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The increasing global demand for dried sea cucumber products (beche-de-mer) coupled with lack of policy regulations to regulate
harvesting from natural populations has resulted in decreased capture production across the Philippines. Stichopus cf. horrens
locally known as â??hanginanâ?? is one of the commercially-exploited sea cucumber species needing management intervention which
would benefit from the availability of genetic data for delineation of management stocks. Phylogenetic analysis of mitochondrial
DNA cytochrome oxidase I (CoI) sequences from S. cf. horrens identified two mitochondrial lineages (Clade A and Clade B). Clade A
individuals which are more abundant and geographically widespread, were studied to examine demographic history and population
genetic structure across the Philippine archipelago. We used partial CO1 gene sequences and multilocus microsatellite data to
investigate historical and contemporary regional scale population structure and gene flow patterns across the archipelago. Analysis
of mitochondrial data and microsatellite loci demonstrated significant genetic structure among Clade A individuals (ФST = 0.37109,
P=0.00; FST=0.0788, P=0.00) and identified seven distinct populations (K=7) which is consistent with the basin isolation hypothesis
and pre-identified marine biogeographic regions in the country. Genetic markers also suggest a retained historical structure due to
stable demography during the Pleistocene epoch. Despite the high dispersal potential for S. cf. horrens, due to long planktonic phase
(27-30 days), the presence of unique oceanographic and ecological barriers in the country restricts connectivity in the country.
Stock delineation is crucial for the identification of putative management units and conservation of S. cf. horrens. This may aid in the
formulation of policies for science-based management of fishery resources in the country.