Abstract
High-quality ancient DNA (aDNA) is crucial for advancements in molecular paleontology. However, current research is often limited to fossil samples less than 1 million years old (Ma) due to DNA degradation and contamination by environmental DNA (eDNA). To overcome these limitations, we used nanoparticle affinity beads to successfully extract DNA from Lycoptera davidi fossils dating back to the Early Cretaceous period, approximately 120 Ma. Utilizing high-throughput sequencing technology, we obtained 1,258,901 DNA sequences. To ensure the accuracy and authenticity of these sequences, we established the rigorous “mega screen method.” This approach allowed us to identify 243 original in situ DNA (oriDNA) fragments likely belonging to the Lycoptera genome. These fragments have an average length of over 100 base pairs and show no signs of “deamination”. Additionally, we discovered 10 transposase coding sequences, which provide insights into a unique self-renewal mechanism within the Lycoptera genome. The update of protein-coding sequences was responsible for the significant divergence of ray-finned fishes in the Cretaceous. Surprisingly, we identified numerous hominid aDNA fragments from the fossil extracts. These fragments, probably from the environmental source during later epochs, had been deposited in the voids that formed after the fossil rocks developed. Notably, these fragments also exhibited no signs of “deamination”. This study provides invaluable data to further our understanding of fish evolution. Also, the non-remain DNA evidence offers crucial clues for anthropologists in their quest for undocumented human-like skeletons in various locations. It also shows the potential for transforming the field of molecular paleontology via studying aDNA in exceptional old rocks.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Numerous hominid aDNA fragments were identified from Lycoptera fossil extracts. These fragments may have been introduced from later environmental sources, deposited in voids that formed after the fossil rock had developed. Remarkably, these fragments exhibited no signs of deamination, challenging Paabo's team's ancient, in situ DNA identification criteria. This finding also provides an important clue for anthropologists to search for undocumented human-like skeletons in various locations and opens up a new field of paleontological research.
