Back in 2010, Svante Pääbo’s group from the Max-Planck Institute for Evolutionary Anthropology in Leipzig Germany published the first big chunk of Neanderthal DNA. This was a big deal, because it was the first time so much ancient DNA had been sequenced so completely and what they found when they compared this DNA to that of modern humans. It became pretty obvious early on that everyone except Africans shared around 2% of their DNA with Neanderthals.
The simplest (although by no means only) explanation for this result is that humans and Neanderthals had babies together before Neanderthals went extinct. Based on this idea, scientists in two separate studies (here and here) searched the DNA of over 1,000 modern humans to find what Neanderthal DNA still lurks in non-African DNA today.
These scientists found that 20-40% of Neanderthal DNA is still hanging out somewhere in these folks’ DNA. That is a whole lot of DNA that's still around after tens of thousands of years!
A close look at this Neanderthal DNA suggested that some of the DNA stayed because it gave the hybrids an advantage. It also suggested that the hybrids had trouble having kids. Neanderthal DNA giveth and it taketh away.
Better at Surviving in Europe, Worse Fertility
Neanderthals arrived in Europe and Asia hundreds of thousands of years before modern humans did. This gave Neanderthals plenty of time to adapt to the cold and to all of the bacteria, viruses and so on that they had to live with.
When modern humans ventured out of Africa all those years later, they were undoubtedly assaulted by a range of bacteria and viruses they had never seen before (think smallpox in the New World). One way to survive the onslaught would be to have kids with the locals who had already adapted. Sure, you might still have problems, but your kids would definitely do better.
When you look at the Neanderthal DNA that has survived, you see a whole lot of immune genes. (The same is true for another ancestor, the Denisovans.) This strongly suggests that interbreeding gave the hybrids the immune genes they needed to survive in this new environment.
You also see a lot of genes that have to do with skin and hair (keratinocyte genes). Although not yet proven, one idea is that some modern humans still have these because they helped them deal with the cold of the northern parts of Asia and Europe.
There has also been a recent study that suggests that a bit of Neanderthal DNA that helps deal with ultraviolet light is very common in East Asians. This makes sense given the lighter skin needed to get vitamin D up north. And scientists keep finding more genes like this (click here for one dealing with fat metabolism in Europeans).
Of course nothing in life is free. If you are going to breed with Neanderthals, you are probably going to have some problems too.
When you look for Neanderthal DNA in human DNA, you quickly realize that there is hardly any of it on the chromosomes that determine gender, the X and the Y. When this sort of thing is seen in the lab with fruit flies, it comes from something called hybrid sterility. Basically while humans and Neanderthals weren’t quite horses and donkeys, they were close. In other words, the hybrid kids weren’t sterile but they may have had trouble having kids themselves.
Taken together these results suggest that the interbreeding of humans and Neanderthals gave enough useful traits to overcome the lowered fertility. Of course this assumes that Neanderthals and humans did have kids together.
Ancient vs. “Recent” Mingling
The results showing Neanderthal DNA in some modern human DNA does not necessarily mean the two had kids together when modern humans left Africa. Another less likely but plausible possibility is that the similarity between non-Africans and Neanderthals has to do with them having common ancestors a bit different from those of modern Africans. Both have human ancestors they just come from different gene pools.
In a simplified version, imagine that a few hundred thousand years ago or so our ancestors in Africa split into two groups. One group stayed in Southern Africa and one left to go north. Some of northern folks went on to Europe and Asia and some stayed behind.
The group that left Africa went on to become Neanderthals while both groups in Africa went on to become humans (there was obviously some mingling between the African groups). Then a group of humans from the northern group leaves Africa to settle Europe and Asia. Once they got there, these folks wiped out the Neanderthals that had left their group a few hundred thousand years before.
In this scenario, European and Asian DNA would share more in common with Neanderthal DNA than they would with African DNA. The Neanderthals and the Europeans/Asians all started from the same pool of DNA.
As I said, this scenario is much less likely. And now a new study shows that it probably didn’t happen this way as humans and Neanderthals almost certainly had kids together.
By comparing small bits of the DNA of a human, a Neanderthal and a third ancestor, a Denisovan, these authors provide strong evidence that all three are related because of interbreeding. In the absence of stumbling on a fossil from one of the original hybrids, this is about as strong of evidence as we are going to get for interbreeding.
Our randy ancestors bred with whomever they came across to birth hybrids that went on to become Europeans and Asians. And the same is probably true for Africans although their interbreeding would have been with other nearby relatives instead of Neanderthals. One day soon we may be able to pull those ancestors’ DNA out of modern African DNA the way we did with Neanderthal DNA in European and Asian DNA. This method is critical for this as we probably won’t get much useable DNA from fossils in tropical areas.