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Most of us living humans have a small percentage of Neanderthal DNA in our genomes. That's the result of a long history of interbreeding between the ancestors of modern humans, and our extinct cousins, the Neanderthals.

So in a small way, Neanderthals shaped our DNA and left their mark on the species we are today. But a new study in the journal Science uncovers new genetic clues to the flip-side of this exchange. It turns out our ancestors shaped Neanderthal DNA in return, and their influence may have been much greater.  In fact, it looks like entire sections of the Neanderthal genome were ultimately replaced by human DNA through interbreeding with our ancestors.

But before we dive deeper into the new research, a quick refresher on our extinct relatives. For hundreds of thousands of years, our species, Homo sapiens, lived alongside two other closely related human lineages: Neanderthals and Denisovans.  Our DNA and theirs contain evidence that our lineages interbred -- both Neanderthal and. Denisovan DNA sequences can be found within living humans.  We know this because we've been able to find enough of their DNA preserved in fossils to sequence their genomes, and by comparing them to modern humans, we can see where a given sequence comes from.

When we compare DNA across all chromosomes, we see that Neanderthals and Denisovans were more closely related to each other than to modern humans. But that doesn't always tell the whole story. When we start to break things down by maternal and paternal lineages, our history starts to look a little different.

There's a slight imbalance in this genetic record, though, making it hard to get a full sense of both sides of the family. Most of our fossil data just happens to come from females. In this case, here we're referring to male and female in the genetic sense — so, males being those who have and pass on Y chromosomes, and females being those who don't.

This genetic gap isn't a huge problem, really, but it does mean that we're missing out on the parts of the genome that are only inherited by males — most notably, the Y chromosome. So in the current study, researchers used a DNA sequencing method specialized for locating and amplifying genes located on the Y chromosome. Doing so, they were able to sequence DNA from two Denisovan individuals from Denisova Cave in Siberia, and three Neanderthals from sites in Spain, Belgium, and western Russia, most from within the last hundred thousand years.

And what they found is that these Y chromosomes tell a different story than the rest of the chromosomes. While whole-genome research suggests Neanderthals are much more closely related to Denisovans overall, the Y chromosomes of the Neanderthal males look much more similar to us. The scientists hypothesized that early Neanderthals probably had Y chromosomes that resembled those of Denisovans, but over time, genetic exchange with our ancestors ultimately led to a total replacement of the Neanderthal Y chromosome.

This is a dramatic finding, but it's not a complete surprise — we see the same pattern in mitochondrial DNA. So the mitochondria in cells have their own genomes, which are inherited from the female parent— this is the opposite of Y chromosomes.  Previous research has found that Neanderthals started out with mitochondrial DNA much like. Denisovans, but later Neanderthals have a full mitochondrial genome inherited from an early lineage related to Homo sapiens.

What this tells us is that Neanderthal DNA was heavily shaped by interbreeding with both males and females from among our own ancestors. And for some reason, certain parts of our genome kind of took over. Now, we should be clear: these replaced genes aren't quite like the DNA of living humans.

Instead, Neanderthals appear to have inherited them from ancestors of modern humans more than 300,000 years ago. No one alive today has the same Y chromosomes seen in these Neanderthals. Exactly why this replacement happened isn't totally clear.

It could be that there was some sort of evolutionary advantage to be had by upgrading the Y chromosome. The scientists point out that Neanderthals had smaller population sizes than our ancestors, which might have been a recipe for the build-up of harmful mutations.  That could have decreased the overall evolutionary health of their chromosomes, so natural selection favored a replacement. It's very hard to know that for sure, but the researchers ran some genetic simulations that found that even a small benefit in one chromosome sequence over the other could have resulted in eventual replacement.  As for the Denisovans, it could be that they just didn't interact with our ancestors very much -- they are thought to have lived further east than the humans that lived at the same time.

This is the kind of finding that raises a lot of questions, but fortunately those questions are testable.  The researchers are hoping that the next step will be to look at older Neanderthal DNA. If this really is a case of replacement, they should see that older Neanderthal Y chromosomes are more like Denisovans. If DNA is preserved well enough, they might even be able to look for signs of harmful mutations or other factors that might have influenced whose chromosomes won the evolutionary contest.  One of the big takeaways here is that interbreeding between ancient humans isn't just a scandalous secret hidden in our family tree.  That genetic exchange has actually been a key feature of our history, fundamentally changing the.

DNA of our ancestors and our extinct cousins. The more we understand our complex extended genealogy, the better we'll understand how we came to be the way we are today. Thanks for watching this episode of SciShow News, and a huge thanks once again to our perennial President of Space, Matthew Brant.

Your support helps us do so much -- like airing out the skeletons in Neanderthal closets. If you'd like to help support SciShow, you can go to patreon.com/scishow to learn more about how you can do that. [♪ OUTRO].