How Human Y Chromosomes Replaced Those of Neanderthals in a Quiet Genetic Takeover

When the two early human species mated, their genomes changed forever

A human skull is on display with a mural-size rendering of a Neanderthal man on the wall behind the display.
When human men mated with Neanderthal women a hundred thousand years ago, Neanderthals inherited the human Y chromosome. Photo by Alain Pitton/NurPhoto via Getty Images

Tens of thousands of years ago, Homo sapiens—the modern-day human—roamed the world with at least two archaic human species: the famous Neanderthals and their lesser known cousins, the Denisovans. Untangling the relationship between these groups has been an ongoing challenge for scientists.

One hurdle in deciphering human prehistory is the absence of evidence of a Neanderthal Y chromosome in the genetic record. Now, a new study, published Friday in the journal Science, suggests that the modern human Y chromosome completely replaced the Neanderthal Y chromosome when male Homo sapiens’ began mating with female Neanderthals at some point between 100,000 and 370,000 years ago, reports Ann Gibbons for Science magazine.

So far, scientists have only been able to sequence about a dozen Neanderthal specimens’ DNA—and most of the samples are from women. The male DNA from Neanderthals that does exist is damaged or contaminated, Science reports. Using a new breakthrough method of “binding” fragmentary chromosome sample, the team of evolutionary geneticists sequenced Y chromosome DNA from three Neanderthals and two Denisovans that lived in Eurasia.

“The most striking thing that immediately popped up is that all three Neanderthal Y chromosomes are more closely related to the modern human or present-day human Y chromosomes than the Denisovan Y chromosomes,” lead author Martin Petr, a Ph.D. student at the Max Planck Institute for Evolutionary Anthropology in Germany, tells Jef Akst for The Scientist.

Long after the three species diverged on the evolutionary tree, they crossed paths again—and began mating. This mixture of Neanderthal and human DNA was “a defining feature of hominin history,” population geneticist Josh Akey, who was not involved in the research, tells Science. And it changed Neanderthal genomes from there on out.

Since the Y chromosome is passed from fathers to sons, when male Homo sapiens mated with female Neanderthals, future generations of Neanderthals inherited the Homo sapiens version of a Y chromosome, reports Kiona Smith for Ars Technica. But why the Homo sapiens Y chromosome persisted is still unclear.

The team theorizes that the human Y chromosome may have had a slight fitness advantage over their Neanderthal comrades. Because Neanderthals had a smaller population size than humans, they likely accumulated more deleterious—or harmful—mutations in their genome, especially on the sex chromosomes. Early modern humans, however, were more genetically diverse and likely had Y chromosomes that were free of undesirable mutations. These mutation-free chromosomes could have given humans a slight genetic advantage that was just enough to edge out the Neanderthal’s Y chromosome.

But this triumph isn’t the first time a genetic takeover has occurred in the Neanderthal lineage. A 2017 study in Nature discovered that a Neanderthal specimen from 38,000 to 100,000 years ago had mitochondrial DNA (mtDNA) from an early modern human woman. Since mtDNA is inherited maternally, the researchers suggested that a human woman mated with a Neanderthal man more than 220,000 years ago, creating a lineage of Neanderthals with human mtDNA.

“It is remarkable to see that both uniparental markers, so both [the] Y chromosome and mitochondrial DNA, they show the same story,” Cosimo Posth, a paleogeneticist at University of Tübingen in Germany and lead author of the 2017 study, tells The Scientist. This new research proves just how dynamic hominin history is, he says.

The researchers say that the next step in understanding Neanderthal evolution is to sequence more archaic human Y chromosomes and study Neanderthals from a wider geographic range. “This will help us narrow down the timing of the replacement and test how far did the Y chromosome replacement spread geographically,” Petr and coauthor Janet Kelso, also an evolutionary geneticist at Max Planck, tell Ars Technica.

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