Dental Plaque Helps Anthropologists Reconstruct Ancient Human Mitogenome

31-03-2016

During the nascent stages of Prof. Christina Warinner’s career in the field of paleogenomics, she took a risk. Instead of utilising conventional techniques to extract ancient DNA – which often requires destruction of fossil specimens—she took an alternate route and investigated the potential of calcified dental plaque from fossil teeth.

Researchers found trace amounts of human DNA stored in the dental calculus.

“Although dental calculus had been long noted in archaeological reports, it was largely neglected and often discarded,” Warinner, anthropology professor at University of Oklahoma and co-director of the Laboratories of Molecular Anthropology and Microbiome Research, told R&D Magazine.“It was widely believed to be virtually abiotic, containing no DNA or proteins, and until very recently the only real interest in it was in using it to search for chance entrapped plant microfossils, such as pollen, starch granules, and phytoliths.”

She had her doubts, but her curiosity was rewarded and led to, in her own words, “a biomolecular treasure hiding in plain sight.” In addition to microbial DNA, Warinner and colleagues found trace amounts of human DNA stored in the dental calculus. It was enough to stoke the flames of knowledge.

Publishing in The American Journal of Physical Anthropology,Warinner and colleagues recently reported their success reconstructing full human mitochondrial genomes from dental calculus, which yielded results comparable to ancient DNA from dentin and bone extraction.

Using capture enrichment technology, the team, which included collaborators from Arizona State University and Pennsylvania State University, extracted DNA from six individuals from Illinois’ 700-year-old Norris Farms No. 36 cemetery, which was used by the Oneota people.

“When collecting dental calculus, we use the same tools as a dental hygienist and essentially give a very belated tooth cleaning to the ancient individuals in our study,” said Warinner.

Full mitogenomes were compiled for all six individuals, including three who had previously tested negative for DNA preservation in bone samples, according to the researchers.

“Dental calculus contains more DNA than any other known archaeological material,” said Warinner. “Archaeological bone typically contains less than (two ng) of DNA per milligram of tissue. By contrast, dental calculus typically contains more than 40 (ng) of DNA per milligram of tissue, and we’ve even measured samples that contain more than 500 (ng) per milligram of tissue. No other material in the archaeological record contains so much DNA.”

Dental calculus collection from a 1,000-year-old tooth. Courtesy of Christina Warinner

Further, the samples gleaned from dental calculus contain DNA not only from the human, but also the microbiome and the diet. Armed with this new technique, anthropologists and archaeologists have a new avenue to acquire mitochondrial DNA, the sequences of which can help them trace the history of the human species and provide glimpses at population movements.

“I am fascinated by the human condition,” said Warinner. “Being an anthropologist means that I am able to study what it means to be human from multiple angles, drawing on biological and cultural observations from time periods spanning from the present day to tens of thousands of years ago. I can’t imagine a more exciting and rewarding profession.” – Greg Watry