Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern humans. (Wikimedia Commons)
Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern humans. (NASA/Wikimedia Commons)

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.

Neanderthals had time to adapt to chilly northern Europe and Asia and kindly contributed genes to help humans survive when they moved there.  (Wikimedia Commons/pixelfehler/Matthias Süßen)
Neanderthals had time to adapt to chilly northern Europe and Asia and kindly contributed genes to help humans survive when they moved there. (Wikimedia Commons/pixelfehler/Matthias Süßen)

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.

Scientists may soon be able to pull ancient DNA out of modern Africans' DNA without any fossils. (Wikimedia Commons)
Scientists may soon be able to pull ancient DNA out of modern Africans’ DNA without any fossils. (NASA/Wikimedia Commons)

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.

Surprising Amount of Neanderthal DNA Still Evident in Modern European and Asian Populations 16 June,2014Dr. Barry Starr

  • bikebsk

    I dare to make a Biblical interpretation of the now accepted Neanderthal DNA residue residing in modern humans, as the account in Genesis of Noah and his family provides a bottle-neck from which the gene pool descended and if true complicates the DNA theories offered as to why only 2% is now found in modern humans. Beyond the pale of accepted scientific thinking perhaps, but until this year so was interbreeding of species.

    • Barry

      Studies have suggested a bottleneck around 75,000 years ago where we were down to somewhere between 1000 and 10,000 breeding pairs. Not quite Noah but definitely close to extinction!

    • Carlos Geary

      Please, stop mixing religion with science.

      • Pat Dizazzo

        The funny thing is I was just reading this the other day and thinking how science is actually is starting to sync with the Bible.

        “Genesis 6

        1 When human beings began to increase in number on the earth and daughters were born to them, 2 the sons of God saw that the daughters of humans were beautiful, and they married any of them they chose.3 Then the Lord said, “My Spirit will not contend with[a] humans forever, for they are mortal[b] (or corrupt).”

        This sounds alot like this quote from the above article “Our randy ancestors bred with whomever they came across to birth hybrids that went on to become Europeans and Asians.”

        The word Marry meant to mate with

        • L.A.M


      • L.A.M

        Shut up dummy. The only reason you don’t want us to, is because you’re scare that it will fit in.

  • George Lyon

    I read somewhere that the Neanderthal DNA in modern humans could have resulted from as few as 300 mating events. That doesn’t suggest interbreeding on a very large scale to me. Of course, there are so many gaps still in our understanding, that well-researched fiction is often a fun way to analyse all these discoveries. Best science thriller in this regard I’ve come across thus far, is ANCESTOR by RAYMOND STEYN (published 2014). Then there was JOHN DARNTON’s NEANDERTHAL, but that has become a bit dated (more than 10 years old I think).

  • Carlos Geary

    I think pretty soon, we will discover that we are really, the supposed extinct Neanderthals. I guess modern men has genetic differences with both Neanderthal and their contemporary Homo Sapiens or archaic Homo Sapiens, due to mutations, interbreeding and adaptations.

  • Carlos Geary

    DNA is Still Evident in Modern European and Asian Populations, but also in
    Amerindians (American Indians from Alaska to Argentina/Chile).

  • SPM

    Actually humans and neanderthals were exactly like horses and donkeys. Male hybrids are infertile and female hybrids have very low fertility, but can be fertile. Indeed this type of hybrid infertility would explain the reason why human-neanderthal interbreeding seems to be limited to only a few instances based on DNA analysis of modern humans.

    There are no recorded cases of fertile mule stallions. A few female mules have produced offspring when mated with a purebred horse or donkey.[9][10] Herodotus gives an account of such an event as an ill omen of Xerxes’ conquest of Greecein 480 BC: “There happened also a portent of another kind while he was still at Sardis,—a mule brought forth young and gave birth to a mule” (Herodotus The Histories 7:57).

    Since 1527 there have been more than 60 documented cases of foals born to female mules around the world.[9] There are reports that a mule in China produced a foal in 1984.[11][12] In Morocco, in early 2002, a mare mule produced a rare foal.[9]In 2007 a mule named Kate gave birth to a mule son in Colorado.[13][14] Blood and hair samples were tested verifying that the mother was a mule and the colt was indeed her offspring.

    A 1939 article in the Journal of Heredity describes two offspring of a fertile mare mule named “Old Bec”, which was owned at the time by the A&M College of Texas (now Texas A&M University) in the late 1920s. One of the foals was a female, sired by a jack. Unlike its mother, it was sterile. The other, sired by a five-gaited saddlebred stallion, exhibited no characteristics of any donkey. That horse, a stallion, was bred to several mares, which gave birth to live foals that showed no characteristics of the donkey.[15]

  • Machete Greg

    What they are not saying is that the other 95% of genes on each chromosome are shared by everything apelike. Those could have come from apes or, more recently, they could have come from Neanderthals. Scientist just can’t say anything until they are absolutely sure and rarely speculate.


Dr. Barry Starr

Dr. Barry Starr (@geneticsboy) is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA and runs their Stanford at The Tech program. The program is part of an ongoing collaboration between the Stanford Department of Genetics and The Tech Museum of Innovation. Together these two partners created the Genetics: Technology with a Twist exhibition.

You can also see additional posts by Barry at KQED Science, and read his previous contributions to QUEST, a project dedicated to exploring the Science of Sustainability.

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