Contrasting Evolutionary Trajectories: Differential Population Dynamics and Gene Flow Patterns in Sympatric Halimeda discoidea and Halimeda macroloba

Calcareous tropical green macroalgae of the genus Halimeda are key reef-builders, yet the drivers of their diversification and population dynamics remain poorly understood. This study analyzed the species diversity of Halimeda in the Xisha Islands based on tuf A gene sequences, focusing on evaluating the genetic diversity, population structure, and historical dynamics of two widespread species— Halimeda discoidea and Halimeda macroloba . The results indicate new records of Halimeda cylindracea and Halimeda cf. stuposa in the Xisha Islands. More importantly, H. discoidea and H. macroloba exhibited significantly different evolutionary histories. Specifically, H. discoidea showed a highly fragmented population structure, restricted gene flow, and a multimodal mismatch distribution, suggesting a complex historical process or long-term stability. In contrast, H. macroloba exhibited lower population differentiation, extensive gene flow, and non-significant neutrality test results, indicating long-term demographic stability without recent, drastic population events. Further validation based on gene flow analysis and divergence time estimation revealed that the lineage divergence of H. discoidea is older, while the dispersal events of H. macroloba are relatively more recent. This striking dichotomy clearly illustrates the interplay between intrinsic species-specific traits (e.g., dispersal capacity) and extrinsic historical factors (e.g., paleo-oceanographic events), leading to contrasting evolutionary outcomes among widespread marine taxa. By elucidating how differing evolutionary histories influence patterns of genetic diversity, this study provides a predictive framework for evaluating the resilience and guiding conservation priorities for critical marine calcifiers in the context of rapid environmental change.