The key to this new result lies in the researchers’ assumption that Neanderthals had a much more diverse gene pool, but that it was divided into small, isolated, inbred groups of genetically similar individuals. This kind of fragmentation would have skewed the earlier genetic results: Estimates like that two-in-10,000 number described the local populations and their regional histories but missed the big picture.
Rogers looked to make up for this shortcoming by adapting and extending a model of population mixing that other researchers had used. Instead of analyzing a single individual’s genome, he and his team compared genetic variants shared by modern Africans, modern Eurasians, Neanderthals, and Denisovans. An earlier version of this model had been designed to estimate how much modern humans and Neanderthals interbred. Rogers’s main innovation was to add the Denisovans into the mix and significantly increase the number of ways different populations could combine and mingle. Doing so allowed him to ask questions that extended far beyond interbreeding to population size and other concerns.
The increase in genetic diversity that Rogers and his colleagues found corresponds to a roughly tenfold increase in effective population size. Although there is no way of knowing how many more Neanderthal individuals that number may represent, it could go a long way toward meeting the estimates from the fossil data.
“The study provides DNA evidence of what we were seeing in the archaeological record,” said Joshua Akey, an evolutionary biologist at Princeton University.
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Working from the genetic sequences and their revised model, the researchers gleaned new insights into how Neanderthal, Denisovan, and modern human populations grew, shrank, separated and periodically merged through prehistory. “We want to have a nice family tree, to be able to tell neat stories about how these groups were related,” said Steven Churchill, an anthropologist at Duke University. “But it’s clear these relationships are a lot more complicated.”
Approximately 750,000 years ago, according to Rogers, the forerunners of Neanderthals and Denisovans left the ancestors of modern humans behind in Africa to make their way across Eurasia’s expansive territory. Once on their own, something nearly wiped them out entirely; the genetic data shows the population passed through a severe bottleneck, never observed in previous studies. But whatever caused that brush with disaster, the archaic humans bounced back from it, and just a few thousand years later—by 744,000 years ago—they separated into two separate lineages, the Neanderthals and the Denisovans. The former then split further into the smaller regional groups that so fascinated Rogers.
The dating of that schism between the Neanderthals and the Denisovans is surprising because previous research had pegged it as much more recent: A 2016 study, for instance, set it at only 450,000 years ago. An earlier separation means we should expect to find many more fossils of both eventually. It also changes the interpretation of some fossils that have been found. Take the large-brained hominid bones belonging to a species called Homo heidelbergensis, which lived in Europe and Asia around 600,000 years ago. Paleoanthropologists have disagreed about how they relate to other human groups, some positing they were ancestors of both modern humans and Neanderthals, others that they were a nonancestral species replaced by the Neanderthals, who spread across Europe.