Impacts of the Three Gorges Dam on gene flow among <i>Phragmites australis</i> populations

Abstract River damming alters hydrochorous conditions and induces habitat fragmentation, thereby impacting ecological processes in aquatic plants. However, the genetic connectivity and consequences of plant populations under such disturbances remain poorly characterized. In this study, we investigated the Three Gorges Dam’s (TGD) impacts through genetic analyses of 379 Phragmites australis individuals from 11 riparian populations along the Yangtze River, China, using microsatellite markers. Among three sections (upstream, midstream, and downstream), downstream populations exhibited the highest genetic diversity (He = 0.534). STRUCTURE analyses revealed two distinct genetic clusters corresponding to upstream and mid-downstream populations, with considerable genetic differentiation emerging between them. Although historically downward gene flow across the basin was significant (from upstream to midstream: m = 0.0030, 95% CI: 0.0018–0.0039; from upstream to downstream: m = 0.0036, 95% CI: 0.0023–0.0047), contemporary gene flow yielded mostly non-significant estimates, except for a pronounced dispersal signal from midstream to downstream groups (M = 0.0876, 95% CI: 0.0592–0.1160). This shift highlights TGD-mediated distinct consequences of recent genetic connectivity. Notably, downstream populations maintained substantial genetic diversity, likely sustained through persistent genetic connectivity with adjacent populations despite hydrological modifications. These findings elucidate the distinct impacts of large-scale dams on riparian plant genetics, propose prioritized conservation strategies for vulnerable upstream populations, and provide empirically grounded insights for biodiversity management in dam-regulated riverine landscapes.