Neanderthals interbred with humans three different times

Humans and Neanderthals interbred. This happened during at least 3 distinct periods as humans spread around the world.

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The Neanderthals were our closest living relatives. At least, they were until they went extinct ~30,000 years ago. But a little piece of them lives on in us because our ancestors interbred with them.

This interspecies hook-up was more important than a one-night stand. We inherited some of the genes we needed to flourish out of Africa from the Neanderthals (and a few bad habits too).

But it seems like the Neanderthals also felt the same way. New data suggests they kept coming back for more; with there being at least three different periods of Neanderthal/human hanky-panky.

Excavating the Neanderthal genome

We’ve known for about a decade that our ancestors interbred with the Neanderthals. But when, where, why, and how often have remained a mystery.

Ok, that’s a bit of an exaggeration. We actually know a fair bit about this interbreeding. Genetic studies show it happened relatively soon after we left Africa (perhaps ~60,000 years ago). As a result the first non-Africans all got a healthy dose of Neanderthal genes; which they still have (with 3 – 4% of their DNA coming from Neanderthals). So scientists have been delving deeper, trying to find out more about this early period of inter-species love.

An old family tree of humans, Neanderthals, and Denisovans; showing the single case of interbreeding between humans and Neanderthals

An “old” family tree of humans, Neanderthals, and Denisovans; showing the single case of interbreeding between humans and Neanderthals

But it turns out palaeoanthropologists were thinking too small. New research has found evidence of two additional times during which humans and Neanderthals interbred.

This discovery was made possible by the 1,000 genome project. Which, as the name suggests, is a database of 1,000 human genomes (because scientists are bad at coming up with creative names for things). This allowed researchers to look at the Neanderthal DNA present in all of these people. This revealed some interesting facts.

First, is that a lot of the Neanderthal genome lives on. Whilst each individual only has 3 – 4% Neanderthal DNA, different groups have a different 3 – 4%. So when you put it all together it adds up to about half of the entire Neanderthal genome continuing to exist.

The second – and perhaps more interesting point I’ve already spoiled – is that they found two extra periods of Neanderthal/human interbreeding. The way each population had a different bit of Neanderthal genome didn’t match the pattern expected if there was only one period we interbred. Instead, it looked like there was at least two extra periods of mating between us.

Our new (incesty) family tree

The graph bellow (labelled C because I’m bad at cropping) shows the new family tree of humans, Neanderthals and Denisovans produced by this research. And there’s a lot of crossover.

Our new family tree, showing all the instance humans (right) interbred with Neanderthals (left)

Our new family tree, showing all the instance humans (right) interbred with Neanderthals (left)

  1. The top arrow represents the case of interbreeding we already knew about. This happened just after our species left Africa. Hence why the African branch didn’t get any of these genes. But all the non-Africans did. The fact that they all got it confirms it was an early case of interbreeding, before regional populations had emerged outside of Africa. It probably happened just as we left home.
  2. The second period of interbreeding was something that had been speculated about. It happened after some regional populations had emerged  outside of Africa, but we hadn’t fully split up into the populations we know and love today. As such it could have happened in Central Eurasia, allowing for all the interbreeding babies to split off in different directions and eventually split into the regional populations.
  3. The final case of interbreeding was between Neanderthals and the branch which ultimately became East Asian populations.

What makes this new family tree extra interesting is that these events are spread out in time and place. Humans and Neanderthals were having a bit of fun all over the globe. Including areas that seem to be outside the traditional Neanderthal heartland of Europe.

As an interesting aside, they also found some other reasons we don’t all have the same segments of Neanderthal DNA. Natural selection had resulted in some bits being stripped out of our genome. It seems that a lot of Neanderthal DNA was harmful so was soon selected against. Different bits were more or less harmful in different places; hence why different populations wound up with a slightly different pattern of Neanderthal DNA.

This is something we already sort of knew; with previous studies finding many “harmful” genes we inherited from the Neanderthals. But this research helps find the genes that were so bad they were killed off. Although they didn’t look at this area in much detail, this research could form the basis for a new study that finds some of the really nasty stuff the Neanderthals gave us.

Maybe as punishment for driving them extinct?

