How one way was human-neanderthal interbreeding?

Human-neanderthal interbreeding introduced a lot of Neanderthal DNA into humans, but why did none of it go the other way? It mya have after all.


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Our species evolved in Africa, but it didn’t stay there. We took a dramatic journey around the world, expanding onto every continent. But we weren’t the first to leave our homeland, several hominin species had left before. And when our species met up with them, things got spicy. Famously, there was a fair bit of human-neanderthal interbreeding.

As a result of this most non-Africans (and thanks to gene flow, a fair few Africans) have a healthy serving of non-human DNA in their genome. But curiously, most of the interactions between our species seems to have been one way. Next to no human genes wound up in the Neanderthals, for instance.

The Neanderthal family tree, with newly identified human genes jumping into them

All that changed with the recovery of DNA from a 120,000-year-old Neanderthal femur. It revealed that Neanderthals did get a few genes from us after all. However, not that many made the jump, suggesting most of the human-neanderthal interbreeding was still one way. What’s up with that?

Default stance

The obvious explanation for the one way flow of human-neanderthal interbreeding is that it actually just was one way. It’s a shocking idea, I know. For whatever reason, the surviving “hybrids” of our species stayed in human groups. This kept Neanderthal genes in our gene pool but prevented the human genes from entering the Neanderthals.

Saying much more than that enters the realm of wild speculations. But that hasn’t stopped people trying. Since the one-way pattern became apparent I’ve heard all sorts of ideas. Some suggest that it was human kindness that kept this pattern going. We adopted Neanderthals into our group, introducing their genes into our populations. Perhaps we took pity on Neanderthals lost and alone in the ice age tundra and brought them in from the cold. But Neanderthals never returned the favour, keeping their lineage “pure”.

Others have argued that our interactions may not have been quite so altruistic. Perhaps we forcibly kidnapped Neanderthals, keeping them prisoner in our tribes. The resulting mix of their genome into our gene pool might have been similarly forceful.  But whilst the Neanderthals would happily engage in cannibalism, they never stooped to that level. Or if they did, they didn’t keep any resulting offspring around.

Neanderthals hunted humans

Angry bigfoot or human relative? The Neanderthal predation theory can’t decide!

(As a great aside, the delightfully wacky “Neanderthal Predator Theory” argues for that last point. Neanderthals were horrible rapists who never took responsibility for the resulting offspring. The fact our interbreeding was so one way was taken as proof of the “theory”).

As fun as it is to speculate about these things, it must be remembered that it is just speculation. All we can say for sure is that, for whatever reason, gene flow into the Neanderthals was rare to non-existent. Or was it?

Time heals all genes

Neanderthals live a long time ago. Any interbreeding with humans also happened a long time ago. This simple fact can be easy to forget. The timescales involve just boggle the mind! But this does mean there’s plenty of time for some big changes to happen.

After all, for us to get evidence of interbreeding then the resulting genes must remain in the gene pool long enough for us to find it. In the case of humans, most of our evidence comes from the present day. So the descendants of any interbreeding must survive for tens of thousands of years for us to spot them. If they were to die out earlier, their lineage would be lost. And with it that evidence of interbreeding, making it seem like we were interacting a lot less than we actually were.

This femur from Siberia is part of an extinct human family that did extra Neanderthal interbreeding

And this isn’t hypothetical speculation either. We’ve found older human genomes that seem to show more Neanderthal DNA than expected. Clearly, there were more cases of human-neanderthal interbreeding than we knew about. Some just died out before we spotted them. A similar problem might plague Neanderthal data. Most of our DNA samples from them comes relatively late in their history. Earlier interbreeding events might have since gone extinct.

In Neanderthals, the issue is further compounded by the way they live. That same genetic evidence suggests they lived in small, isolated groups. That isolation would make it harder for any human genes to spread through the population, putting them at higher risk of going excting. And just like that it looks like they never got any of our genes.

Human-neanderthal interbreeding going the other way

These caveats mean we can’t be sure that human-neanderthal interbreeding was one way. But at the same time, that isn’t an excuse to start speculating about possible “lost” relationships between our species. I’ve already done more than enough speculation for one article. We need evidence.

Luckily for me, there is some. Neanderthal fossils from the Altai mountains of Siberia have yielded useful DNA. When compared to other Neanderthal fossils and modern Africans it looks like up to 7% of their DNA comes from humans. However, the other Neanderthal groups examined appeared to have minimal contact with humans, even via the Altai group.

A new Neanderthal family tree, showing the introduction of human DNA into the Altai group. Note how the Neanderthal groups remain separated, prevented the human genes from further spreading into other Neanderthal groups.

Crucially, this evidence seems to match what would be expected, based on the aforementioned caveats. Human-neanderthal interbreeding took place in one group of Neanderthals. Their isolation and small population sizes prevented the resulting human genes from spreading. The group then died out, taking that evidence with them.

This raises the possibility that other isolated groups might also have hooked up with humans more than expected. Because when you’re as similar to humans as Neanderthals were, how can they not be trying to have sex with everything?

References

Kuhlwilm, M., Gronau, I., Hubisz, M.J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H.A., Lalueza-Fox, C., de La Rasilla, M. and Rosas, A., 2016. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature530(7591), pp.429-433.

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 communications8.

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