Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science

Ancient DNA (aDNA) research has revolutionised archaeology and forensic science by enabling genomic recovery from highly degraded remains. This review explores the biochemical and environmental factors influencing aDNA preservation, alongside methodological advances that have improved data yield and authenticity. Techniques such as next-generation sequencing (NGS), single-stranded library preparation, and hybridisation capture have transformed the field, allowing recovery from ultrashort fragments and challenging contexts such as warm climates. Authentication strategies-including cytosine deamination profiling, fragment length analysis, and rigorous contamination controls-remain essential to ensure reliability. Applications of aDNA extend beyond ancestry reconstruction and population genetics to include forensic identification, kinship analysis, and pathogen detection. Lessons from forensic genetics, such as stringent validation and contamination mitigation, have informed best practices in archaeological contexts. However, ethical considerations are central to both domains. Issues of Indigenous data sovereignty, consent, repatriation, and culturally sensitive interpretation demand transparent, community-led research frameworks. These principles align with international agreements such as the Nagoya Protocol and emerging guidelines for equitable benefit-sharing. Despite significant progress, challenges persist, including geographic sampling bias, interpretive uncertainty, and the need for interdisciplinary integration. Future directions emphasise long-read sequencing, metagenomic approaches, and artificial intelligence-driven analytics, alongside robust ethical governance. By combining technological innovation with culturally responsible practices, aDNA research continues to advance our understanding of human history while reinforcing the importance of ethical stewardship in forensic and archaeological science.