Neanderthal Y-chromosome genes disappeared from the genome of modern humans long ago, suggests a new study published this week in the American Journal of Human Genetics.
Reconstruction of a Neanderthal. Image credit: Neanderthal Museum.
The Y chromosome is one of two human sex chromosomes.
Unlike the X chromosome, the Y chromosome is passed exclusively from father to son.
“This is the first study to examine a Neanderthal Y chromosome,” said lead author Dr. Fernando Mendez, from Stanford University.
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 Y chromosome was the main component remaining to be analyzed from the Neanderthal genome,” Dr. Mendez said.
“Characterizing 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.”
Dr. Mendez and his colleagues analyzed the Y chromosome from a Neanderthal male found in El Sidrón, Spain.
Other research has shown that the DNA of modern humans is from 2.5 to 4% Neanderthal DNA, a legacy of breeding between humans and Neanderthals 45,000 – 35,000 years ago.
Dr. Mendez’s team was excited to find that, unlike other kinds of DNA, the Neanderthal Y chromosome DNA was apparently not passed to modern humans during this time.
“We’ve never observed the Neanderthal Y chromosome DNA in any human sample ever tested,” said co-author Dr. Carlos Bustamante, also from Stanford University.
The scientists estimate that the time to the most recent common ancestor of Neanderthal and modern human Y chromosomes is approximately 588 thousand years ago.
“The fact that the Neanderthal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct,” they said.
They also found some intriguing protein-coding differences between genes on the Neanderthal and modern human Y chromosomes.
Three of those changes are mutations in genes known in humans to produce male-specific minor histocompatibility antigens.
Antigens derived from one of these genes, known as KDM5D, are thought to elicit an immune response in some pregnant mothers against their male fetuses and lead to miscarriages.
“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,” the scientists said.
“The functional nature of the mutations we found suggests to us that the Y chromosome may have played a role in barriers to gene flow,” Dr. Bustamante added.
“The finding that most of the functional differences associate with these genes, rather than with genes involved in sperm production, came as a surprise,” Dr. Mendez said.
According to the team, additional research is required to confirm the role of those Y-chromosome mutations in discouraging the formation of a hybrid Neanderthal and Homo sapiens.
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Fernando L. Mendez et al. 2016. The Divergence of Neandertal and Modern Human Y Chromosomes. American Journal of Human Genetics, vol. 98, no. 4, p728-734; doi: 10.1016/j.ajhg.2016.02.023