Don’t forget the Denisovans

Neanderthals get all the attention. And since they were so special to our ancestors, I think that’s justified. However, our ancestors also had a fling with another member of the human family.

A denisovan tooth

A denisovan tooth

The Denisovans get their name from Denisova cave in Siberia (confirming once again scientists are awful at naming things). A finger bone was found there which at first appeared normal; but actually contained the DNA of a whole other species of hominin. As if that wasn’t odd enough, they also discovered that the ancient Siberians also interbred with modern humans.

However, the Denisovans had left before we woke up in the morning. Initial surveys revealed that the interbreeding between our two species was a lot more limited than with the Neanderthals. Denisovan genes were only found in Melanesian populations. So it looks like the ancestors of those modern populations had a brief run in with the Denisovans, whilst we avoided it.

This most recent study confirms that picture. Evidence of only period of interbreeding was found; and it only appears to have involved the ancestors of Melanesians and the Denisovans.

But whilst we might not have spent too long with the Denisovans, we still inherited a few interesting traits from them. The researchers found that Melanesian populations had several Denisovan genes linked to blood glucose and metabolism (although they have no idea precisely what they do). Previous research also revealed that Tibetan populations have some Denisovan genes that help them deal with the high altitude.

Based on all this, I’m now in favour bringing the Neanderthals and Denisovans back from extinction. Only to get them interbreeding again to create the perfect hominin hybrid that WILL RULE THE GALAXY.


Humans and Neanderthals interbred. This happened during at least 3 distinct periods as humans spread around the world. Clearly we couldn’t keep our hands to ourself.


Hackinger, S., Kraaijenbrink, T., Xue, Y., Mezzavilla, M., van Driem, G., Jobling, M.A., de Knijff, P., Tyler-Smith, C. and Ayub, Q., 2016. Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas. Human genetics, pp.1-10.

Meyer, M., Kircher, M., Gansauge, M.T., Li, H., Racimo, F., Mallick, S., Schraiber, J.G., Jay, F., Prüfer, K., de Filippo, C. and Sudmant, P.H., 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science, 338(6104), pp.222-226.

Reich, D., Green, R.E., Kircher, M., Krause, J., Patterson, N., Durand, E.Y., Viola, B., Briggs, A.W., Stenzel, U., Johnson, P.L. and Maricic, T., 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468(7327), pp.1053-1060.

Vernot, B., Tucci, S., Kelso, J., Schraiber, J.G., Wolf, A.B., Gittelman, R.M., Dannemann, M., Grote, S., McCoy, R.C., Norton, H. and Scheinfeldt, L.B., 2016. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science, p.aad9416.

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20 thoughts on “Neanderthals interbred with humans three different times”

  1. Charles A. Bishop says:

    If nearly half the Neanderthal genome continues to survive today, it suggests to me that mating was almost continuous between incoming moderns and resident Neanderthals from 65,000+ years to 35,000 years. I’m of the old school and think that you can’t discount the fossil and archaeological evidence. Some Neanderthals have modern-like traits (incipient chins, absence of occipital buns, smaller molars, more linear long bones, etc.) that are highly suggestive of gene flow. The Chatelperonian archaeological tradition dating to about 43,000 years also suggests that the Neanderthals borrowed and adapted some tool types from moderns to fit their own repertoire.

    1. Adam Benton says:

      The continuation of half the Neanderthal genome is a byproduct of the different lineages that led to modern human populations. It doesn’t indicate a lot of interbreeding.

      That said, all of these studies examine modern human genomes. There could well have been other lineages with more interbreeding that went extinct so we don’t know about them.

  2. Cynthia Echterling says:

    Every time I read an article about the number of times Modern Humans got together with Neanderthals it brings back a funny story. I am the middle of five children. It fell on me to explain the birds and bees to my two younger brothers. Afterwords, they were disgusted and one said, “You mean, Mom and Dad had to do that five times!” Think of all the fun our ancestors had that didn’t result in viable offspring.

    1. Adam Benton says:

      Ignoring viable offspring, think of all the lineages that just might not have survived to the present day. All of this research is based on modern genomes after all. What if there was another group that was doing a lot of interbreeding, but was just in the wrong place when the glacial maximum hit so we don’t know about it.

