Neanderthal Y chromosome was replaced after mating with Homo sapiens

A new study found that Homo sapiens males essentially emasculated Neanderthal males when they mated with Neanderthal females over 100,000 years ago. These unions forced modern Y chromosomes to infiltrate future generations of Neanderthal boys, eventually replacing the Neanderthal Y chromosome with the Homo sapiens Y chromosome.

The new discovery could solve a long-standing mystery as to why researchers were unable to locate the Neanderthal Y chromosome. Part of the problem was a lack of male DNA: of the dozen Neanderthals whose DNA has still been sequenced, most are female, as the DNA in male Neanderthal fossils is poorly preserved or contaminated with bacteria. “We started to wonder if there were any male Neanderthals at all,” says Janet Kelso, a biologist at the Max Planck Institute for Evolutionary Anthropology.

But in a technical breakthrough, Max Planck’s graduate student Martin Peter developed a set of probes that used DNA sequences from small fragments of the Y chromosomes of modern men to “fish” and bind to DNA from the Y chromosomes of archaic men. The new method works because the chromosomes of Neanderthal and modern humans are largely similar; DNA probes also form slightly different base pairs.

The researchers examined the fragmented Y chromosomes of three Neanderthals from Belgium, Spain and Russia, who lived 38,000 to 53,000 years ago, and two male Denisovans, close relatives of the Neanderthals, who lived in Denisova Cave in Siberia from 46,000 to 130,000 years ago. When the researchers sequenced the DNA, they got a surprise: the Neanderthal Y chromosome “looked more like modern humans than Denisovans,” says Kelso.

This was “a mystery,” says Peter, since earlier studies showed that the rest of the Neanderthal’s nuclear genome is closer to Denisovans.

Scientists estimate that the two groups split off from modern humans about 600,000 years ago. But the emergence of the unusual Y chromosome comes in parallel with another genetic upheaval: Neanderthal remains dating from 38,000 to 100,000 years ago contain the inherited mitochondrial DNA (mtDNA) of a modern woman instead of the ancient Neanderthal mtDNA found in earlier fossils.

In this case, an early female Homo sapiens probably interbred with a Neanderthal male over 220,000 years ago, and their descendants carried modern mtDNA. The best scenario to explain this is to assume that early modern human males mated with Neanderthal females over 100,000, but less than 370,000 years ago.

Their sons would carry the modern human Y chromosome, which is passed down through the paternal line. The modern male Y chromosomes then quickly spread through their offspring to small populations of Neanderthals in Europe and Asia, replacing the Neanderthal male Y chromosome, the researchers report in the journal Science.

Interestingly, modern humans were not the ancestors of today’s Homo sapiens, but were probably part of a population that migrated from Africa and then became extinct. Traces of Neanderthal DNA in living humans were inherited from a single mixing event between 50,000 and 70,000 years ago.

Researchers don’t know why this change happened.

Meanwhile, the study shows that the mixing of modern humans and Neanderthals was “a defining milestone in hominin history,” says geneticist Josh Eiki of Princeton University.

This event not only gave modern humans the DNA of Neanderthals, but also fundamentally changed the Neanderthals themselves.

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