A recent genetic analysis of the male Neanderthal sex chromosome reveals that modern humans have less DNA in common with our ancient cousins than once thought. According to a report from Discovery News, the study suggests that the Neanderthal Y chromosome disappeared because of a growing rift between the two species that resulted in more frequent miscarriages.

The study, published in the American Journal of Human Genetics, offers new insights into how the Neanderthals and modern humans continued to grow apart. Previous genetic analyses of the Neanderthal genome had been done exclusively on female samples, and the recent study, led by Dr. Fernando Mendez of Stanford University, offers a glimpse into the other side of the story.

“Characterizing the Neanderthal Y chromosome helps us to better understand the population divergence that led to Neanderthals and modern humans,” said Mendez. “It also enables us to explore possible genetic interactions between archaic and modern variants within hybrid offspring.”

Previous research tells us that modern non-African humans have up to four percent Neanderthal DNA in their genes, but the Y chromosome is unique in that either the whole thing is passed along, or none of it is.

The study compared a Y chromosome taken from a 49,000 year-old Neanderthal discovered in Spain with the Y chromosome of two modern-day humans. Researchers found that the Neanderthal chromosome was entirely different from the one taken from modern humans. The study confirms earlier estimates that place the divergence of humans and Neanderthals at roughly 588,000 years ago.

The team found mutations on three of the genes from the Neanderthal Y chromosome that were linked to immune functions known as minor histocompatibility antigens. When these antigens are mismatched they can result in complications in women related to organ transplants from men in addition to miscarriages after the birth of their first child.

As Neanderthals and humans coexisted and likely engaged in interbreeding thousands of years ago, these mutations could have sealed the fate of a long-standing hybrid species between the two. Over time, the Neanderthal Y chromosome would have disappeared completely from the gene pool.

A press release describing the details of the study can be found here.