Razib Khan on Denisovans

Razib Khan does a good job of summing up some of the things that we've learned in recent years about Denisovans, an archaic hominin clade.

[I]n 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%.

 

Partial skull of Homo longi, AKA a Denisovan

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.