Browning developed a technique that compares the genomes of many modern people, and looks for stretches of DNA that are unusually varied, relative to their neighboring segments. These varied stretches are likely to have been inherited from ancient hominins like Neanderthals, Denisovans, or as-yet-undiscovered groups. Browning can then compare these segments to the genomes of those ancient hominins to work out exactly which group the DNA came from. 
 
 In the genomes of people from Japan and China, Browning found several segments that closely match the genome of the Denisovan woman whose pinky was found in the Altai Mountains. But to her surprise, she also found segments that were clearly Denisovan in origin, but were much weaker matches to the Altai female. “They’re close enough that we’re sure they’re Denisovan, but they’re not as close,” she says. 
 
 This suggests that modern humans inherited DNA from two separate groups of Denisovans. The way Browning sees it, the ancestors of today’s Melanesians encountered Denisovans as they expanded through South Asia and the Malay Peninsula. The two groups interbred, with the result that 5 percent of modern Melanesian DNA has a Denisovan origin. 
 
 At roughly the same time, the ancestors of today’s East Asians were taking a more northerly route through the continent, and met a different group of Denisovans, perhaps somewhere close to that Altai cave. Again, there was sex. Again, Denisovan DNA infiltrated the human genome. 
 
 But this contribution was much smaller, and today’s East Asians retain much less Denisovan ancestry than Melanesians do—just 0.2 percent of their genome. “Maybe it was a large group of East Asians meeting a small number of Denisovans,” Browning speculates. And complicating matters further, some Melanesians likely migrated north and mixed with East Asians, uniting the two waves of Denisovan ancestry in one lineage. 
 
 “Once I found two Denisovan waves, I thought we’d see something similar in the Neanderthals,” Browning says. To her surprise, she didn’t. People from Eurasia can trace around 2 percent of their DNA to Neanderthals, and it seems that this legacy comes from a single wave of interbreeding with one particular group—one that likely lived in the European part of their range. 
 
 That goes “somewhat against the grain of current knowledge,” says Emilia Huerta Sánchez, from the University of California at Merced. Some scientists have suggested that several groups of Neanderthals donated DNA to modern humans, which might explain why East Asians contain considerably more Neanderthal DNA than Europeans do. Browning and her colleagues argue otherwise, “and they have a considerable level of evidence to support their conclusions,” Huerta Sánchez says. 
 
 That seems counterintuitive, especially since we know that Neanderthals lived throughout Europe and Asia, whereas Denisovans have only been found in a single Siberian cave. But that picture might be deceptive. Scientists have sequenced the genomes of two Neanderthals—one from Vindija Cave, in Croatia, and another from the Altai region, in Siberia—and the differences between them are smaller than between the two Denisovan populations Browning identified in her work. “Maybe the Neanderthals were more nomadic and their populations were mixing a lot, while the Denisovans stayed in particular places and didn’t mix,” she says. 
 
 It’s also possible that Denisovans were more widespread than their limited bones suggest. “They may have overlapped in range with Asians and Papuans, as these populations had multiple encounters,” says Priya Moorjani, from University of California, Berkeley. “Since we only know about Denisovans from genetic material from one cave, any additional insights are exciting.” 
 
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 Our ancestors mated with another species of ancient hominins, the Denisovans, on at least two occasions. The discovery suggests that Denisovans were widely across Asia, and apparently co-existed happily with modern humans, to the point of having children with them in two different parts of the ancient world. 
 
 The Denisovans were unknown until 2010, when researchers described a fragment of a girl’s finger bone found in Denisova cave in Siberia. Soon afterwards, researchers sequenced its genome from the surviving DNA. The DNA did not belong to any known hominins, such as Neanderthals, so it had to be something new. 
 
 What’s more, around 5 per cent of the DNA of some Australasians – particularly people from Papua New Guinea – is Denisovan. Humans evidently mated with Denisovans 50,000 or more years ago. 
 
