Biology Magazine

How Did Humans and Neanderthals Stay Separate Species?

Posted on the 13 April 2016 by Reprieve @EvoAnth

In the not too distant past there were several species of human, all living side by side. Humans, Neanderthals and Denisovans happily co-existed for several thousands of years. In fact, they did a lot more than just co-exist. They actually interbred.

Ongoing research is revealing how this interbreeding was surprisingly prevalent and played a key role in our species' evolution. All of this leads to this weeks question; asked by Leo. They're curious how those three species remained separate given all this interbreeding.

I set out to ask you clarify something - I read three articles that made me wish someone would explain the reason species maintain an identity even though everybody breeds with every body

There's a surprisingly simple answer to this: mating with another species is difficult.

Remember, if you have a question you want answered (even if it isn't this simple) you can get in touch via the contact form.

Challenges of inter-species love

Humans and Neanderthals interbred during at least three separate periods. During this time we inherited many genes from them, many of which still persist to this day. So why did humans stay so different to Neanderthals?

The secret lies in those genes we got from Neanderthals.

The fact is that most genes don't come in only one form. Most have a few different variants, called " alleles ". For a rather crude example, people have a gene for eye colour. Brown, blue, grey, etc. would be alleles of that gene. Your eye colour this depends on which allele you inherit from your parents.

When we interbred with the Neanderthals we got many alleles of existing genes from them. In some populations these variants were beneficial, so those with them became more successful. Thus they gradually replaced the original form of that gene we had. In other cases these alleles might be neutral. So it's down to chance whether or not you wind up with a Neanderthal allele for a particular gene.

Where things get interesting is when we find genes that are missing Neanderthal alleles entirely. This would indicate that variant was harmful, so those with it died off (and the allele went with them). These reveal where the problems with Neanderthal interbreeding was.

A genetic kick in the nuts

It turns out that many of the missing Neanderthal alleles are linked to reproduction. This indicates that interbreeding between the two species caused major fertility problems in the hybrid offspring. Hence why all those alleles were purged.

The entire Y chromosome (inherited only in men) is missing Neanderthal alleles. Related to this, most of the genes linked to male reproduction in the rest of the genome are also missing their Neanderthal alleles. This indicates that Neanderthal genes really mucked up the fertility of any male hybrid babies born.

In fact, this problem may have been so severe that it effectively made reproduction down the male line (hence why there's no Y chromosome). An examination of the Neanderthal Y chromosome has identified many alleles that would have caused major problems if they were present in the hybrid offspring (including some that could cause a miscarriage).

And that's probably why Neanderthals and humans remained separate. They simply couldn't interbreed successfully very often. And even when they did, that offspring probably had reduced fertility (especially if they were male). This stopped the genes of our two species being properly mushed together; causing us to remain separate.

Why did we have so many difficulties? Well it's not really surprising when you consider that all these species were isolated for almost half a million years. That's half a million years of differences building up, pushing us further apart and making it harder for us to interbreed.


Humans and Neanderthals had spent 500,000 years apart. The resulting genetic differences mucked with our reproduction, preventing our species successfully interbreeding very often.


Mendez, F.L., Poznik, G.D., Castellano, S. and Bustamante, C.D., 2016. The Divergence of Neandertal and Modern Human Y Chromosomes. The American Journal of Human Genetics, 98(4), pp.728-734.

Sankararaman, S., Mallick, S., Patterson, N. and Reich, D., 2016. The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans. Current Biology.

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