Modern men have no traces of Neanderthal DNA on their Y chromosome, the first-ever analysis of the male Neanderthal sex chromosome has revealed.

Key points: All sequencing of Neanderthal genome had until now been done on females

All sequencing of Neanderthal genome had until now been done on females Chromosome is different to modern human Y chromosome

Chromosome is different to modern human Y chromosome Contains mutations in immune system genes

Contains mutations in immune system genes Genetic incompatibility may have caused miscarriages of male hybrid offspring

The disappearance of the Neanderthal Y chromosome may be due to genetic incompatibilities between the two species that led to miscarriages, suggests a study published today in the American Journal of Human Genetics.

The Y chromosome is passed exclusively from father to son.

Until now, all sequencing of the Neanderthal genome had been done on females because those happened to be the specimens that provided enough good-quality DNA, the study's lead author, Dr Fernando Mendez of Stanford University, said.

"Characterising the Neanderthal Y chromosome helps us to better understand the population divergence that led to Neanderthals and modern humans," he said.

"It also enables us to explore possible genetic interactions between archaic and modern [gene] variants within hybrid offspring."

It is widely known that modern non-Africans have around 2.5 to 4 per cent Neanderthal DNA in their genes, but the Y chromosome is special, Dr Mendez said.

"Either you get the whole Y chromosome, or you get nothing," he said.

Analysis compared ancient and modern Y chromosomes

Dr Mendez and his colleagues compared the Y chromosome of a 49,000 year-old Neanderthal male found in El Sidron in Spain, with the Y chromosome from two modern humans.

Their analysis supports earlier data that estimated Neanderthals and modern humans diverged from their common ancestor around 588,000 years ago.

They also found the Neanderthal Y chromosome was distinct from any Y chromosome observed in modern humans, suggesting the lineage is extinct.

The researchers then searched for evidence that would explain why the Neanderthal Y chromosome disappeared.

"The Y chromosome has a number of genes that are specific for male functions, like making sperm, so we said maybe we'd find something in one of those, but we didn't," Dr Mendez said.

These genes did contain mutations that distinguished Neanderthals from modern humans, but none would have adversely affected their function.

Genetic incompatibility may have caused miscarriages

But the team identified mutations on three genes on the Neanderthal Y chromosome connected to immune factors called the minor histocompatibility antigens.

When these antigens, which are only found in males, are mismatched they can cause women to reject organ transplants from men as well as have miscarriages after the birth of their first child, Dr Mendez said.

This may have had serious consequences for the offspring of Neanderthal and modern human interbreeding; a male foetus could have sensitised his mother's immune system so any subsequent male offspring would be at greatly increased risk of being miscarried.

"If they have fewer boys than other couples, then systematically boys are likely to have fewer boys," said Dr Mendez.

Over time the Neanderthal Y chromosome would be lost in favour of the modern human Y chromosome.

However, Dr Mendez stressed this was still only a hypothesis.

"The amount of Neanderthal DNA in modern humans nowadays is relatively low so it could have been lost by drift," he said.

But reduced fertility or viability of hybrid offspring with Neanderthal Y chromosomes is consistent with an observation known as Haldane's rule.

"Haldane's rule says basically that when you have a cross of differential populations, the male offspring are the ones that have more trouble," Dr Mendez said.

Dr Mendez said he hoped other Neanderthal samples would reveal more about the Neanderthal man.