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 But this posed a puzzle: why were the present-day descendants of Denisovans so far from the Denisovans’ Siberian home? The simplest explanation was that Denisovans lived throughout much of Asia, including South East Asia, not just Siberia. 
 
 Sharon Browning of the University of Washington in Seattle and her colleagues have now found evidence of a second instance of human-Denisovan interbreeding – on the Asian mainland. 
 
 Hidden in the genes 
 
 Browning’s team used a new technique to trawl for segments of ancient DNA in the genomes of 5600 living humans from Europe, Asia, America and Oceania. The chunks of older DNA stand out because they are unusually rich in mutations, which would have built up for hundreds of thousands of years in the genomes of Denisovans, but would not have been present in the human lineage. So when humans and Denisovans mated, their children would inherit these mutation-rich regions of DNA. 
 
 After Browning had isolated the ancient DNA, she then used the reference genomes of Denisovans and Neanderthals to establish where it came from. She found that some East Asians carry Denisovan DNA, especially Han Chinese, Chinese Dai and Japanese people. 
 
 But this Denisovan DNA is distinct from that carried by Australasians. It is more closely related to the Denisovan sample. “Although the Papuans ended up with more Denisovan ancestry, it turns out to be less similar to the sequenced Denisovan,” says Browning. 
 
 The upshot is that Denisovans bred with modern humans in at least two places: in east Asia, and further south-east in Indonesia or Australasia. “Our research demonstrates that there were at least two distinct populations of Denisovans living in Asia, probably somewhat geographically distant,” says Browning. 
 
 Even more interbreeding 
 
 “The fact that two episodes of interbreeding occurred suggests that at least in some instances, Denisovans and modern humans were willing to live in proximity and interact,” says Browning. 
 
 As well as mating with Denisovans, there is strong evidence that humans interbred with Neanderthals, which were a sister species to the Denisovans. 
 
 “This new work is important because for the first time it unambiguously demonstrates a third interbreeding [of modern with ancient hominins],” says David Reich of Harvard Medical School in Boston. “Up to this point, we only had data for two.” There have been claims of a second, earlier instance of interbreeding with Neanderthals, but not everyone is convinced. 
 
 Tantalisingly, breeding with Neanderthals and Denisovans may not be the end of our ancestors’ promiscuity. A quarter of the chunks of ancient DNA that Browning found in living humans didn’t match either Neanderthal or Denisovan DNA. So we may have also had children with other, unidentified hominins. 
 
 “At this point, we have no way of knowing if these derive from an as-yet-unknown archaic group, or are simply false positives,” says Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 
 
 Journal reference: Cell, DOI: 10.1016/j.cell.2018.02.031
– Ancient humans weren't against knocking boots with other species: We know they had sex with Neanderthals. We also know they mated with the mysterious Denisovans, as some Australasians (those from Papua New Guinea in particular) have 5% Denisovan DNA. But a "breakthrough" study shows the interbreeding wasn't limited to those two instances. While looking for ancient DNA in the genomes of 5,600 living humans, a team at the University of Washington in Seattle came across evidence of a third interbreeding event, reports New Scientist. A smaller contribution of Denisovan DNA in Han Chinese, Chinese Dai, and Japanese people—about 0.2% of their genome—suggests humans mixed with a distinct population of Denisovans in not one but two locations: Indonesia or Australasia and East Asia. Though the only four Denisovan fossils that have been found come from the same cave in Siberia, the research published in the journal Cell shows Denisovans were spread across Asia and "suggests that at least in some instances, Denisovans and modern humans were willing to live in proximity and interact," lead author Sharon Browning says. Her research also backs the theory that there was a single "wave" of interbreeding between humans and one population of Neanderthals, reports the Atlantic. But Browning couldn't link other ancient DNA found in living humans to Neanderthals or Denisovans, suggesting humans may have mated with hominins we haven't even discovered yet. Harvard geneticist David Reich, who was not involved in the research, says the finding of "a definite third interbreeding event" makes this "a breakthrough paper," per the Washington Post. (Here's how a bit of cave dirt changed archaeology.)