The Ayta Magbukon people of the Bataan peninsula on Luzon Island, the Philippines, have the world’s highest proportion of Denisovan genes a new study has discovered, despite centuries of interbreeding with later arrivals to Luzon. The discovery reveals a fourth known encounter between Denisovans and modern humans. It also suggests the ancient humans who inhabited the islands of South East Asia may have been descendants of the Denisovans, and at least some of them may have also bred with modern humans.
Ancient humans such as Neanderthals and Denisovans have shaped the human genome through what geneticists call admixture, changing our immune systems and teeth. Indeed these genes are so common in modern humans as to created debate about whether these archaic humans should be considered subgroups of Homo Sapiens, rather than their original designation as different species. Homo floresiensis (nicknamed hobbits) and the recently discovered Homo luzonensis, on the other hand, have been considered more remote relations, most likely unconnected to us for hundreds of thousands of years.
Neanderthal genes are widespread outside Africa, but the Denisovan contribution to the genome is concentrated in South East Asia and Australia. Past studies have found allele (gene varieties) inherited from Denisovans are most common among Papuan Highlanders in what is now New Guinea and Indigenous Australians. However, a new paper in Current Biology reports something other researchers overlooked: an even higher Denisovan inheritance among the Ayta Magbukon, a Philippine Negrito ethnic group.
Philippine Negritos are thought to be the earliest human population to migrate to the Philippines. There are at least 30 self-identified Negrito groups, 25 of which were involved in this study. The researchers found the higher the Negrito ancestry a person had, the higher their Denisovan ancestry.
This discovery is surprising, and significant, because the Ayta Magbukon have had much more contact, and interbreeding, with the rest of the world than Papuan highlanders, who were largely isolated until very recently.
“Philippine Negritos were recently admixed with East Asian-related groups — who carry little Denisovan ancestry, and which consequently diluted their levels of Denisovan ancestry,” said Dr Maximillian Larena of Uppsala University. Once Larena and co-authors accounted for such dilution they found the Ayta Magbukon once had 30-40 percent more Denisovan ancestry than Papuans or Indigenous Australians. Admixture almost certainly occurred in the Philippines, in addition to the three previously identified encounters; two on the Asian mainland before people fanned out through the islands, and a more recent one in New Guinea or nearby.
Some other Luzon Indigenous populations also exceed Papuan levels of Denisovan DNA, but the Ayta Magbukon stand out.
Geneticists estimate the timing of admixture events from the length of DNA tracts left behind. The Ayta Magbukon’s Denisovan tracts are of similar length to those of Australasian peoples, indicating the admixture was not substantially more recent.
The paper notes no Denisovan fossils have been found in the Philippines (or indeed anywhere outside Siberia and Tibet). However, we know almost nothing about the ancestry of H. luzonensis. Perhaps, the authors suggest, the two were genetically related, and H. luzonensis were still present in Luzon when modern humans arrived.
This then raises the question of whether H. floresiensis, who appear to share many characteristics with H. luzonensis, might also have been of Denisovan descent. A people known to us only from four bones, and the DNA inside, may have adapted to many island environments and survived there for hundreds of thousands of years.
Earlier this year Larena and colleagues were accused of not complying with Philippine guidelines on informed consent from the people whose DNA they studied for previous work and not gaining proper ethical clearance. Larena and a colleague responded, noting five that independent investigations have cleared them of these allegations and their indigenous partners remain supportive. A Filipino scientist conducting similar research has not been satisfied by this response..