Humans weren’t just making babies with Neanderthals back in the day. A new study that compares the genomes of different groups of modern humans has found that our ancestors interbred with another close relative, the Denisovans, more than once.
The findings, published in the journal Cell, demonstrate a special method that scientists can use to find these hidden fragments of DNA from our long-gone cousins — and shed fresh light on the complexities of human evolution.
Denisovans, close cousins of modern humans and Neanderthals, were first described in 2010 after the discovery of a fossil finger bone from a cave in the Altai mountains in Siberia. That roughly 41,000-year-old fossil allowed researchers to extract some of its DNA and sequence the genome of its former owner, a young female Denisovan.
Those DNA samples revealed a number of matches in the genome of some modern humans — including a gene that helps Tibetans adapt to high-altitude environments. This means that at some point in time, modern humans and Denisovans had sex. The same goes for Neanderthals, whose DNA is also embedded in our own genome. (That ability to mate and produce viable offpsring is a large part of why some scientists are starting to avoid calling Neanderthals and Denisovans separate “species.”)
But it’s difficult to learn a whole lot about the mark that Denisovans left on modern humans based primarily on the Altai Denisovan girl’s finger bone. (There are only a handful of other fossils, mostly teeth and a toe, which means scientists don’t have a great idea of what they looked like, either.)
So for this paper led by Sharon Browning, a biostatistician at the University of Washington in Seattle, scientists tried another approach — one that could pick out Denisovan DNA without needing an ancient genome for reference. Her method compared modern human genomes from different regions (Europe, Asia and Oceania) to look for shared segments of DNA with telltale levels of genetic variation that indicated they came from an archaic human.
The researchers found that Oceanian people, particularly Papuans, had the most Denisovan DNA — it made up about 5% of their genomes. East Asians were a distant second, with about 0.2%.
But the odd thing about the East Asian DNA is that it held two genetically distinct groups of Denisovan DNA — one that was more related to the Altai Denisovan, and one that was far less similar. This meant that those two types of Denisovan DNA actually came from two different populations that had been separated over time, allowing random mutations to emerge and their lineages to diverge.
“I definitely wasn’t going and looking specifically for this,” said Browning, who’d simply been looking to see if this statistical method would work. “It was a surprise when it popped out of the results.”
The scientists also found Neanderthal DNA using this method, though they didn’t find two waves the way they did with the Denisovans.
What this means for how humans and our fellow hominins moved around and interacted is unclear, Browning said. The scientists can’t say which interaction happened first, although it does seem to imply that Denisovans had spread farther than previously thought.
“It makes it clear that there were at least two populations living over an extended geographical distribution, whereas the only remains we have are from that one cave in Siberia,” Browning said.
It also strengthens the growing understanding that humans and their close relatives interacted with each other far more than we once thought.
It “says something about them not being so different from us,” she said.
Browning said the next step is to apply this to other populations — perhaps in Africa, where there are few genomic sequences of archaic humans available — and to see whether other hints of ancient hominin matings show up.
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