Sedimentary Ancient DNA from Subtropical Cave Sites in Japan

SAWAFUJI Rikai

Sedimentary ancient DNA (sedaDNA) analysis has been widely applied to cave sites in cold and temperate regions such as Europe and Siberia, providing insights into past ecosystems and human presence. However, its application in subtropical environments remains limited due to the challenges of preserving DNA under warm, humid conditions. In this study, I present sedaDNA analyses from three cave sites in Japan: Sakitari Cave on Okinawa Island and two cave sites (Komori-Iyo and Shimotabaru) on Tokunoshima Island. Sediment samples were collected from multiple layers, including layers dating from the Late Pleistocene to the Holocene (the oldest at around 30 ka). DNA was extracted, shotgun sequenced, and aligned to reference databases including bacteria, fungi, viruses, animals, and plants. Across all sites, the most abundant taxa are bacteria, along with some plant and animal taxa. Plant DNA, including Celtis, Crateva, and Ficus, showed DNA damage and fragmentation, and some of these findings were consistent with macrofossil evidence. It is also revealed that there is a difference in taxon abundance between layers, possibly due to human activities.  These results demonstrate that sedaDNA can be successfully recovered from subtropical cave environments despite challenging preservation conditions. This study highlights the potential of sedaDNA to reconstruct past environments and human–environment interactions in warm and humid regions.