Tens of thousands of years ago, as modern humans migrated into northerly territories inhabited by our ancient cousins, the Neanderthals, the two species met – and sometimes mated.
Now, genetic evidence has revealed a striking imbalance in these prehistoric trysts, suggesting that interbreeding was mostly between male Neanderthals and female humans.
This ancient mating pattern, they have concluded, explains why Neanderthal DNA is largely missing from the human X chromosome.
“We found a pattern indicating a sex bias: gene flow occurred predominantly between Neanderthal males and anatomically modern human females,” said Dr Alexander Platt, a senior research scientist at the University of Pennsylvania and first author of the research.
The ancestors of modern humans and the closest related species, the Neanderthals, diverged, forming two distinct groups, about 600,000 years ago.
“Our ancestors evolved in Africa, while the ancestors of Neanderthals evolved in and adapted to life in Eurasia,” said Sarah Tishkoff, the David and Lyn Silfen University professor in genetics and biology at the University of Pennsylvania, who led the research. “But that separation was far from permanent.”
Over hundreds of millennia, human populations migrated into Neanderthal territories and back again, and when these groups met, they mated, swapping segments of DNA. Today, individuals of non-African heritage typically have a few per cent Neanderthal DNA, while those of African heritage typically have a lower proportion.
“It’s hard to say how many times these events occurred,” said Tishkoff. “But I’m just getting the sense that this was happening more than we originally speculated.”
However, Neanderthal DNA carried by modern humans is not evenly distributed across the genome. In particular, there are missing areas of Neanderthal DNA, known as “Neanderthal deserts”, along the X chromosome.
Platt said: “For years, we just assumed these deserts existed because certain Neanderthal genes were biologically ‘toxic’ to humans – as tends to be the case when species diverge – so we thought the genes may have caused health problems and were likely purged by natural selection.”
However, the latest research, published in the journal Science, puts forward an alternative explanation.
The researchers studied the presence of modern human DNA preserved in three Neanderthals – the Altai, Chagyrskaya and Vindija – and compared this dataset with genetic data from specific sub-Saharan African populations that lack Neanderthal ancestry.
If the two species were biologically incompatible, modern human DNA should have been missing from Neanderthal X chromosomes as well. However, the analysis revealed that Neanderthal X chromosomes had a 62% excess of modern human DNA compared with their other chromosomes – a mirror-like reversal of the distribution of Neanderthal DNA in human populations.
Because females carry two X chromosomes and males carry only one, mating direction matters. If Neanderthal males partnered more often with modern human females, fewer Neanderthal X chromosomes would enter the human gene pool, and more human X chromosomes would enter Neanderthal populations.
“Mating preferences provided the simplest explanation,” Platt said.
The findings did not, Platt said, suggest that Neanderthal males were particularly attractive to modern human females or vice versa. “It could be that everybody considered the interspecies matings as gross – or attractive,” he said. “But it seems that one direction was viewed as better, or less worse, than the other.”
The strength of the effect suggested that it also went beyond the first mating event and that males with Neanderthal heritage would be preferred over females with Neanderthal heritage, within a predominantly modern human population. “It’s something that had to continue within a population after the first mating had already happened,” Platt said.
