Sat. Sep 24th, 2022
Comparison of modern human and Neanderthal skulls from the Cleveland Museum of Natural History.

Comparison of modern human and Neanderthal skulls from the Cleveland Museum of Natural History.

We know that Neanderthals have left their mark on the DNA of many modern humans, but that exchange worked both ways. The groups of Neanderthals that our species encountered in Eurasia about 45,000 years ago already had some with them Homo sapiens genes as souvenirs of many previous encounters. A recent study suggests that those early encounters Homo sapiens version of the Y chromosome to completely replace the original Neanderthal sometime between 370,000 and 100,000 years ago.

Evolutionary geneticists Martin Petr, Janet Kelso and their colleagues used a new method to sequence Y chromosome DNA from two Denisovans and three Neanderthals from locations in France, Russia and Spain (all three lived 38,000 to 53,000 years ago). The oldest Neanderthal genomes in Eurasia have Y chromosomes much more similar to Denisovans. Later Neanderthals, however, have Y chromosomes that are more like our humans.

Gene flow is a two-way street

Tens of thousands of years ago, our species shared the world with at least two other hominids. The tools, beads and art they left behind indicate that these other people probably looked a lot like us. And we were certainly all equal enough to, apparently, have a little sex.

That resulted in a really complicated population history spanning thousands of years and different continents. We’ve met the daughter of a Neanderthal and a Denisovan in the archaeological record, and our species’ DNA records ancient encounters with both Neanderthals and Denisovans. And Neanderthal genomes also carry the genetic legacy of many previous encounters with early Homo sapiens

Most of what we know comes from the DNA of our regular chromosomes – there is less data on sex chromosomes. Geneticists can use the differences in this DNA to estimate when two populations, such as: Homo sapiens and Neanderthals, who last had a common ancestor. Count the small differences in their DNA and compare that to how quickly human DNA accumulates mutations, and you can come up with a rough date for when the populations split. (Feel free to take a moment to realize how cool it is that we actually know that.)

The DNA data we have from the non-sex chromosomes tells us that Neanderthals and Denisovans share a branch of the human family tree, which split off from our branch sometime between 700,000 and 550,000 years ago. But the Y chromosomes tell a different story, suggesting that our most recent common ancestor lived about 370,000 years ago.

That suggests that long after the groups went their separate ways and evolved into different populations, they met and swapped genes (what they called it natural at the time). Over time, our version of the Y chromosome genome eventually replaced the Neanderthal version.

“A big advantage of [studying] Y chromosomes and mitochondrial DNA is that while they only provide a simple picture of human history through a single sire/mother line, they can make some aspects of it (such as gene flow) stand out much more clearly,” Petr and Kelso told Ars. “This is the case with the gene flow from early modern humans to Neanderthals that our study shows, which is extremely clear. Finding something like this in autosomal DNA is much more difficult and requires advanced statistical methods (which are now finally being developed).”

A slight evolutionary advantage

There’s a reason that non-African people today only have a small number of Neanderthal alleles — about two to four percent — in their genome. When two groups like Homo sapiens and Neanderthals intermingle, alleles from both parents are passed on to their offspring. But there is a good chance that an allele from one group will become “fixed” (meaning it becomes the dominant form) in the gene pool of the other group. First, the new allele must be passed on to a large enough percentage of offspring, which is rare unless extensive inter-mating occurs over time.

But things may be different if the new allele has natural selection on its side. If the new allele somehow makes it more likely that a person will pass their genes on to a new generation (or if it’s linked to another gene that does), then it will likely persist.

Previous studies indicated that the alleles from our species probably entered the Neanderthal gene pool at a fairly slow rate: about a single-digit percentage of the population. That’s not enough to get stuck. So Petr, Kelso and their colleagues suggest that the Homo sapiens Y chromosome alleles probably offered some sort of fitness advantage compared to the Neanderthal versions.

“This is the model we propose for substitution as an alternative to substitution purely by chance, without relying on natural selection (which is rather unlikely),” Petr and Kelso told Ars. How much difference does a small selective advantage really make? They performed a computer simulation in which a Y chromosome allele of Homo sapiens was passed to just five percent of the Neanderthal population in a single burst of admixture. When the simulation increased the fitness advantage of that allele by just one percent, the odds of replacing the older Neanderthal version over a 50,000-year period rose to about 25 percent.

That suggests that any selective advantage Homo sapiens alleles offered, it may have been small, but that’s enough to stick around.

More ancient DNA, please

At the moment there is not enough information for archaeologists or geneticists to say what selective advantage is written in Homo sapiensY chromosome DNA. To understand that, we need more genomes from Denisovans and Neanderthals — and especially more Y chromosomes, which were rare until recently. So far, the handful of Neanderthals and Denisovans with the best-preserved genomes have turned out to be female.

“It’s really just a random chance. So far, we’ve taken with high coverage of three Neanderthals and one Denisovan. The chance that they’re all female is actually not that small,” they said. Petr, Kelso and their colleagues had to use a newly developed DNA extraction method to extract enough Y chromosome DNA from their specimens to actually study.

They also used the method on a 46,000 to 53,000-year-old Neanderthal from Spain’s El Sidron Cave, whose genome had been sequenced previously. The new method helped revise an earlier estimate of the most recent common ancestor of Neanderthal Y chromosome with our species, illustrating why it’s sometimes important to revisit old specimens with new methods. But we also need more Neanderthal and Denisovan genomes to fill in the details of their history.

“The most obvious step is to sequence more archaic human Y chromosomes, especially those from older Neanderthals than those analyzed in our study and also those from a wider range of known Neanderthal habitats (all three Neanderthals in our study are from western Eurasia),” Petr and Kelso told Ars. “This will help us narrow down the timing of the replacement and test how far the Y chromosome replacement spread geographically.”

They added: “By having access to Y chromosomes with a high coverage of pre-introgressed Neanderthal (and also Denisovan) Y chromosomes it will be possible to investigate more about what the drivers were behind the replacement than the theoretical simulations in our current study.”

Science2020 DOI: 10.1126/10.1126/science.abb6460 (About DOIs).

By akfire1

Leave a Reply

Your email address will not be published.