Plaque and People: Reconstructing Diet, Microbiome, and Host Genetics from Ancient Dental Calculus

Dental calculus is an underutilized resource preserving host DNA, bacterial DNA from the oral microbiome, and microscopic food particles. Building on advances in SNP capture and extraction techniques for degraded samples, this project would develop a specialized pipeline for calculus analysis. It would track how the introduction of farming, evident in plant DNA trapped in calculus, correlated with shifts in microbial communities and selection on human immunity and metabolism genes. Questions include whether a high-carbohydrate diet selected for different oral bacteria and whether those bacteria created new selective pressures on human immunity genes. This approach investigates human evolution as part of a complex, evolving ecosystem and provides direct evidence of dietary change from the same individuals whose genomes are studied.

References:

1. Tracing the Evolution of Human Immunity Through Ancient DNA.. E. Patin, L. Quintana-Murci (2024). Annual Review of Immunology.
2. Ancient DNA: a direct window into the human past. João C. Teixeira (2024). Antropologia Portuguesa.
3. Eight thousand years of natural selection in Europe. I. Mathieson, Iosif Lazaridis, N. Rohland, Swapan Mallick, B. Llamas, Joseph K. Pickrell, H. Meller, M. Guerra, Johannes Krause, David, Anthony, Dorcas Brown, Carles Lalueza Fox, Alan Cooper, K. Alt, W. Haak, N. Patterson, David Reich (2015).
4. Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?. Evan K. Irving-Pease, R. Muktupavela, M. Dannemann, F. Racimo (2021). Frontiers in Genetics.
5. An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples. Daniel R. Cuesta-Aguirre, A. Malgosa, Cristina Santos (2024). PLoS ONE.