Foraminiferal environmental DNA reveals late Holocene sea-level changes

Reconstructing past relative sea level provides critical insight into mechanisms driving sea-level change and informs future projections. Foraminifera are widely used sea-level proxies, but their application is often limited by poor preservation. Here, we demonstrate that foraminiferal environmental DNA and sedimentary ancient DNA provide a complementary approach to traditional morphological methods for relative sea-level reconstruction. By analyzing surface sediments and a core from subtropical intertidal environments in the Pearl River Delta, we found a clear vertical zonation in the environmental DNA assemblage consistent with morphological results. An environmental DNA-based transfer function enabled reconstruction with decadal temporal and decimeter vertical resolution for two periods: 290–1703 CE and 1956–present. Notably, sedimentary DNA preservation extended the reconstruction beyond morphological methods, which was limited by taphonomic processes. The environmental DNA reconstruction closely matched tide-gauge and geological records, underscoring its potential as a robust tool for reconstructing past relative sea level and its driving mechanisms. © The Author(s) 2025.