Pathogens, microbiomes and sedimentary DNA as windows into past lives and environments.
Human remains and archaeological sediments preserve DNA not only from people, but also from the microbes that lived with them and the environments they inhabited. Ancient pathogen genomes can reveal how diseases spread and evolved, while sedimentary ancient DNA (sedaDNA) can recover traces of past ecosystems even where no skeletal remains survive. I am interested in bringing these approaches to Anatolian archaeology, where they remain almost unexplored.
Projects
Leprosy in Anatolia: A Palaeopathological and Archaeogenomic Study Advisor · TÜBİTAK 1001 · 2023–2026 Combines palaeopathology with ancient DNA to study leprosy in Anatolia. As part of this work, Arda Sevkar’s MSc thesis (2023), which I co-supervised, analysed Mycobacterium leprae in leprosy-affected individuals from Medieval to Late Ottoman Anatolia.
Collaborations
I contributed to aMeta, an accurate and memory-efficient workflow for profiling microbial DNA in ancient samples that reduces false discoveries in ancient metagenomic analyses (Pochon et al., 2023). I also co-authored a perspective on integrating sedaDNA into archaeological research, outlining its potential for studying the origins, lifestyles and environments of past populations and the challenges that remain (Özdoğan et al., 2024).
References
2024
Archaeology Meets Environmental Genomics: Implementing sedaDNA in the Study of the Human Past
Kadir Toykan Özdoğan, Pere Gelabert, Neeke Hammers, and 3 more authors
Archaeological and Anthropological Sciences, Jun 2024
Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.
@article{Ozdogan2024-wm,title={Archaeology Meets Environmental Genomics: Implementing {sedaDNA} in the Study of the Human Past},author={Özdoğan, Kadir Toykan and Gelabert, Pere and Hammers, Neeke and Altınışık, N. Ezgi and de Groot, Arjen and Plets, Gertjan},journal={Archaeological and Anthropological Sciences},publisher={Springer Nature},volume={16},number={7},pages={108},month=jun,year={2024},doi={10.1007/s12520-024-01999-2},}
2023
aMeta: An Accurate and Memory-Efficient Ancient Metagenomic Profiling Workflow
Zoé Pochon, Nora Bergfeldt, Emrah Kırdök, and 10 more authors
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
@article{Pochon2023-ak,title={{aMeta}: An Accurate and Memory-Efficient Ancient Metagenomic Profiling Workflow},author={Pochon, Zoé and Bergfeldt, Nora and Kırdök, Emrah and Vicente, Mário and Naidoo, Thijessen and van der Valk, Tom and Altınışık, N. Ezgi and Krzewińska, Maja and Dalén, Love and Götherström, Anders and Mirabello, Claudio and Unneberg, Per and Oskolkov, Nikolay},journal={Genome Biology},publisher={Springer Nature},volume={24},number={1},pages={242},month=oct,year={2023},doi={10.1186/s13059-023-03083-9},}