Hiding in plain sight: uniting Denisovans’ famous DNA with a set of mysterious physical remains
The Denisovans were always right in front of us
Fifteen years ago, a humble genome sequence revealed a never-before detected human lineage. The Siberian cave, Denisova, where DNA was extracted from unidentified trace hominin remains, lent its name to this newly discovered people. Called “Denisovans,” everything we have so far gleaned of them has come from the slow accretion of data in a mere handful of genomes that have come to light since, including that of a 13-year-old teen girl given the unimaginative nickname “Denny,” who lived 90,000 years ago and astonishingly happens to have had a pure Denisovan father and a pure Neanderthal mother. The 2010 discovery of this class of hominids, accomplished by genome sequence alone, occurred in tandem with the sequencing of Neanderthals, published six months earlier; together they revealed that all humans outside of Africa harbored some ancestry from this long recognized people, whose fossils were first discovered more than two centuries ago. But the Neanderthals were not the only now extinct contributors to the genomes of modern humans; comparisons between various human populations and Denisovans have shown that an average of some 5% of people’s ancestry in New Guinea, thousands of miles from Siberia, actually derives from Denisovans. Further comparing the genomes of Neanderthals, Denisovans and modern humans, we’ve seen that our ancestors parted ways with the Neanderthals’ and Denisovans’ ancestors about 600,000 years ago, and that Neanderthals and Denisovans diverged from one another about 400,000 years ago.
In the space of less than a year, in 2010, paleoanthropology’s model of human evolutionary history over the last few hundred thousand years was utterly transformed. Neanderthals were not just primitive dead-ends, they were part of our own heritage (subsequent work showed that Africans as well have at minimum trace amounts of Neanderthal ancestry due to members of our anatomically modern lineage back-migrating from Eurasia). But the Denisovans presented different questions: they were a wild card, unexpected and unaccounted for. More critically, while Neanderthals had long been a well-characterized fossil lineage in the paleoanthropological literature, we were left to conjure Denisovans solely from their distinctive genomic sequence. Homo neanderthalensis is a human species defined by taxonomists; Denisovans were an ad hoc label of convenience for geneticists, a sort of species in waiting.
All of that officially changed this month; in June 2025, Chinese paleogeneticist Qiaomei Fu published data finally connecting specific fossil remains to Denisovans, utilizing both mtDNA and protein sequencing methods. And so now we know that Denisovans and Homo longi, are one and the same. A rather well preserved fossil from Harbin, China, a nearly complete skull, first identified as a new species in a 2021 publication, and colloquially dubbed Dragon Man, turns out to have DNA that we can now see neatly matches the sequences extracted from Denisova cave. For fifteen years, the label Denisovan only applied in a genomic context. No longer. Denisovan physical remains were in fact in plain sight all along.
This is not entirely a surprise. Some geneticists and paleoanthropologists have long assumed that many among the wealth of the fossils languishing yet to be identified, catalogued or named in East Asian collections today were Denisovans (I said as much in a podcast with Vagheesh Narasimhan of UT Austin, when H. longi was announced four years ago). Also, since 2010, we have established that Denisovans are the ancestors of more than Papuans and other Australasians. The Negrito peoples of the Philippines have a substantial contribution from Denisovans, the same as their Papuan neighbors from New Guinea to the south. But when you set aside their majority Austronesian ancestry (a much more recent overlay), it appears their forager ancestors (today some 35% of their ancestry) carried even more Denisovan ancestry than Papuans, on the order of 7-8%. It is also clear that low, but detectable, levels of Denisovan ancestry appear today in populations across South, East and Southeast Asia, at fractions of 0.1-0.3%.
The attested presence of Denisovan ancestry across a vast triangle stretching from Pakistan to Japan to Australia argues that they were present across vast territories. Deeper analysis of the Denisovan fragments in the genomes of Asians, Melanesians and Australians suggest at minimum two admixture events with two very distinct Denisovan populations. One population is clearly related to the genomes we have from Denisova cave. These northern Denisovans mixed with the ancestors of modern East Asians. But the Denisovan ancestry in South and Southeast Asians, as well as in Melanesians and Australians, is clearly from a population with a distinct ancestry; likely one that split off from the northern subspecies as long as more than 350,000 years ago. And the plot thickens, because tentative evidence gleaned from comparing the segments carried by these populations with southern Denisovan ancestry suggests distinct admixtures here as well; one in South Asians, another in Southeast Asians (a common one with Melanesians and Australians), and perhaps even one or two further ones in the outer reaches of prehistoric Sundaland and Sahul.