Status: it’s complicated —
Newly sequenced Neanderthal Y chromosomes hint at a complex history of mixture.
We know that Neanderthals left their mark behind in the DNA of many modern humans, but that exchange worked both ways. The groups of Neanderthals our species met in Eurasia around 45,000 years ago already carried some Homo sapiens genes as souvenirs of much earlier encounters. A recent study suggests that those early encounters allowed the Homo sapiens version of the Y chromosome to completely replace the original Neanderthal one 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 sites in France, Russia, and Spain (all three lived 38,000 to 53,000 years ago). The oldest Neanderthal genomes in Eurasia have Y chromosomes that look much more like those of Denisovans. Later Neanderthals, however, have Y chromosomes that look more like those of us humans.
Gene flow is a two-way street
Tens of thousands of years ago, our species shared the world with at least two other hominins. The tools, beads, and art they left behind hint that these other humans were probably a lot like us. And we were definitely all alike enough to have, apparently, a bit of sex.
That resulted in a really complicated population history spanning thousands of years and several 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 much earlier meetings with early Homo sapiens.
Most of what we know comes from the DNA of our regular chromosomes—there’s less data on sex chromosomes. Geneticists can use the differences in this DNA to estimate when two populations, like Homo sapiens and Neanderthals, last shared 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 second to appreciate 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 our most recent common ancestor lived around 370,000 years ago.
That suggests that long after the groups had gone their separate ways and evolved into different populations, they met and swapped genes (which is definitely what they called it back then, of course). Over time, our version of the Y chromosome genome ended up replacing the Neanderthal version.
“A big advantage of [studying] Y chromosomes and mitochondrial DNA is that, although they offer only a simple view of human history through a single paternal/maternal lineage, 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 into Neanderthals evident from our study, which is extremely clear. Finding something like this in the autosomal DNA is much trickier and requires sophisticated statistical methods (which are now finally being developed).”
A slight evolutionary edge
There’s a reason that non-African people today only have a tiny number of Neanderthal alleles—about two to four percent—in their genomes. When two groups like Homo sapiens and Neanderthals mingle, alleles from both parents get passed down to their offspring. But the odds are against an allele from one group getting “fixed” (meaning becoming the dominant form) in the gene pool of the other group. First, you need to have the new allele getting passed to a large enough percentage of offspring, which is rare unless there’s extensive inter-mating over time.
But things can be different if the new allele has natural selection on its side. If the new allele somehow makes it more likely that one person will pass their genes on to a new generation (or if it’s linked to another gene that does), then it’s likely to stick around.
Previous studies indicated that our species’ alleles probably entered the Neanderthal gene pool at a fairly low rate: roughly single-digit percentage of the population. That’s not enough to become fixed. So Petr, Kelso, and their colleagues suggest that the Homo sapiens Y chromosome alleles probably offered some kind of fitness advantage compared to the Neanderthal versions.
“This is the model that we propose for the replacement as an alternative to replacement purely by chance without invoking natural selection (which is rather unlikely),” Petr and Kelso told Ars. How much of a difference does a tiny selective advantage really make? They ran a computer simulation in which a Y-chromosome allele from Homo sapiens got passed along 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, its chances of replacing the older Neanderthal version over a 50,000-year period shot up to about 25 percent.
That suggests that whatever selective edge Homo sapiens alleles offered, it may have been tiny, but that’s enough to stick around.
More ancient DNA, please
At this point, there’s not enough information for archaeologists or geneticists to say what selective advantage was written into Homo sapiens‘ Y chromosome DNA. To understand that, we’ll need more genomes from Denisovans and Neanderthals—and specifically more Y chromosomes, which have been 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 have high-coverage genomes of three Neanderthals and one Denisovan. The odds of them being all female is actually not that low,” they said. Petr, Kelso, and their colleagues had to use a newly developed DNA extraction method to get 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 man from El Sidron Cave in Spain, whose genome had previously been sequenced. The new method helped revise a previous estimate of that Neanderthal’s Y chromosome’s most recent common ancestor with our species, which illustrates 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 habitat (all three Neanderthals in our study are from West Eurasia),” Petr and Kelso told Ars. “This will help us narrow down the timing of the replacement and test how far did the Y chromosome replacement spread geographically.”
They added, “Having access to high-coverage Y chromosomes of pre-introgression Neanderthal (and also Denisovan) Y chromosomes will make it possible to look more into what were the drivers of selection behind the replacement beyond the theoretical simulations in our current study.”