“What’s quite clear is that 40,000 years ago, Southeast Asia was already a patchwork of peoples with and without Denisovan ancestry,” Reich said. The limited interbreeding that took place on the main Asian continent still shows up in populations there today as a small piece of the Denisovan hominin puzzle.
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In tracing the steps of the Denisovan, we find evidence that the species migrated to Southeast Asia in a concentrated enough amount to impart a high degree of hybridization with groups in the region. From the location of the Denisova Cave, we can trace a path from modern day Russia into Southeast Asia and Australia.
What’s perhaps more surprising is that there is a low rate of interbreeding in China, Mongolia, Nepal and other countries on the main continent. If the Denisovans were in the area for long, they certainly didn’t interact with Homo sapiens in quite the same way as they did in Southeast Asia. But the fractions of a percent of shared DNA seen in modern Asian populations have imparted beneficial adaptations to some groups there—even if it’s just from a great-to-an-unknown-power grandfather. And all this adds up to more clues, however small, explaining the migration of the Denisovan.
DNA mixture in mainland Asia isn’t entirely absent. Some groups still have the markers of Denisovans, however small. For native Tibetans, ancient hominin interbreeding—however small a portion of their overall genome—may have impacted their ability to live in climates and altitudes hostile to other groups. Rasmus Nielsen, a faculty member of the Center for Theoretical Evolutionary Genomics, previously worked on tracing how Tibetans can withstand the effects of hypoxia in low-oxygen environments. In 2010, his team published a paper indicating the EPAS1 gene as the culprit behind this beneficial mutation. The gene regulates the body’s reaction to low oxygen environments, allowing Tibetans to produce fewer red blood cells and less hemoglobin.
When comparing Tibetan DNA to other human groups, no one could find where the EPAS1 gene might have arisen. It didn’t show up in other Homo sapiens populations. It would seem that it came from another species entirely. So Nielsen went looking for the other hominin.
“The difference between the DNA sequence in Tibetans and all other human human populations was simply too large,” Nielsen said. “Our models of natural selection and mutation just couldn’t explain that. So we started to look for other explanations, and we compared first to the Neanderthal sequence, and we can show that there’s no match to the Neanderthal sequence.” So on a longshot bet, Nielsen compared the recently uncovered Denisovan genome to the Tibetans. The Denisovan ancestry was fractional, but the EPAS1 was an exact match between the two populations.
Prior to dispersing to the islands, the Denisovans hung around just long enough to give Tibetans the gene they needed to survive the Himalayas.
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With scant fossil evidence, it’s hard to know what to look for when it comes to learning more about the Denisovan.
It would take a DNA match in a fossil to positively identify any fossil found as Denisovan. The low temperatures of the Denisova Cave helped preserve much of the DNA in the scant fossil record, but the same can’t be said of a number of human species whose lineage has to be resolved based on physical fossil evidence because DNA is too far decayed to prove useful.
There are a few suspicions on Denisovan fossil matches, however.
“There’s a very enigmatic fossil record in China that contains possible candidates for Denisovans, and that’s sort of a very interesting place to look aside from Southeast Asia,” Reich said, specifically referring to the Dali and Maba Man, two enigmatic fossils found in two different areas of China. Pääbo also sequenced DNA from a 400,000 year old femur bone found in a cave in Spain. While Neanderthals were known to dominate Europe prior to the arrival of humans, mtDNA in the femur was a closer match to Denisovans, complicating the existing picture of migration. In the absence of nuclear DNA, though, it’s hard to determine the extent of a match.
There may also be existing specimens not yet tested. “So you have a large amount of potential candidates from museum collections that you could investigate to see if there’s some match to the Denisovan DNA,” Nielsen said.
Even if the mystery of the Denisovan is solved, there are plenty more unknowns. In the DNA of the Siberian Denisovan there were the markers of a third species. Where there was interbreeding between Neanderthals and Denisovans, there was also gene flow from another unidentified species more ancient than either Neanderthals and Denisovans, meaning a very old species likely lived alongside and at the same time as both.
“The gene flow from Denisovans was from another archaic population that was extremely distantly related to the Denisovan from the Denisova Cave,” Reich said. In other words, whatever the mystery species was, it shared a common ancestor that wasn’t Denisovan. “What becomes clear is that there were at least three highly divergent archaic populations. And who knows, there could have been more in Eurasia at that time.”
Until a fossil is identified, we won’t conclusively know what the Denisovan looks like. But the quest to learn more is starting to generate even more questions. In tracking the Denisovan, scientists have found evidence of other archaic groups, predating humans, Neanderthals and Denisovans.