Emerging Challenges in Molecular Paleontology: Misapplication of Environmental DNA Fragments and Misconception of Deamination as a Key Criterion for In Situ DNA Identification

This article critically examines the methodologies applied in ancient DNA (aDNA) research, particularly those developed by Dr. P\"a\"abo's team, which have significantly influenced the field. The focus is on the challenges of distinguishing original in situ DNA (oriDNA) from environmental DNA (eDNA) contamination in fossil samples. Recent analyses indicate that even with rigorous extraction and sequencing protocols, a considerable amount of eDNA remains present, often misinterpreted as oriDNA. This misidentification risks the accuracy of species ascription and evolutionary interpretations derived from fossil analyses. The paper explores fossil preservation's physical and chemical dynamics, which allow eDNA from similar and disparate species to infiltrate bone matrices. We propose enhancements to methodological frameworks, such as broader BLAST database usage and stringent E-value criteria, to improve species-specific aDNA identification. Additionally, the article critiques the reliance on deamination patterns as a definitive marker for aDNA, suggesting a reevaluation of this criterion due to its inconsistency and the potential for misleading sequencing results. Ultimately, our findings advocate for a more cautious and refined approach to aDNA research, ensuring more reliable and verifiable scientific outcomes