ABSTRACT Halodule uninervis plays a critical role in the seagrass ecosystem because its opportunistic traits facilitate expansion and persistence under changing environmental conditions. Yet the population genetic structure and connectivity of this species in the Philippines remain poorly understood. Using genome‐wide single‐nucleotide polymorphisms (6952 SNPs) generated from MIG‐seq data, we assessed clonal reproduction, genetic diversity, population structure, isolation by distance, and recent migration across 10 populations in the Bohol Sea and adjacent waters. Clone detection revealed pronounced spatial variation ranging from predominantly sexual populations with high genotypic richness to populations with strongly clonal populations dominated by relatively few multilocus genotypes. Genetic diversity was generally low to moderate across populations. A geographically separated population from the Visayan Sea exhibited comparatively higher nucleotide diversity and distinct ancestry patterns relative to most Bohol Sea populations. Population structure analyzes showed weak but detectable genetic structuring, with the first two principal components explaining 6.3% and 5.1% of the total variance. ADMIXTURE analyzes showed partially shared ancestry profiles among several populations. Genetic differentiation was low to moderate, with no significant association between geographic distances. These results suggest that geographic distance alone may not fully explain connectivity patterns within the study area. Recent migration analyzes revealed generally high self‐recruitment together with asymmetric migration estimates among several populations, including comparatively higher incoming migration into Mambajao. These overall findings suggest a partially connected population dynamics influenced by clonal reproduction, localized recruitment, and regional dispersal processes. This study provides baseline genetic information that may support future conservation, monitoring, and restoration planning for tropical seagrass ecosystems in the Philippines.
SINGSON et al. (Fri,) studied this question.