Show Notes
️ Episode 55: Denisovan DNA in Dental Calculus — Linking Morphology and Genetics in a 146,000-Year-Old Hominin
In this episode of Base by Base, we delve into a groundbreaking study by Fu et al. (2025) published in Cell, which reports the first successful retrieval of hominin mitochondrial DNA from dental calculus on the Harbin cranium, dated to over 146,000 years ago. Through targeted enrichment and high-throughput sequencing, the team recovered endogenous mtDNA fragments despite extensive modern contamination, establishing a direct genetic link to Denisovan populations in northeastern China .
Highlights:
The researchers treated the dental calculus with bleach to minimize modern DNA, then extracted and sequenced two libraries, ultimately recovering 6.6-fold coverage of ancient mtDNA amidst contaminating human sequences . By focusing on short, deaminated fragments, they assembled a partial consensus genome covering over 8,000 nucleotide positions aligned to an ancestral Denisovan reference . Phylogenetic analyses using Bayesian, maximum likelihood, and parsimony methods consistently place the Harbin mtDNA within the Denisovan clade, clustering it with older Denisovan individuals (e.g., Denisova 2, 8, 19, 20, 21), thereby extending the known Denisovan geographic range to the Middle Pleistocene of China . This direct association of mtDNA with a nearly complete cranium offers a unique opportunity to correlate Denisovan morphology with genetic identity and suggests that similar morphological traits in other East Asian fossils may mark additional Denisovan specimens .
Conclusion:
The study not only demonstrates dental calculus as a valuable reservoir for ancient hominin DNA but also firmly links a distinctive Middle Pleistocene cranium to Denisovan lineages. By merging genetic and morphological evidence, BayesMRnet opens new avenues for identifying Denisovan fossils and understanding hominin diversity across prehistoric Asia .
Reference:
Fu, Q., Cao, P., Dai, Q., Bennett, E. A., Feng, X., Yang, M. A., Ping, W., Pääbo, S., & Ji, Q. (2025). Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium. Cell, 188(1), 1–8. https://doi.org/10.1016/j.cell.2025.05.040
License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/
