Dormancy Season Is Key to Submergence Tolerance of Annual Plant Seeds in the Drawdown Zone of the Three Gorges Reservoir

Large reservoir construction generates vast drawdown zones characterized by novel hydrological regimes that impose unprecedented selective pressures. While annual plants serve as pioneer colonists during secondary succession in these ecosystems, the mechanisms allowing their seeds to persist through prolonged anti-seasonal flooding remain poorly understood. We investigated how seed germination responses to extreme submergence are influenced by dormancy traits and phylogenetic history. We conducted a field experiment on 44 common annual plant species in the Three Gorges Reservoir drawdown zone. Seeds were subjected to maximum submergence depths of 0 m (control), 5 m, 10 m, 15 m, and 20 m, along the reservoir’s hydrological gradient. Post-submergence germination percentages were measured and analyzed using linear and Bayesian phylogenetic mixed-effects models, with seed dormancy status, seed type, season, and species’ phylogenetic relationships as explanatory variables. Submergence significantly reduced overall seed germination (p < 0.001), but more than 75% of species retained germination capacity even after 20 m of submergence. Germination percentage distributions shifted from near-normal to bimodal with increasing depth. Although the regression of squared PIC values against phylogenetic branch lengths showed a significant relationship, phylogenetic signal for germination percentages was weak and non-significant across all depths (Pagel’s λ < 0.101, Blomberg’s K < 0.228, p > 0.05). Bayesian models revealed that dormancy season significantly interacted with submergence depth (Estimate = −1.41, 95% CrI [−2.16, −0.67]). Seeds dormant during autumn-winter maintained stable germination percentages across depths, while germination of spring-summer dormant seeds declined significantly with increasing depth. Our findings demonstrate that annual plant seeds possess widespread, species-specific tolerance to extreme submergence. This tolerance is primarily driven by environmental filtering rather than phylogenetic history. The seasonality of dormancy is a crucial adaptive mechanism, enabling seeds, particularly those dormant in autumn-winter, to withstand the harsh conditions of the Three Gorges Reservoir drawdown zone. This study provides a functional trait-based framework for selecting suitable species for the ecological restoration of reservoir drawdown zones globally.