A neanderthal chromosome passed from father to son is no longer present in modern humans, meaning we’re not quite as caveman as we think.

Modern men carry traces of cavemen DNA but do not have the Y chromosome as it may have drifted out of the human gene pool over millennia of breeding , a study found.

The Y chromosome is one of two human sex chromosomes and unlike the X chromosome, the Y chromosome is passed exclusively from father to son.

But experts believe the Neanderthal Y chromosome was incompatible with other human genes so died out.

The Stanford University study was the first to examine a Neanderthal Y chromosome.

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.

The DNA of modern humans is from 2.5 to 4 per cent Neanderthal DNA and the Neanderthal Y chromosome was not passed to modern humans during breeding 50,000 years ago.

The study found unlike other kinds of DNA, the Neanderthal Y chromosome DNA was apparently not passed to modern humans during this time.

Professor Dr Carlos Bustamante said: “We’ve never observed the Neanderthal Y chromosome DNA in any human sample ever tested.

“That doesn’t prove it’s totally extinct but it likely is.”

The study was the first in-depth genetic analysis of a Neanderthal Y chromosome from the remains found in Spain .

The findings offer new insights into the relationship between Neanderthals and modern humans and some of the genetic factors that might have kept the two lineages apart.

Postdoctoral research fellow in genetics Dr Fernando Mendez added: “Characterising the Neanderthal Y chromosome helps us to better understand the population divergence that led to Neanderthals and modern humans.

“It also enables us to explore possible genetic interactions between archaic and modern gene variants within hybrid offspring.”

Yet why this gene was not passed on remained unclear.

The Neanderthal Y chromosome genes could have simply drifted out of the human gene pool by chance over the millennia.

Another possibility was Neanderthal Y chromosomes include genes that are incompatible with other human genes.

These incompatibilities at one or more of these genes might have played a role in driving ancient humans and Neanderthals apart by discouraging interbreeding between them.

Prof Bustamante said: “The functional nature of the mutations we found suggestions to us that Neanderthal Y chromosome sequences may have played a role in barriers to gene flow, but we need to do experiments to demonstrate this and we are working to plan these now.”

Sequencing the Neanderthal Y chromosome may shed further light on the relationship they shared with humans.

The Y Neanderthal chromosomes that differ from humans function as part of the immune system.

Three chromosomes are minor histocompatability antigens, known as H-Y genes which resemble the HLA antigens that transplant surgeons check to ensure organ donor recipients have similar immune profiles.

Because Neanderthal antigen genes are on the Y chromosome they are specific to males.

The study, published in The American Journal of Human Genetics, shows evidence that a woman’s immune system may attach a male foetus carrying the Neanderthal H-Y genes.

The absence of the Y chromosome also sheds light on the divergence of humans and Neanderthals showing that stopped breeding with apes between 400,000 and 800,000 years ago.

After the split from apes human lineage branches into a series of different types of modern humans.

The last common ancestor of Neanderthals and humans, based on the data, was roughly 550,000 years ago.

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