Neanderthals were flourishing when humans arrived

The size of the Neanderthal population at the time humans arrived in Europe is debated. New evidence indicates they were actually doing quite well.

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Modern humans arrived in Europe around 45,000 years ago. There, we met the Neanderthals who had been living on the continent for nearly 1 million years. Despite this long history, we “won” this encounter and the Neanderthals went extinct within a few tens of thousands of years. A rapid end for an ancient species.

Some have suggested the extinction of Neanderthals was actually a long time coming. It turns out their population may have been on the decline before we even showed up. Perhaps they were already vulnerable to extinction and we just tipped them over the edge.

Or at least, that’s what preliminary reports suggested. A recent, thorough review has revealed the opposite might be true. Neanderthals were actually flourishing as humans arrived.

Neanderthals on the decline

The first indicators Neanderthals were in trouble as humans arrived come from the distant past of 2014 when a Neanderthal toe was found in the Altai Mountains. Specifically, in Denisova Cave; notable for containing another mysterious species.

Now, a Neanderthal toe on its own isn’t that interesting. Even one from a cave where another hominin lived. However, they managed to extract some DNA from it, revealing the owner was a woman. It also revealed that she was a little bit too Lannister-y. Their parents were at least half-siblings, and similar levels of interbreeding seem to have been common in her recent past.

Possible family trees of the Altai inbreeding Neanderthal

This level of interbreeding implies Neanderthal populations may have been small. This fact seemed to be backed up by the lack of diversity in the genome. They had ~20% the number of heterozygous genes of modern Africans. Based on this, the discoverers of this Neanderthal Cersei estimated that the Neanderthal population was on the decline, trending towards extinction.

Additionally, Neanderthals had a higher number of deleterious mutations.  This indicates there was a lot of genetic drift in the population, a tell-tale sign of a small population. It may also explain why so many of the genes we inherited from them through interbreeding were harmful.

So Europe was occupied by a small, inbred population of Neanderthals when humans arrived. Is it any surprise that we survived whilst they went extinct?

Estimates of the population size of human and Neanderthal populations. Neanderthals appear to be on the decline well before the eventual extinction

Neanderthals were actually doing well

So that’s all the evidence things weren’t going great for Neanderthals. What changed? Well, nothing really. It’s still fairly clear that the Altai Neanderthal was the result of inbreeding and part of a declining population.

However, new evidence indicates these were problems unique to the Altai group, rather than Neanderthals as a whole. Those living in the Siberian Mountains were in the decline and inbreeding. Neanderthals elsewhere were actually flourishing.

The evidence for how additional populations were doing comes from, well, additional population. Data from the Altai Neanderthals was compared with Denisovans and hundreds of humans. This, combined with improvements to the methodology, failed to find the evidence of the widespread population decline looking at Altai alone found. Instead, there were likely tens of thousands of Neanderthals across Europe. Hardly the dwindling group that could easily pushed over by arriving humans.

Population size estimates for different populations. Neanderthals may have been almost as large as contemporary humans

Early troubles for Neanderthals

That chart above has a very interesting point you may have missed. The population size estimates for the last common ancestor of Neanderthals and Denisovans is very small. This isn’t a mistake. Shortly after the Neanderthal/Denisovan branch split from the modern human branch, their population plummeted.

It is worth noting that the population estimate for before this split was also quite small. As such, this isn’t quite as dramatic as it looks. But it still indicates a fairly substantial population decrease in early Neanderthals/Denisovans.

The exact significance of this is unknown. The split happened close to 750,000 years ago. We don’t have an awful lot of fossils from this period, and no DNA. For all we know there might be something super interesting happening. But what is clear is that Neanderthal populations eventually recovered.

Humans arrived to find a continent occupied by a whole other species. But that didn’t stop us.


Prüfer, K., 44. authors (2014). The Complete Genome Sequence of a Neanderthal from the Altai Mountains. Nature505(7481), pp.43-49.

Rogers, A.R., Bohlender, R.J. and Huff, C.D., 2017. Early history of Neanderthals and Denisovans. Proceedings of the National Academy of Sciences, p.201706426.

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4 thoughts on “Neanderthals were flourishing when humans arrived”

  1. Zachary J Fisher says:

    Can you explain the notation used on the nifty chart showing pop over time? SHeeesh! Kind of opaque and I have game in (other) technical disciplines. Maybe this cryptic notation is a sign of Lanisterism (and Targarianism!) among evolutionary anthropologists!

    Intrigued by the focus on various modern pops. I’m guessing that the ones chosen (Mbouti, Sardinian etc) have vestige, unique aspects to their genomes that can be traced back as far as Neanderthals and their Denisovian cousins.

    1. Adam Benton says:

      The y axis is log transformed population estimates, so all the populations will reasonably fit on the same graph. The X axis is time but measured in degree of genetic divergence, rather than years. These are loosely translated to years at the top of the graph.

  2. clayton says:

    I really don’t get the graphs with their weird u’s and such, but a couple things bother me a little. One is that doesn’t it sound just a little ridiculous to base a whole theory of extinction on a single toe? Don’t they think of things like geography, or the fact that they are indeed basing everything all on one toe? How does that happen?
    OK, the other thing: You mentioned that the Neanderthals were doing well, with a population in the tens of thousands-that sounds to me like they were doing well enough, I suppose, but for a whole continent? That doesn’t sound like a hell of lot of people. And, weren’t they pretty well scattered about in small groups? And, now that I’m thinking, I’m gonna cheat and add another thing: Now that we know Moderns and Neanderthals have met and inter-bred, at least twice that we know of and who knows how many other times, evidenced by populations that have died out and left no trace, might have not the Moderns known of the “Others”, or at least had some inklings, legends passed down or traveler’s tales, or something? I think so. The same would probably go for the Neanderthals, too.

    1. Adam Benton says:

      It’s worth noting these people were all hunter-gatherers. They need a lot more space to live in than sedentary populations. As such, population density is very low and it’s normal for a whole continent to just have a few tens of thousands of people. For context, the population size of humans before they left Africa (which is 3x the size of Europe) is estimated to be <100,000 people.

      However, you are right that, in retrospect, it was a bit silly to draw huge conclusions from a single sample of DNA (although it is worth noting that the original research did include many caveats and warnings, but over the years people have got more confident in it as more data became available). But it should be remembered that at the time this was the first proper Neanderthal genome we'd found, so people naturally got a bit excited over it.

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