Bencao archaeology of “<italic>Haitongpi</italic>” from imperial pharmacy in Qing Dynasty: Common evidence based on ancient DNA information and chemical characteristics

<p indent="0mm">Bencao archaeology applies modern archaeological theories and methods to explore the intricate relationship between humans and medicinal substances, with a particular focus on unearthed drugs, medicinal sites, and related relics. This field aims to reconstruct the temporal and spatial frameworks of cultural remains and trace the historical evolution of Traditional Chinese Medicine (TCM). From ancient to modern times, the origin of medicinal materials has often undergone changes. A critical task in bencao archaeology is the accurate identification of the origins of medicinal relics. Conducting research on the origins of ancient medicinal materials can promote the inheritance and development of TCM, providing a foundation for ensuring clinical efficacy and safety. <italic>Haitongpi</italic>, first recorded in the <italic>Haiyao Bencao</italic> during the Five Dynasties period, has a long history of medicinal use. It was later recorded in the Qing Dynasty’s <italic>Yizong Jinjian</italic>, where it was featured as a key ingredient in <italic>Haitongpi</italic> Decoction, used to dispel wind-dampness and alleviate pain. However, the precise botanical origin of <italic>Haitongpi</italic> is difficult to determine based solely on historical texts, as the modern medicinal use of this term encompasses plants from four families and six species distributed across different regions. The imperial palace, as the residence of the highest rulers in China’s feudal society and the center of state power, maintained a meticulous standard for the selection and quality of medicines used in the Qing imperial pharmacy. Medicinal relics of <italic>Haitongpi</italic> preserved in the National Palace Museum provide crucial material evidence for exploring its historical usage and origin during the Qing Dynasty. In this study, a multidisciplinary approach combining molecular archaeology, and chemical profiling was employed to identify the origin of <italic>Haitongpi</italic> relics (GU233758) from the Qing imperial pharmacy. Initially, ancient DNA was extracted from the relics, and shotgun metagenomic sequencing was conducted, identifying the sample as belonging to the genus <italic>Zanthoxylum</italic>. Complementary chemical analysis using UPLC-Q-TOF-MS/MS revealed 20 characteristic compounds, including alkaloids, flavonoids, lignans, and coumarins, consistent with the chemical profile of <italic>Zanthoxylum</italic>. To further narrow down the species, a molecular phylogenetic tree was constructed using ITS, ETS, and <italic>trnH-psbA</italic> sequences. The results demonstrated a close genetic relationship between the <italic>Haitongpi</italic> sample and <italic>Zanthoxylum ailanthoides</italic> Sieb. et Zucc. By integrating morphological analysis, molecular techniques, and chemical characterization, this study established a systematic identification model for Qing Dynasty medicinal relics, progressing from family to genus to species. The findings confirmed that <italic>Haitongpi</italic> (GU233758) originated from the bark of <italic>Z</italic>. <italic>ailanthoides</italic>. This research not only provides a robust bencao archaeological foundation for tracing the origins of <italic>Haitongpi</italic> but also contributes to the preservation of Qing medical records and the inheritance of classic formulations. Moreover, it holds potential for improving clinical efficacy and medication safety through a deeper understanding of historical medicinal practices.