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"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. Professor 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.