Hank: Neanderthals and modern humans, Homo sapiens, have shared a long and intertwined history. We split from a common ancestor around 700,000 years ago, spent some time apart, but then hooked back up again before the Neanderthals died out 40,000 years ago. Even though they’re gone, a part of them lives on – their DNA.

That’s because for some of our history together, early humans had occasional... dalliances with Neanderthals. Our species were similar enough that the resulting offspring were still fertile. And so that history is still within us today.

Scientists estimate that for many of us, about 2% of our DNA is from Neanderthals. And it’s not just sitting there, doing nothing. A paper out this week in the journal Cell shows that those bits of Neanderthal DNA can control how active your genes are.

In some cases, it turns out, your Neanderthal genes get turned on more, while in others, the Neanderthal versions get turned on less -- especially in your brain, and if you have them, your testicles. These findings reveal a new way that ancient interbreeding is still showing up today, in you body.

Because we’ve sequenced the Neanderthal genome from fossils, we already know about a bunch of gene variants that we’ve inherited from our archaic cousins. Some of these relate to height or how well our immune systems work. Others change our risk for diseases like schizophrenia and lupus. There are probably a lot that we don’t even know about yet, and different people have different ones. But one way these genes might affect us is by altering how often these genes are expressed, or turned on.

Turning on a gene means using that DNA sequence to make a kind of copy, in the form of RNA, which is then used ultimately to make proteins. If a gene is highly expressed, that means it’s getting used to make lots of RNA, which usually means more of that gene’s protein is getting made. So if the remaining bits of Neanderthal DNA in our genome are changing how genes are expressed, that could be really important for human health.

To find out what’s going on, geneticists at the University of Washington measured levels of RNA in different tissues from more than 200 people who had Neanderthal ancestry. They looked at over 5,000 spots in their genomes, where the people had inherited both a Neanderthal version of a gene -- from either their mom or dad -- and a modern human copy, from the other parent. This way, they could see whether one was expressed more than the other.

We usually think of these two versions of a gene -- what geneticists call alleles -- as being used pretty much equally. But it turned out, a quarter of the time, there was a difference in how much the Neanderthal copy was expressed compared to the modern human version. That’s a lot of places where having Neanderthal DNA might change something!

The geneticists also noticed something else. Sometimes Neanderthal sequences were used less than the modern human counterparts, and sometimes they were used more, but overall, they balanced out.

But when they compared different kinds of tissues, from different parts of the body -- and they tested more than 50 of them -- some interesting patterns emerged. In brains and testicles, specifically, Neanderthal variants weren’t expressed as much. This included a gene whose protein helps develop neurons and create synapses, and another one that works in the whip-like tail of sperm.

For some reason, we’re just not using those genes that much. This, the scientists say, is a sign that the brain and testicles have evolved pretty rapidly since Neanderthals and modern humans diverged some 700,000 years ago. After all, our brains are structurally quite different from Neanderthals. And as for the testicles, well, reproduction tends to be very species specific – that’s why cross-species hybrids are often less fertile.

What scientists think happened is that in many cases, when Neanderthal genes got mixed in with ours, the proteins that help turn on a gene were no longer as compatible with some of the Neanderthal DNA, which led to a lower expression of those genes. But there are still plenty of instances where Neanderthal genes are going strong.

And since early humans also had... you know, special relations... with other early hominins, like the Denisovans as well, the research team plan next to check whether a similar thing might have happened with them, as well.

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