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Ancestors of Neanderthals, Denisovans Interbred With 'Superarchaic' Hominin

NEW YORK – The ancestors of Neanderthals and Denisovans interbred with a so-called "superarchaic" hominin population that split from the rest of the human lineage about 2 million years ago, according to a new analysis.

The ancestors of modern-day Eurasians interbred with Neaderthals and Denisovans, and recently evidence has arisen suggesting there was even admixture between Neaderthals and the ancestors of modern-day Africans. But looking further back in time at the ancestors of Neaderthals and Denisovans has produced differing conclusions from researchers.

In 2017, the University of Utah's Alan Rogers reported in the Proceedings of the National Academy of Sciences that the Neaderthal and Denisovan lineages might have diverged from each other much earlier than previously proposed and that that split was followed by a population bottleneck. But researchers from Max Planck Institute for Evolutionary Anthropology noted that their own analyses led to different results.

"Both of our methods under discussion were missing something, but what?" Rogers said in a statement.

In this new analysis, appearing in Science Advances, Rogers and his colleagues tried to address that issue by including possible admixture with a superarchaic population in their models and analysis.

For their analysis, the researchers focused on nucleotide site patterns, which they said enabled them to peer further back in time as the patterns are unaffected by recent population history. They evaluated eight models of interbreeding between modern Africans and Europeans and Neanderthals, Denisovans, and a superarchaic population. All these models included gene flow from Neanderthals into Europeans and various combinations of gene flow from a superarchaic population into Denisovans, from the ancestors of modern Africans and Europeans into the ancestors of Neanderthals and Denisovans, and from a superarchaic population into the ancestors of Neanderthals and Denisovans.

The best model, they reported, includes all four of those admixture events. 

This idea of gene flow from a superarchaic population into the ancestors of Neanderthals and Denisovans is novel, the researchers noted. They added that the evidence for it does not appear to be artifactual or due to sequencing error or somatic mutations.

The researchers could also time when these admixture events took place. The superarchaic population split from the rest of the human lineage about 2 million years ago, an estimate the researchers said was in line with archaeological findings of human fossils in Eurasia that are 1.85 million years old. Admixture between the ancestors of Neanderthals and Denisovans and the superarchaic population likely took place about 700,000 years ago.

In all, there were likely three waves of human migration into Eurasia: 2 million years ago when the superarchaic population arrived, then 700,000 years ago when the ancestors of Neanderthals and Denisovans migrated and then interbred with the superarchaic population that was already there, and about 50,000 years ago when modern humans expanded into Eurasia and also interbred with Neanderthals and Denisovans.

The superarchaic population was also likely quite large. The researchers estimated it had an effective population size of about 20,000 individuals. At the same time, the effective population size of the ancestors of Neanderthals and Denisovans was quite small, about 500 individuals. Following the divergence of ancestors of Neanderthals and Denisovans, the size of the Neanderthal effective population size fluctuated from about 16,000 down to 3,400 individuals.

"We've never known about this episode of interbreeding and we've never been able to estimate the size of the superarchaic population," Rogers said. "We're just shedding light on an interval on human evolutionary history that was previously completely dark."

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