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…
Read More: Not-so-hostile takeover: Human Y chromosome displaced the Neanderthals’ version