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

Calcareous tropical green macroalgae of the genus <i>Halimeda</i> are key reef-builders, yet the drivers of their diversification and population dynamics remain poorly understood. This study analyzed the species diversity of <i>Halimeda</i> in the Xisha (Paracel) Islands based on <i>tuf</i>A gene sequences, focusing on evaluating the genetic diversity, population structure, and historical dynamics of two widespread species-<i>Halimeda discoidea</i> and <i>Halimeda macroloba</i>. The results indicate new records of <i>Halimeda cylindracea</i> and <i>Halimeda</i> cf. <i>stuposa</i> in the Xisha (Paracel) Islands. More importantly, <i>H. discoidea</i> and <i>H. macroloba</i> exhibited significantly different evolutionary histories. Specifically, <i>H. discoidea</i> 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, <i>H. macroloba</i> 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 <i>H. discoidea</i> is older, while <i>H. macroloba</i> represents a lineage with a relatively younger evolutionary origin restricted to the Indo-Pacific region. 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.