Regional genetic structure of sandfish Holothuria (Metriatyla) scabra populations across the Philippine archipelago

The sandfish, Holothuria (Metriatyla) scabra Jaeger, 1833 is a commercially-valuable tropical sea cucumber species which is overexploited throughout much of its distributional range, the Philippine archipelago included. The need for management interventions to sustain the fishery is recognized. However, the lack of knowledge on the genetic structure of natural populations needs to be addressed to guide management initiatives. The present study examined genetic diversity and spatial patterns of genetic structure of sandfish populations across the Philippine archipelago. Population genetic analysis using 11 microsatellite markers revealed weak yet significant regional genetic structure among 15 H. scabra populations across the Philippine archipelago (FST = 0.016; P <  0.0001). Six genetic groups broadly concordant with marine biogeographic regions were identified. Genetic connectivity was strongest among populations situated in the center of the archipelago (internal seas; FST = 0.002, P >  0.05). Peripheral locations exhibited limited gene flow (Philippine Sea, South China Sea, Sulu Sea and Celebes Sea; mean FST = 0.023, P <  0.0001), with significant genetic relatedness further suggesting relative isolation or high levels of self-recruitment. Excluding the two most divergent Sulu Sea populations, there was a significant signal of isolation-by-distance for the rest of the Philippine populations, suggesting that geographic distance between coastal habitats coupled with oceanographic circulation largely influence genetic structure. There was no signature of genetic bottlenecks for any population, although effective population sizes (Ne) were larger for central populations compared to peripheral populations. This study provides information on genetic stocks which has important implications to genetic resource management of Philippine sandfish populations to support sustainability of the fishery.