      1. Cynthia Echterling says:

        Speaking of which, I saw something once that suggested there was a decline in population of modern humans with the next glatial maximum, but now I can’t find it. Any resources on that? I was wondering if the initial population that interbred with Neanderthals was partially wiped out, then replaced by further immigration from Africa in the next interglatial period, that would partially account for the low percentage of Neanderthal genes in modern populations?

        1. Adam Benton says:

          There’s a few genetic studies that seem to indicate some population shrinkage (and maybe even the ultimate replacement of some populations by others). Unfortunately a lot of this genetic stuff goes over my head so I couldn’t telkl you more.

  3. Joachim says:

    Why not say, that Neanderthals and modern humans were sub-species rather than separate species? That would make the vanishing of Neanderthal genes a case of selection against certain genes within one population and not one of extinction of a species.

    1. Adam Benton says:

      The differences between humans and Neanderthals are fairly substantial; so I’m not convinced they can really be lumped together so easily. However, there are some who would agree with you and group them all together.

  4. Wyrd Smythe says:

    A friend recently told me about how, when he was in the Navy, he heard some farm boys talking about how it was no big deal spending “quality time” with sheep. Given that, anything that looked human would certainly be no big deal. I’d have to agree with others that think the interbreeding must have been pretty continuous!

    1. Adam Benton says:

      It would be interesting to see where on the spectrum contemporary humans placed Neanderthals. Were they stone age “sheep” or did people actually view them at least on the human scale.

      1. Wyrd Smythe says:

        If it walks like a duck, looks like a duck,… then duck it! 🙂

        1. Adam Benton says:

          That certainly explains the logic behind certain autocorrects

  5. Charles A. Bishop says:

    I think that Neanderthals were seen as slightly different humans by Moderns. Our modern Western concept of beauty tends to see Neanderthals as ugly, but this may not have been true of early Upper Paleolithic Moderns. There is also an enormous technological gap between Neanderthals and present day society. Consequently, many today classify Neanderthals as less than human. But we can’t be sure how Moderns of 40,000 years ago might have viewed them. At that time, Moderns and Neanderthals were just two different groups of hunter gatherers, although Moderns made better tools and were better hunters, two main reasons why they survived. Because there were many more similarities between the two groups that at present, I believe that Moderns would have accepted Neanderthals as basically human and acceptable mating partners by Upper Paleolithic society’s norms, as the DNA evidence indicates.

  6. Cynthia Echterling says:

    Unlike the Discovery Channnel reinactments, I imagine that the first contact was probably made after the two types of humans spotted the smoke from each others fires. This would give them time to check each other out before making contact. Hey, they’ve got fire, they wear clothes, walk on two legs. They’re people, not animals. And, hey, check out those long legs. Oh and, those folks have interesting long hair. So somebody kills an antelope, the eat, share some of whatever they were using to get high at the time and good times commensed. There wasn’t that much difference in technology, but those Southern folks had some cool beads to trade and the Northerners had some nice worm clothes making techniques. With a little sgn language trade went on in more ways than one.

    1. Cynthia Echterling says:

      That’s Warm clothes, not Worm clothes. Sorry.

      1. Adam Benton says:

        But worms get chilly too.

    2. Adam Benton says:

      One of the interesting things I think we forget is the sheer scale of distances involved. Population densities were likely very low during this period. You probably only bumped into another group a handful of times a year. In that context the Neanderthals might have seemed even less unusual because people wouldn’t have a massive “sample” to compare them too.

  7. Charles A. Bishop says:

    Exact population densities are very difficult to determine given that many sites may have been destroyed by later settlements or remain undiscovered under several feet of loess and dirt. Consequently, much of what we know comes from cave and rock shelter sites. But so far relatively little archaeological work has been done on open air sites which are much more difficult to locate, and it is these that could give us a better picture of population densities at different times during the Middle and Upper Paleolithic. But you are probably right about bumping into other groups 3 or 4 times a year. Charles

  8. QwertyBalls says:

    LOL is that Neanderthal man a pedobear?

  9. Pingback: How did humans and Neanderthals stay separate species? - FMM
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