My genome isn't all human. Neither is that of most non-Africans. As our ancestors migrated around the world they interbred with hominin species they found there. As a result of this, we have a few Neanderthal genes in us. Some have helped more than others. However, there was next to no evidence of Neanderthal interbreeding going the other way. No sign that the Neanderthals inherited some of our genes.
This has led to all sorts of speculation about why our interactions were so one-sided. Perhaps lone Neanderthals were adopted into human groups. Maybe we kidnapped them. But it turns out all of that speculation was exactly that. A deeper dive into our cousin species' genetics has revealed the fingerprints of them inheriting some of our genes. This new data also helps narrow down when and where some of this interbreeding may have happened.
A deeper dive into our cousin species' genetics has revealed the fingerprints of them inheriting some of our genes. This new data also helps narrow down when and where some of this interbreeding may have happened.
Neanderthal genes told the wrong story
As a whole, Neanderthals are more closely related to another contemporary (but now extinct) group of hominins called Denisovans. These two extinct species split from each other around 500,000 years ago. Their ancestors split from our lineage about 750,000 years ago. Once we were all split up, our ancestors worked to bring us back together with a cheeky bit of interbreeding.
However, it turns out the Neaderthal mothers preserve a different record of our interactions. Mitochondrial DNA is only inherited through the maternal line and was some of the first DNA to be recovered from both Neanderthals and Denisovans.
This is because each cell has multiple copies of it, making it more likely to be preserved. But it turns out that the resulting analysis of the mtDNA of recent Neanderthals (as in, lived in the past 50,000 years) it contradicts the rest of the DNA entirely. This isn't the only time the initially discovered mtDNA has told a "wrong" story.
Getting back to the Neanderthals. Whilst the bulk of their DNA shows Neanderthals and Denisovans are more closely related to each other than to us, their mtDNA claims we are closer relatives to the Neanderthals than the Denisovans. Since mtDNA was recovered first the earliest published family trees all put us closest to the Neanderthals, with the Denisovans as a lonely out group.
Neanderthal interbreeding preserved by mothers
Right, so now we're all caught up on how weird recent Neanderthal DNA is? Fortunately, we can look to the old timers for a solution. An ancient chunk of Neanderthal mtDNA has finally helped us understand what was causing all this weirdness.
It comes from the cave of the Swabian Jura in southwestern Germany. It follows the "proper" Neanderthal pattern, being more similar to the Denisovans than to us. This tells us that at some point in Neanderthal history their mtDNA shifted dramatically from being more Denisovan-like to being more human-like.
What could possibly cause such a thing? You guessed right: interbreeding. It now appears that Neandethal mtDNA behaved normally until sometime after the Swabian Jura cave. Then, they interbred with us and got our mtDNA out of the deal. This spread through Neanderthal populations, persisting until the "recent" Neanderthal we examined first. As such, they had more human-like mtDNA than expected, creating the wrong family tree shown above. Now we know about that, we can correct for that and create a correct family tree.
Now we know about that, we can correct for that and create a correct family tree. However, it's worth noting that we've only found mtDNA from Swabian Jura. And we now know how well basing a whole family tree of that can go. Perhaps further work on this sort of super ancient DNA will find further traces of interbreeding going both ways between our species.
Pushing back Neanderthal interbreeding
The other big thing to note about this mtDNA from Germany is that it's very old. Combining this with previous discoveries could help us pinpoint when the extra bit of Neanderthal interbreeding happened. After all, it must have been between them! Such comparisons reveal that it must have happened sometime between 260 - 460,000 years ago.
This is notable for being about 200,000 years older than our previous estimates. This doesn't just shake up the timing of our interbreeding, but perhaps the location as well. At this time we may still have been human but we hadn't left Africa yet. At least, the lineages leading to modern non-African's hadn't. Some may have made earlier, failed migrations. Perhaps the interbreeding happened between them and the Neanderthals.
But there may have been earlier migrations by our species out of our African homeland. These migrations ultimately failed, leaving behind no modern descendants. But perhaps they still managed to have a bit of fun on the way, interbreeding with the unusual species they found! And that's not the end of it. This ancient case of Neanderthal interbreeding might have some even further reaching implications. Whilst these failed migrations that might have mated with Neanderthals did die off, they may have interbred with the successful humans as they passed through.
All of this creates a fascinating mystery. Humans leaving Africa and mating with Neanderthals. The species sharing genes, despite both branches being ultimatley doomed. But not before those humans find more of their own species, allowing their genes (and perhaps some Neanderthal hitchhikers) to survive until the modern day.
It seems that these new discoveries are creating as many new mysteries as they help solve. I'm not complaining though, it keeps me in a job.
References
Posth, C., Wißing, C., Kitagawa, K., Pagani, L., van Holstein, L., Racimo, F., Wehrberger, K., Conard, N.J., Kind, C.J., Bocherens, H. and Krause, J., 2017. Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nature communications, 8.
