The discovery of the Denisovans 15 years ago set off a chain of evolutionary research into how they contributed to modern East Asians and Oceanians. A new study adds evidence. Researchers have confirmed that a nearly complete hominin skull from 146,000 years ago that was discovered near Harbin belongs to the Denisovan lineage even as it is a new species, Homo longi.  

In "The proteome of the late Middle Pleistocene Harbin individual", the authors detail how they linked the Harbin cranium to the early Denisovan lineage from Siberia. By creating a method for automatic identification of human populations based on ancient proteins, creating the most informative ancient human proteome to-date. The mass spectrometric data identified over 308,000 peptide-spectrum, more than 20,000 peptides, and confirmed 95 endogenous proteins.

They also optimized extraction techniques and developed bioinformatic algorithms to trace the evolution of ancient human DNA from Pleistocene dental calculus, successfully retrieving host mitochondrial DNA from the dental calculus of the Harbin cranium.


Harbin cranium (HBSM2018-000018(A)). (A) Anterior view. (B) Lateral view, left side. Scale bar indicates 50 mm. Credit: 10.1016/j.xinn.2021.100132

Prior to the Harbin cranium, Denisovan fossils were limited and fragmentary, which hindered understanding of their morphology and evolutionary history.  The team did their own palaeoproteomic analyses and innovative ancient DNA experiments on the Harbin cranium and its dental calculus and found the fossil fossi shares significant morphological similarities with Denisovan remains found at other locations. They confirmed the Harbin individual’s classification within the Homo genus with discovery of 122 single amino acid polymorphisms (SAPs) unique to Hominidae species.

By identifying three variants unique to Denisovans, they established the phylogenetic link between the Harbin individual and Denisova 3. The mitochondrial DNA from dental calculus further confirmed that the Harbin individual belongs to an early mtDNA lineage of Denisovans, suggesting a wide distribution from Siberia to Northeast China during the late Middle Pleistocene.