Towards predicting the geographical origin of ancient samples with metagenomic data

Area of Science:

• Ancient genomics
• Bioinformatics
• Archaeological science

Background:

• Determining an individual's place of death is crucial for ancient DNA (aDNA) studies but challenging with museum samples.
• Human DNA and isotope analyses offer ancestry and living location clues but not the place of death.
• Exogenous microbial DNA, typically discarded in aDNA studies, colonizes remains post-mortem.

Purpose of the Study:

• To investigate if microbial DNA metagenomes from ancient remains can identify the place of death.
• To develop a method for using shotgun sequencing data to determine geographic origin and detect sample mislabeling.
• To leverage soil-dwelling microbial communities for tracing ancient sample provenance.

Main Methods:

• Hypothesized that geographically proximate samples share similar microbial metagenomes.
• Employed a k-mer-based approach to calculate metagenomic similarity scores.
• Utilized dimensionality reduction and logistic regression for geographical origin assignment.

Main Results:

• Individual samples from closer geographic locations exhibited higher metagenomic similarities.
• The method achieved accurate geographical predictions for test samples.
• The bacterial genus *Streptomyces* was identified as a reliable biomarker for geographic origin.

Conclusions:

• Metagenomic data from ancient remains can effectively determine the place of death.
• This approach provides a novel tool for resolving sample mislabeling in museum collections.
• *Streptomyces* serves as a valuable indicator for tracing the geographic provenance of ancient samples.