Indigenous Group in Philippines Has Highest Denisovan Ancestry in the World

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The remains of a Denisovan jaw.
The remains of a Denisovan jaw.Credit: Dongju Zhang
Ruth Schuster
Ruth Schuster

The more we dive into our innermost selves, the more we discover others lurking there – specifically, other types of humans.

It is becoming ever clearer that our ancestors mixed with other types of humans, including but not confined to Neanderthals and their cousins the Denisovans. We also previously learned that indigenous Southeast Asians feature relatively high Denisovan ancestry compared with Europeans (sub-Saharan Africans are considered to have no Denisovan ancestry).

Now a new paper in Cell Current Biology reports that the Ayta Magbukon Negritos of the Philippines have the highest level of Denisovan ancestry in the world, insofar as is known. They have significantly more than the nearby Papuans.

The report is based on the genomic analysis of 1,107 people in 118 ethnic groups in the Philippines.

How great is the Denisovan contribution to Ayta Magbukon Negritos? About 30 to 40 percent greater than in Australopapuans – meaning indigenous Australians and nearby Papuans, who have a relatively high concentration to begin with: 4 to 6 percent.

The degree of Neanderthal ancestry is the same in all the Philippine ethnic groups; and is also about the same as in other non-African populations. So all non-sub-Saharans have a roughly similar Neanderthal signature in their genes.

Not so the Denisovan contribution: it's not the same in everyone, and was not only highest in (self-proclaimed) Negritas: it decreased in proportion to the level of non-Negrito ancestry.

“We find a strong correlation between Negrito ancestry and Denisovan ancestry,” write Maximilian Larena of Uppsala University, Sweden, and the team.

The Ayta Magbukon group had the most Denisovan ancestry of all despite a later influx of East Asians who didn’t have strong Denisovan signatures. When that contribution from East Asian modern humans (10 to 30 percent in the Ayta Magbukon) is statistically discounted, the team extrapolates, then the Denisovan contribution to the Ayta Magbukon people is 46 percent higher than to Papuans.

Denisova Cave in Siberia.Credit: Xenochka

The requisite inference is that there had been an independent admixture event into the ancestors of the Negritos with Denisovans, the team explains. An extra one – i.e., there had been more than one interspecies sexual encounter.

Multiple encounters with Denisovans

One has to wonder if the unusually high degree of Denisovan ancestry in the Ayta Magbukon people could indicate a quite recent interaction, accounting for the 24 percent excess Denisovan ancestry relative to Papuans. Could it mean the Denisovans went extinct much later than we thought?

The answer is apparently not. If the intermixing event had been recent, the Denisovan sequences in the Ayta Magbukons would be longer than the Denisovan sequences in the Papuans. But they’re not.

“Our findings imply that the admixture is of similar age in the two populations,” the team writes (which doesn’t mean the same time, just a similar one). However, the significantly higher level of Denisovan ancestry in Ayta Magbukon versus Papuans suggests an independent Denisovan introgression event in the Philippines among the ancestral Negritos, which was distinct from the Denisovan introgression event into the ancestral Australopapuans. 

A map showing Denisovan dispersal.Credit: John D. Croft

Further supporting that hypothesis, the pattern of Denisovan ancestry in Negritos isn’t the same as in Australopapuans. It does not seem, the team adds based on their genetic analysis, that the difference stemmed from the Australopapuans mixing with peoples with low Denisovan signatures – while if anything, prior generations of Negritos did exactly that.

So what do we have? Two distinct Denisovan lineages mixing, separately into the ancestors Ayta Negritos and Papuans, after the Negrito-Papuan divergence about 53,000 years ago, the team suggests.

“Upon entry of the first modern human migrants into Sunda and Sahul (ancestors of Negritos and Australopapuans), these ancestral Australasian groups likely experienced admixture with deeply divergent Denisovan-related populations scattered all throughout the ISEA and the Oceania region,” the team sums up.

This would support the big picture taking shape that when different human types met, they weren’t fussy. In the least.

It bears adding that we have no fossil evidence whatsoever for Denisovan presence in Southeast Asia, though we barely have any remains at all – recognized that is – of this enigmatic group. A few bones have been found in the famed Denisova Cave in Siberia, where the species was first detected. A jaw was found in Tibet. The odd hominin fragment of bone found elsewhere in Asia might be theirs or might not.

A Denisovan molar.Credit: Thilo Parg

Recent speculation suggests that “Dragon Man,” a proto-Neanderthal-type skull found in China, could be a Denisovan.

The hobbit and the Denisovan?

It is basically genomic analyses that led to the postulation that Denisovans, an eastern sister species of Neanderthals, had successfully spread throughout Asia. It bears adding that Neanderthals and Denisovans were distinct hominin variants and, in fact, a first-generation Neanderthal-Denisovan hybrid was also discovered in Denisova Cave. This find was so extraordinary that the patriarch of ancient-DNA research, Svante Pääbo, told Nature: “I thought they must have screwed up something.”

And now for something not-quite-completely different. Clearly, Southeast Asia was thronged with multiple species of archaic humans. Among them are Homo floresiensis, the famed “hobbit,” a mini-species occupying the island of Flores; and another mini-species on the island of Luzon, sensibly named Homo luzonensis. Both the Flores and Luzon hominins were primitive types with small brains, no more than about 400 cubic centimeters compared with our 1350 to 1400ccs; both stood about three and a half feet (just over a meter) in height. And both have baffled science. Who were their ancestors?

A recreation of what Homo floresiensis may have looked like.Credit: Cicero Moraes et alii

This new paper suggests that the diminutive Flores and Luzon archaic humans were, after all, offshoots from the Denisovan tree.

Yet previous research, reporting that the two tiny hominins survived until a mere 60,000 to 50,000 years ago, argues powerfully against Denisovan ancestry for them. It seems the ancestors to the two archaic humans of Flores and Luzon likely reached the region around 750,000 years ago, which predated the evolution of the Denisovans by a few hundred thousand years.

Some suggest the Flores and Luzon hominins arose from Homo habilis, which lived between 2.4 million to 1.65 million years ago: the proportions between the hobbits’ upper arm and upper leg seem more similar to australopiths and Homo habilis than to modern humans. Its feet also seem more Australopithecus-like but its shoulder is more like Homo erectus. In other words, we still don’t have a clue. We have no idea where, or who, the Flores and Luzon hominins came from.

Even without suspecting that Luzon and Flores hominins stemmed from Denisovans, there are signs the Denisovans were a hardy lot that could adapt to a broad range of environments, including great altitudes. The present-day Tibetan tolerance of high altitude is thought to have been inherited from Denisovans.

A Homo floresiensis skull.Credit: Daderot

With our ancestors’ bed linen on display in our genomes, do mysteries remain? They sure do. For instance, genomic data indicates that Papuans experienced a distinct Denisovan introgression event as recently as 30,000 to 25,000 years ago. This is utterly inexplicable based on the fossil evidence.

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