Although it’s widely known that modern humans carry traces of Neanderthal DNA, a new international study led by researchers at the Stanford University School of Medicine suggests that Neanderthal Y-chromosome genes disappeared from the human genome long ago.

The study was published April 7 in The American Journal of Human Genetics, in English and in Spanish, and will be available to view for free. The senior author is Carlos Bustamante, PhD, professor of biomedical data science and of genetics at the School of Medicine, and the lead author is Fernando Mendez, PhD, a postdoctoral scholar at Stanford.

The Y chromosome is one of two human sex chromosomes. Unlike the X chromosome, the Y chromosome is passed exclusively from father to son. This is the first study to examine a Neanderthal Y chromosome, Mendez said. Previous studies sequenced DNA from the fossils of Neanderthal women or from mitochondrial DNA, which is passed to children of either sex from their mother.

Other research has shown that the DNA of modern humans is from 2.5 to 4 percent Neanderthal DNA, a legacy of breeding between modern humans and Neanderthals 50,000 years ago. As a result, the team was excited to find that, unlike other kinds of DNA, the Neanderthal Y chromosome DNA was apparently not passed to modern humans during this time.

“We’ve never observed the Neanderthal Y chromosome DNA in any human sample ever tested,” Bustamante said. “That doesn’t prove it’s totally extinct, but it likely is.”

Why no Neanderthal DNA?

Why is not yet clear. The Neanderthal Y chromosome genes could have simply drifted out of the human gene pool by chance over the millennia. Another possibility, said Mendez, is that Neanderthal Y chromosomes include genes that are incompatible with other human genes, and he and his colleagues have found evidence supporting this idea. Indeed, one of the Y chromosome genes that differ in Neanderthals has previously been implicated in transplant rejection when males donate organs to women.