Semi-connected structure and asymmetric gene flow of Nypa fruticans Wurmb. across the Philippine archipelago

The Philippine archipelago is one of the most geographically complex coastal systems in the Indo–West Pacific, comprising numerous islands and semi-enclosed seas linked by narrow straits that together create a highly diverse setting for nearshore exchange. This complex geography contributes to the Philippines’ status as one of the world’s major biodiversity hotspots. Nypa fruticans is an ecologically important estuarine mangrove palm in the Philippines that contributes to shoreline stability and supports coastal livelihoods. Its dispersal relies primarily on large, buoyant fruits released directly into coastal waters. Therefore, the genetic diversity and connectivity of populations across different islands of the archipelago remain important questions. We collected 118 individuals from seven coastal regions across Mindanao, Bohol, Luzon, and Palawan to investigate genetic diversity and connectivity across the Philippine archipelago. The populations showed moderate expected heterozygosity ( He = 0.584–0.719) and consistently lower mean observed heterozygosity ( Ho = 0.376) than mean expected heterozygosity ( He = 0.666), resulting in a pervasive heterozygote deficit ( F = 0.431) and deviations from Hardy–Weinberg equilibrium. This pattern indicated less realised genetic mixing than expected under random mating. Most genetic variance was partitioned among individuals within populations (43%) and within individuals (48%). The results further supported two major genetic clusters ( K = 2), indicating broad admixture among populations. Directional gene-flow analysis suggested that Palawan acted as a major recipient, whereas western Luzon occupied a key position in the inferred connectivity network. Overall, N. fruticans in the Philippines forms a semi-connected metapopulation with modest regional structure and uneven connectivity, suggesting that conserving dispersal pathways and key connectivity nodes, particularly Palawan-linked routes, should be a management priority.