Towards predicting the geographical origin of ancient samples with metagenomic data

作者：Davide Bozzi, Samuel Neuenschwander, Diana Ivette Cruz Dávalos, Bárbara Sousa da Mota, Hannes Schroeder, J. Víctor Moreno-Mayar, Morten E. Allentoft, Anna‐Sapfo Malaspinas · 发表于：Scientific Reports · 年份：2024 · DOI：10.1038/s41598-023-40246-x · 被引用次数：7 · 研究领域：Forensic and Genetic Research、Archaeology and ancient environmental studies、Forensic Anthropology and Bioarchaeology Studies

Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samp...