Preservation Constraints on aDNA Information Generation and the HSF Posterior Sourcing Framework: A First-Principles Critique of Conventional Methods
Fossil DNA preservation varies with depositional environments and diagenesis, producing fragments of heterogeneous origins and degradation states. We use first-principles biomolecular analysis to classify fossil molecular environments into four system types, distinguished by three orthogonal indicators: origin (H/h: host/heterologous), deamination status (D/d), and similarity ratio (S/s). Conventional aDNA pipelines assume a binary mix of endogenous host DNA and modern contaminants, overlooking multisource complexity from multiple species and time-averaged deposits. This leads to bias: authentic signals suppressed during enrichment, alignment, or damage filtering, and exogenous/ancient admixed fragments misassigned as endogenous, particularly in open systems. We introduce the HSF (Host/Species-specific Fragment) posterior traceability framework to address this. It treats fragments as primary units, maximizes source diversity, detects isolated sequences, defers lineage assignment to preserve uncertainty, and applies phylogenetic consistency to discriminate origins. Combined with preservation characterization (e.g., 3D imaging and volumetric openness assessment), it improves authenticity evaluation and reduces misassignment in mixed-signal samples. Case studies identify novel fossil DNA patterns (CRSRR and SRRA) and demonstrate superior performance compared with conventional methods. The HSF framework enhances aDNA reliability, extends molecular archaeology to challenging contexts, and aids genome evolution and lineage reconstruction.