any from this particular thigh bone, since it was chewed over by carnivores and contaminated with modern DNA. That doesn’t matter as much for mitochondrial DNA — but for nuclear DNA, the contamination makes analysis more challenging. (The scientists are still doing their best to extract ancient DNA from it, though.) So Posth and his colleagues will need more nuclear DNA to create more complete timelines of human and Neanderthal interactions.

Enough DNA samples may make it possible to retrace humans’ very early migration even without a fossil record, Posth says. That’s because we can track the human genes appearing among Neanderthals. “It’s a nice parallelism with what happens later, with the Neanderthals inside of us,” he says.