Genetic analysis reveals new details on ancient human and Neanderthal couplings

NEW YORK– NEW YORK — Humans and Neanderthals rubbed shoulders occasionally when they lived in the same areas tens of thousands of years ago. But we don’t know much about who hooked up with who, or why.

A new genetic analysis reveals some old rumors: the couples were more often human women with Neanderthal men.

Exactly how this happened remains a huge question mark. Did human women venture into Neanderthal populations, or were Neanderthal men drawn to larger human enclaves? Were these interactions peaceful, confusing, secretive, or even violent?

“I don’t know if we’ll ever get a definitive answer on how this happened, because we can’t travel in time,” said Xinjun Zhang, a population genetics expert at the University of Michigan, commenting on the new analysis.

But the study, published Thursday in the journal Science, shows “that whenever Neanderthals and modern humans mated, there was a preference for Neanderthals and modern women, as opposed to the other way around,” said author Alexander Platt, who studies genetics at the University of Pennsylvania.

Scientists know that Neanderthals and humans mated because there is a small but significant percentage of Neanderthal DNA in most modern humans outside of sub-Saharan Africa – including genes that can help us fight certain diseases and make us more vulnerable to others.

But they also know that Neanderthal DNA is not distributed evenly throughout the human genome.

In particular, there is a surprising lack of Neanderthal DNA in the human X chromosome, one of each cell’s sets of genes called the sex chromosome, compared to the amount of Neanderthal DNA in the cell’s other non-sex chromosomes.

Scientists thought that perhaps the genes in these places were simply not beneficial, or even harmful. Perhaps people with these genetic patterns did not survive as well, so these genes were filtered out by evolution over time.

Or, they thought, perhaps the difference could be explained by the way the two species mixed.

To try to solve the puzzle, Platt and his colleagues instead looked at the Neanderthal genome and human DNA that were interspersed during a “mating event” 250,000 years ago.

Comparing these genes, they found more human fingerprints on the Neanderthal X chromosome – the same chromosome that, in humans, contains less Neanderthal DNA than might be expected.

The most likely explanation for this mirror image pattern is mating behavior. This is due to the way sex chromosomes are passed from parents to children, Platt explained. Since genetic females have two X chromosomes and genetic males have one X and one Y chromosome, two out of three X chromosomes in a population, on average, are inherited from people’s mothers.

If more human females mated with Neanderthal males than the other way around, we would expect to see, over thousands of years, exactly what they found: more human DNA in Neanderthal X chromosomes and less Neanderthal DNA in human X chromosomes.

“I think they took some very important steps to fill in the missing pieces of the puzzle,” said Joshua Akey, who studies evolutionary genomics at Princeton University and was not involved in the new study.

The study cannot completely rule out other explanations. For example, Zhang said, it’s possible that the offspring of human males and Neanderthal females simply didn’t survive as well.

But the simplest and most likely explanation, according to the study, is also the most interesting: “It’s not the result of strictly Darwinian survival of the fittest,” Platt said. “It’s really a result of how we interact with each other, as well as our culture, our society and our behavior.”

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