When Neanderthals and modern humans first came together, they preferred a combination of Neanderthal males and human females, a new study of ancient and modern genomes suggests. The discovery helps explain why modern humans (Homo sapiens) have relatively low levels of Neanderthal genes, and why those genes are found in some populations today but not in others.
Ever since the genomes of modern humans and Neanderthals were first sequenced more than 20 years ago, scientists have puzzled over the “Neanderthal desert,” or the rare places in the modern human genome where Neanderthal genes reside. The two groups interbred over several periods after their ancestors diverged about 600,000 years ago. As a result, most non-Africans on Earth now have an average of 2% Neanderthal DNA, but some African groups have up to 1.5% DNA, which they inherited from Homo sapiens who interbred with Neanderthals in Eurasia and then migrated to Africa.
But what puzzles experts is that the genes we inherited from Neanderthals are only found in a small patch on the X chromosome, even though they are more abundant on other chromosomes. There is a region of the X chromosome (the sex chromosome of which all humans have at least one copy) where modern humans do not have Neanderthal ancestry.
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“For many years, we thought these deserts existed only because certain Neanderthal genes were biologically ‘toxic’ to humans,” Alexander Pratt, a population geneticist at the University of Pennsylvania, said in a statement. “As is often the case when species diverge, we thought it was likely that the genes caused health problems and were removed by natural selection.”
But in a study published Thursday (February 26) in the journal Science, Pratt and colleagues concluded that the most plausible explanation for these “Neanderthal deserts” is actually mate preference, an evolutionary mechanism that is a key part of sexual selection. Biologists commonly explain the evolutionary consequences of mate preference with the male peafowl’s large, colorful tail. Early humans and Neanderthals likely also chose their mates for specific reasons.
DNA details
The researchers analyzed the genomes of 73 women from three modern African populations without Neanderthal ancestry, including !Xoo, Ju|’hoansi and Khoisan, and compared them to the genomes of several Neanderthals. First, by examining the Neanderthal X chromosome, it was found that compared to other Neanderthals, it has a significantly larger amount of ancestors from modern humans. The results would reveal that the absence of Neanderthal genes on the human X chromosome is not the result of incompatibility and would suggest that Neanderthal genes caused problems in modern humans and were eliminated by natural selection.
Rather, the researchers concluded that mate preferences explain the surprisingly large amount of modern human DNA found in Neanderthals. Because women have two X chromosomes and men only one, a preference for interbreeding between female Homo sapiens and male Neanderthals would mean fewer Neanderthal X chromosomes would enter the human gene pool, producing the pattern researchers identified in the genome.
However, the reasons for mate preference and its direction remain unclear.
“I have no idea whose preferences are being represented here,” Pratt told Live Science via email.
Previous studies of the Neanderthal Y chromosome (one of the two male sex chromosomes) have shown that there was interbreeding between Homo sapiens men and Neanderthal women. But a new study reveals that male Neanderthals and female Homo sapiens actually liked each other more than female Neanderthals and male Homo sapiens.
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“Right now, we don’t have any further identifying genetic characteristics,” Pratt said.
The researchers did not rule out a more complex evolutionary scenario in which natural selection, sex bias, mate preference, and sex-specific migration may have combined to contribute to a “Neanderthal desert” in the human genome.
Anthropologists and evolutionary biologists who have studied this phenomenon have shown that mate choice is partially learned, so questions about the structure of Neanderthal and modern human societies are also important to answer to more fully understand past mate choice.
The research team plans to “examine the evolution of Neanderthal social structure and gender roles,” which “may shed some light on the bigger picture,” Pratt said. “But I think we still have a long way to go before we know this.”
Neanderthal quiz: How much do you know about our closest relatives?
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