Foraminiferal environmental DNA reveals late Holocene sea-level changes

Reconstructing past relative sea level (RSL) provides critical insight into the mechanisms driving RSL change and informs future projections. Foraminifera are widely used sea-level indicators, but their application is often limited by poor preservation. Here, we demonstrate that foraminiferal environmental DNA (eDNA) and sedimentary ancient DNA (sedaDNA) provide a complementary approach to traditional morphological methods for RSL reconstruction. By analyzing surface sediments and a core from subtropical intertidal environments in the Pearl River Delta, we found that foraminiferal eDNA and sedaDNA assemblages exhibit clear vertical zonation, consistent with morphological results. An eDNA-based transfer function enabled high-resolution RSL reconstructions with decadal temporal and decimeter vertical precision from two periods: 290–1703 CE and 1956–present. Notably, eDNA preservation extended RSL reconstruction far earlier than morphological analyses (1956 CE). The eDNA reconstruction closely matched tide-gauge and geological RSL records, underscoring its potential as a robust tool for reconstructing past RSL and its driving mechanisms.