New Publication: Lessons Learned - Recommendations for Reproducible Paleogenomic Data Analyses

We’re excited to share our latest perspective piece published in The American Journal of Human Genetics, offering comprehensive recommendations for ensuring reproducibility in paleogenomics research. This mansucript reflects mine and the experience of my colleagues at ACAD (Australian Centre for Ancient DNA) working in the field. The proposed ideas are aimed to address critical gaps in reporting standards for ancient DNA research.

Paleogenomics has become hugely influential in understanding population history, yet its reliance on destructive sampling of finite and unique skeletal remains makes transparent reporting absolutely crucial. From our collective experience extensively interacting with other researchers in the field, we identified critical information required for reproducible research across key analytical areas.

Key Recommendations

Our perspective provides practical guidance for the paleogenomics community, including:

  • Standardized Data Formats: Use of consistent file formats and metadata standards compatible with FAIR (Findable, Accessible, Interoperable, and Reusable) and CARE (Collective benefit, Authority to control, Responsibility, and Ethics) frameworks
  • Comprehensive Reporting Checklists: Detailed documentation of sample preparation and analytical workflows to ensure transparent and robust conclusions
  • Parameter Documentation: Clear reporting of analytical choices that can meaningfully impact results, from sample usage decisions to data processing parameters
  • Ethical Considerations: Integration of ethical research practices throughout the analytical pipeline

Why This Matters

Given the destructive nature of ancient DNA sampling and the finite availability of archaeological specimens, minimum reporting standards are essential to:

  • Inform the peer review process
  • Improve transparency and reproducibility
  • Increase the usability of research findings
  • Maximize the value gained from unique samples
  • Ensure confidence in paleogenomics research outcomes

This work represents a collective effort to strengthen the field of paleogenomics through better practices and clearer communication of methods and results.

📄 Read the Full Paper

Journal: The American Journal of Human Genetics
Published: November 5, 2025
DOI: 10.1016/j.ajhg.2025.10.011