Ancient DNA Reveals Hominoid Evolution: Intermediate DNA Sequences and Advances in Molecular Paleontology

The study proposes that fossils and ancient pottery can act as physical DNA containers, preserving original in situ DNA (oriDNA) while accumulating environmental DNA (eDNA). Using nano‑affinity bead technology, the authors extracted and sequenced DNA from Lycoptera fossils in the Jehol region and from a round‑bellied jar from the Erlitou period in Guangwu Town, recovering hundreds of thousands of primate-assigned reads. They report that an AFF metric for DNA fragments negatively correlates with host species divergence time, suggesting a quantitative measure of preservation and divergence. They identify ‘intermediate DNA sequences’ (IDS)—fragments that differ from modern genomes—many of which appear to retain features of the last common ancestor of Hominidae. A subtype termed SRRA (Sequence Reversal and Rearrangement), observed in exonic regions, is hypothesized to arise from upstream incorporation of complementary antisense strands, potentially creating hairpins and indels in UTRs or coding regions and acting as a post‑transcriptional regulatory mechanism. The authors propose SRRA events as a ‘genetic switch’ that aided early hominid evolution, with some SRRA segments later excised. They also describe seven non‑human primate species‑specific fragments potentially linked to Asian Homo erectus, and pottery DNA indicating tropical taxa (e.g., zebras, oil palms), which they interpret as evidence for climate‑driven local extinctions and for paleo‑ecological reconstruction. The work argues that non‑skeletal materials can extend molecular paleontology, notes an ‘old‑few, new‑many’ turnover pattern in preserved fragments with frequent non‑deamination, and calls for re‑evaluation of accepted aDNA authenticity criteria and methods.