Modern humans and Neanderthals have a confusing genetic relationship. One set of data suggests our two species diverged around 650,000 years ago—but other clues point to an ongoing close (that is, sexual) relationship between our ancestors that persisted until around 300,000 years ago. This is made all the more muddled by the fact that Neanderthals look like they were living in Eurasia 300,000 years ago while our own ancestors were still in Africa. And then the two groups clearly intermingled once humans did leave Africa.

One way to account for all this contradictory information is to suggest that another group of humans left Africa sometime between the Neanderthals' departure and our own. An analysis of Neanderthal DNA, published this week in Nature Communications, adds new weight to this hypothesis.

Sisters? First cousins? The genes are confusing

When people talk about DNA, most often they’re talking about nuclear DNA. That’s the DNA that combines genetic material from a mother and a father and sits in the nucleus of each cell. But the mitochondria—little energy-producing blobs that sit inside cells—have their own DNA, which comes exclusively from the mother. Mitochondrial DNA (mtDNA) is a fantastically useful tool for understanding evolutionary lineages, in part because there's so much more of it that it's still detectable in very old samples.

The picture painted by nuclear DNA (nDNA) is that, between 765,000 and 550,000 years ago, our ancestors in Africa diverged into two groups. One group would eventually lead to our own species, although we wouldn't make an appearance until around 200,000 years ago. The other group would lead to Neanderthals and the closely related Denisovans. This proto-Neanderthal/Denisovan group left Africa for Eurasia at some point; sometime around 430,000 years ago, they diverged into distinct Neanderthals and Denisovans.

But the picture painted by mtDNA is different. Neanderthal mtDNA is more similar to modern humans than it is to Denisovan mtDNA. And the divergence date between us and them, when estimated based on mtDNA, is much more recent—between 498,000 and 295,000 years ago.

Some researchers have suggested that you can explain this mixed genetic evidence if Neanderthals interbred with another, more recent African group of humans. This would provide them with different mtDNA after they split from Denisovans. And that, in turn, means that there must have been humans, closely related to our own species, who left Africa for Europe far earlier than previously suspected.

Out of Africa, earlier than we thought

Some archaeological evidence supports this scenario: African and Eurasian technologies in this time period have some important similarities. There’s also corroborating evidence from very old Neanderthal DNA from Spain, which has Denisovan-like mtDNA. That matches up with the picture that Neanderthals started out with both nuclear and mtDNA closely related to their cousin Denisovans, but had their mtDNA replaced through breeding with other humans.

But there are some plausibility issues here. We know that our own species interbred with Neanderthals more recently, so that’s not a problem—but could low-level interbreeding on this small scale really result in such drastic changes to Neanderthal mtDNA, without leaving much of a mark on its nuclear genome? It also hasn’t been possible to narrow down the window of when all this interbreeding might have happened. This makes assessing the feasibility of the mtDNA-replacement scenario difficult.

A Neanderthal thigh bone from southwestern Germany has offered up some answers. The bone has been dubbed HST, after the Hohlenstein-Stadel cave where it was found in 1937. It is the only human fossil from this region and time. Of course, a bone that has been handled by humans for that long is bound to have been subject to genetic contamination, and the researchers accounted for this in their analyses.

HST seems to have lived around 124,000 years ago, making this the second-oldest Neanderthal mtDNA to have been analyzed. The evidence pointed toward HST’s family line having diverged from other Neanderthal groups around 270,000 years ago.

That helps to narrow down the time frame of the genetic mixture with African humans: the mixing must have happened before 270,000 years ago. This suggests that the early migration out of Africa must have happened sometime before that. Given this timeframe, the researchers calculated that a huge mtDNA shift, based on low-level interbreeding, was, in fact, plausible.

It’s a new point in favor of this early-migration hypothesis, but a lot more evidence is needed. The story is inordinately difficult to piece together because data is so scarce. Analyzing genomic DNA from the HST thigh bone would be fantastic, if it were possible, but modern contamination and the decay of its incredibly ancient DNA make this a challenging prospect. We might get no more stories from HST—we’ll have to look to other Neanderthals for new puzzle pieces.

Nature Communication, 2016. DOI: 10.1038/ncomms16046 (About DOIs).