Mitochondrial Genomes Reconstructed from Teeth of Prehistoric Native Americans

Using advanced technologies, physicial anthropologists succeeded to enrich human mitochondrial DNA (mtDNA) from dental calculus (calcified plaque on teeth) in amounts that enabled reconstruction of whole mitogenomes for maternal lineage ancestry analysis, providing an alternative to skeletal remains in ancient DNA investigations of prehistoric human ancestry and health.

Christina Warinner and Cecil M. Lewis, Jr., professors at University of Oklahoma (Norman, OK, USA), collaborated with researchers from Arizona State University (USA) and Pennsylvania State University (USA) on the capture, enrichment, and high-throughput sequencing of DNA extracted from 6 individuals at 700-year-old Oneota cemetery (Norris Farms #36), including 3 who had previously tested negative for DNA preservation in bone using conventional PCR.

The results provided high-resolution, whole mitochondrial genome information for the Oneota, a Native American archaeological culture that rose to prominence ca. AD 1000–1650, but declined sharply following European contact.

“We can now obtain meaningful human, pathogen, and dietary DNA from a single sample, which minimizes the amount of ancient material required for analysis,” said Prof. Warinner. In recent years, dental calculus has emerged as an unexpected valuable reservoir of ancient DNA from dietary and microbial sources. This study demonstrates that it is also an important source of human DNA. Very little dental calculus was required for analysis—fewer than 25 milligrams per individual.

Although dental calculus preserves alongside skeletal remains, it is not tooth tissue. Dental calculus, also known as tartar, is a calcified form of dental plaque that acquires human DNA and proteins passively, primarily through the saliva and other host secretions. Once mineralized within dental calculus, human DNA and proteins can preserve for thousands of years.

Conventional techniques for recovering ancient human DNA typically require the destruction of bone or tooth tissue during analysis, and this has been a cause of concern for many Native and indigenous communities. Obtaining DNA from dental calculus does not damage or disturb the integrity of skeletal remains. In addition, because dental calculus is the richest known source of DNA in the archaeological record, it presents unique opportunities for investigating archaeological sites with preservation challenges.

“Dental calculus may enable researchers to retrieve ancient DNA from samples where bone or other biological tissues are too degraded for analysis. This is particularly exciting to those of us who work in tropical or extremely old contexts, where traditional sources of DNA may be poorly preserved or even non-existent,” said Maria Nieves Colón, PhD candidate, ASU.

The study represents an important technological advancement for paleogenomic investigations in prehistoric regions where destructive analysis of skeletal remains is difficult or controversial. “We hope that this research on dental calculus from the Norris Farms site acts as the first step toward future paleogenomic investigations of prehistoric North American remains in a respectful and non-destructive way that interests and benefits both descendent communities and anthropologists,” said Andrew Ozga, OU doctoral graduate, and currently postdoctoral candidate at ASU.

The study, by Ozga AT et al., was published March 16, 2016, in the journal American Journal of Physical Anthropology.

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