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Ancient Humans, Neanderthals Interbred More Than Once, New Analysis Says

NEW YORK (GenomeWeb) – Ancient humans living outside of Africa interbred with Neanderthals more than once, according to a new analysis.

Modern East Asian and European human populations have differing amounts of Neanderthal ancestry — East Asians have between 12 percent and 20 percent more than Europeans — and there are varying theories, including a dilution model, to explain how that came to be.

Two researchers from Temple University have now modeled various scenarios for how ancient human-Neanderthal admixture may have occurred and compared those results to Neanderthal ancestry captured by the 1000 Genomes Project. As they reported in Nature Ecology and Evolution today, they uncovered evidence for an admixture event that occurred before the East Asian and European lineages diverged, as well as for subsequent events that only involved the East Asian lineage or only the European lineage.

"These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated," Fernando Villanea and Joshua Schraiber wrote in their paper.

According to a previous analysis, the genome of the 45,000-year-old Ust'-Ishim, an individual from Siberia who is equally related to East Asians and Europeans, has the same amount of Neanderthal ancestry as some present-day Eurasians, though in longer tracts of DNA. This, the researchers noted, is consistent with an admixture event occurring between 52,000 years and 58,000 years ago.

But to account for the differing levels of Neanderthal ancestry between Europeans and East Asians, some scientists have suggested that it was watered down in Europeans through interbreeding with another population that was lacking Neanderthal ancestry. By contrast, another hypothesis suggests that differing demographic or selective forces exerted themselves on East Asians and Europeans that affected their level of Neanderthal ancestry. Alternatively, there may have been more than one admixture event.

To look into this further, Villanea and Schraiber constructed a joint fragment frequency spectrum (FFS) matrix from Neanderthal ancestry calls identified within the 1000 Genomes Project dataset. Through this, they found East Asians to have an average proportion of Neanderthal ancestry 19.6 percent higher than that of Europeans, as they expected. They then developed analytical models to determine how FFS would look under various demographic models.

Neither the one-pulse admixture nor the dilution model matched with what is observed in modern populations. Instead, the researchers found evidence supporting a two-pulse model.

They also applied a maximum likelihood approach to their models and again found evidence for the two-pulse model from within both the East Asian and European populations. This led them to conclude that there was a complex history of admixture between ancient humans and Neanderthals.

With a supervised machine-learning approach, the researchers further examined how tweaking different demographic parameters affected the joint European and East Asian FFS. The models that best fit the data, the researchers found, were the more complex ones: a three-pulse model of admixture and a three-pulse model of admixture with dilution. Those later pulses of admixture affected East Asian and European populations separately, leading to higher levels of Neanderthal ancestry among East Asians.

As Villanea and Schraiber noted in their paper, the best-fit model involves multiple instances of interbreeding between Neanderthals and humans. This interbreeding was ongoing, they said, though intermittent and likely occurring in a restricted geographical area.

They added, though, that their analysis has some limitations. Namely, their model assumes that Neanderthal ancestry was neutral, when it was likely deleterious. In addition, some Neanderthal ancestry among modern East Asian populations may have been misclassified and could instead be from another ancient hominin group, the Denisovans.

Still, the scenario the researchers described tallies with "the emerging view of complex and frequent interactions between different hominin groups," wrote Fabrizio Mafessoni from the Max Planck Institute for Evolutionary Anthropology in a related commentary. He added that there is evidence that the Denisovans interbred with humans at least twice.