The Y chromosome is a hindrance Will Oliver/PA

Modern humans diverged from Neanderthals some 600,000 years ago – and a new study shows the Y chromosome might be what kept the two species separate.

It seems we were genetically incompatible with our ancient relatives – and male fetuses conceived through sex with Neanderthal males would have miscarried. We knew that some cross-breeding between us and Neanderthals happened more recently – around 100,000 to 60,000 years ago.

Neanderthal genes have been found in our genomes, on X chromosomes, and have been linked to traits such as skin colour, fertility and even depression and addiction. Now, an analysis of a Y chromosome from a 49,000-year-old male Neanderthal found in El Sidrón, Spain, suggests the chromosome has gone extinct seemingly without leaving any trace in modern humans.


This could simply be because it drifted out of the human gene pool or, as the new study suggests, it could be because genetic differences meant that hybrid offspring who had this chromosome were infertile – a genetic dead end.

Four gene mutations

Fernando Mendez of Stanford University, and his colleagues compared the Neanderthal Y chromosome with that of chimps, and ancient and modern humans.

They found mutations in four genes that could have prevented the passage of Y chromosome down the paternal line to the hybrid children.

“Some of these mutations could have played a role in the loss of Neanderthal Y chromosomes in human populations,” says Mendez.

For example, a mutation in one of the genes, KDM5D that plays a role in cancer suppression, has previously been linked to increased risk of miscarriages as it can elicit an immune response in pregnant mothers.

“That could be one reason why we don’t see Neanderthal Y chromosomes in modern human populations,” says Mark Pagel an evolutionary biologist at the University of Reading.

It could also be one factor keeping the two species as separate species.

The researchers also used the new DNA sequences to estimate the time when the most recent common ancestor of Neanderthal and modern human Y chromosomes existed. They came up with a figure of around 590,000 years ago, which agrees with other estimates for the split of the two groups.

Journal reference: The American Journal of Human Genetics, DOI: 10.1016/j.ajhg.2016.02.023