What is that how can a tooth survive the years and bear any intelligible mark of the molecules on its side when bone and other soft tissue have long since decayed?
In the case of ancient-DNA, teeth have ceased to be enduring anatomy. They are compartmentalized archives: enamel protects the internal tissues; dentin provides a mineral scaffold on which biomolecules have the potential to adsorb; and, externally, mineralized plaque which is dental calculus, may entrap a snapshot of the microbes and residual traces of the host. With these niches, an individual tooth is made into a stratified sample, in which one can raise various questions to different materials without having to depend on a single “best” substrate.
Why calculus is important is one thing; it is a calcified biofilm. During a systematic comparison between two paired samples, the total DNA yield of calculus was large in comparison with the dental dentin, the yield of calculus 4.9-214.4 ng/mg being 10 to 100 times less than that of dentin, 0.2-35.7 ng/mg, in immediate post-extraction fluorometric measurements. It is not necessarily a lot of abundance but context calculus mineralizes quickly and interacts with the DNA to form a dense crystalline structure that prevents penetration to deeper layers. This physical organization can be used to understand why calculus can maintain an internally consistent oral message when other tissues have been colonized by the environment following burial.
Such a contrast is evident in microbial profiles. Calculus groups are often tight-knit human oral groups and dentin sterile in life often represents post-mortem environmental microbes. This study also reported that calculus samples contained high human-microbiome contributions (median 98% of microbial DNA), and the median of dentin was 3.7%. That is, calculus is an enclosed community sample; dentin is an exposed surface on porous surface and is subject to whatever a grave offers.
Host DNA is a different story. Human reads may be in much greater proportions in dentin, but the variation is vast between teeth. The percentage of human DNA is always small in calculus, but still can be detected many times; and where retention of dentin fails, the entire richness of the calculus DNA can be made up. This same paired analysis also found that human DNA fragments in calculus are generally shorter than those obtained in dentin, indicative of a more severe pathway of entry into the matrix probably in shedding cells, oral fluids, and immune response instead of intact tissue.
The choice of methods now determines what can be allowed by the museums and field teams. Teeth are often context-rich and unique specimens of teeth and the standard extraction process will often necessitate grinding. In a comparison 2025 of methods, a workflow to non-destructively isolate DNA in human teeth was described, which targets internal spaces, with the least external damage, designed specifically with irreplaceable material. The practical implication is that sampling may be bargained in other ways: the tooth may be left mostly intact so that it still provides DNA that can be used in later tests, and only in instances where it is scientifically warranted may destructive sampling be used.
Other than DNA, another means of getting around the chemical limits of DNA is through teeth. Another breakthrough involved a landmark study that employed mass spectrometry to sequence ancient proteins in dental enamel and position dental enamel of Homo antecessor in the larger family tree of hominin, to a depth of time not accessible to DNA. This is important to human-origins discussions since proteins have a longer persistence than DNA and may even be able to retain phylogenetically informative differences.
Calculus has also turned out to be unexpectedly tough in warm, humid environments, where human DNA degradation is notoriously unreliable. Another metagenomic paper of 102 participants of the Pacific and Island Southeast Asia found that the majority of samples still harbored an indigenous oral microbiome, though skeletal human DNA was much less predictive. It showed also that microbial phylogenies of particular taxa might be geographical as well as supplementary to human-genome studies when population separations are weak and periods are brief.
What comes out is not that fossil teeth include one “best” molecule, but that teeth subdivide information. Microbial ecosystems and small, damaged remnants of host DNA are preferentially preserved in calculus; when preservation works with them, the ratio of host to dentin may be larger; when DNA is lost, enamel proteins may lengthen the molecular horizon. Collectively, these tooth-based vaults are increasing how the human background can be examined with the same specimen to triple-lineage, way of life, and setting.
