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National Committee on Marine Sciences (NCMS)

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AGROVOC Keyword: search.filters.agrovoc.population geneticsScientific name: search.filters.scientificname.Holothuria scabra

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    Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management
    Lal, Monal M.; Macahig, Deo A. S.; Juinio-Meñez, Marie A.; Altamirano, Jon P.; Noran-Baylon, Roselyn; de la Torre-de la Cruz, Margarita; Villamor, Janine L.; Gacura, Jonh Rey L.; Uy, Wilfredo H.; Mira-Honghong, Hanzel; Southgate, Paul C.; Ravago-Gotanco, Rachel (Frontiers Media SA, 2024-06-04)
    The sandfish Holothuria (Metriatyla) scabra, is a high-value tropical sea cucumber harvested from wild stocks for over four centuries in multi-species fisheries across its Indo-Pacific distribution, for the global bêche-de-mer (BDM) trade. Within Southeast Asia, the Philippines is an important centre of the BDM trade, however overharvesting and largely open fishery management have resulted in declining catch volumes. Sandfish mariculture has been developed to supplement BDM supply and assist restocking efforts; however, it is heavily reliant on wild populations for broodstock supply. Consequently, to inform fishery, mariculture, germplasm and translocation management policies for both wild and captive resources, a high-resolution genomic audit of 16 wild sandfish populations was conducted, employing a proven genotyping-by-sequencing approach for this species (DArTseq). Genomic data (8,266 selectively-neutral and 117 putatively-adaptive SNPs) were used to assess fine-scale genetic structure, diversity, relatedness, population connectivity and local adaptation at both broad (biogeographic region) and local (within-biogeographic region) scales. An independent hydrodynamic particle dispersal model was also used to assess population connectivity. The overall pattern of population differentiation at the country level for H. scabra in the Philippines is complex, with nine genetic stocks and respective management units delineated across 5 biogeographic regions: (1) Celebes Sea, (2) North and (3) South Philippine Seas, (4) South China and Internal Seas and (5) Sulu Sea. Genetic connectivity is highest within proximate marine biogeographic regions (mean Fst=0.016), with greater separation evident between geographically distant sites (Fst range=0.041–0.045). Signatures of local adaptation were detected among six biogeographic regions, with genetic bottlenecks at 5 sites, particularly within historically heavily-exploited locations in the western and central Philippines. Genetic structure is influenced by geographic distance, larval dispersal capacity, species-specific larval development and settlement attributes, variable ocean current-mediated gene flow, source and sink location geography and habitat heterogeneity across the archipelago. Data reported here will inform accurate and sustainable fishery regulation, conservation of genetic diversity, direct broodstock sourcing for mariculture and guide restocking interventions across the Philippines.
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    Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra
    Ordoñez, June F.; Ravago-Gotanco, Rachel (Elsevier, 2024-01-30)
    The sandfish, Holothuria scabra is a commercially important fishery and aquaculture species contributing to the high-value sea cucumber industry. Overexploited across many areas throughout its distributional range, natural populations are considered in decline. Accurate genetic assignment to population of origin is becoming increasingly important for genetics-based marine fisheries management and monitoring, especially for species experiencing depletion of natural stocks and decline in fisheries productivity due to overfishing and illegal, unreported, and unregulated (IUU) fishing. Initiatives for genetics-based applications on economically important seafood such as H. scabra have been limited by the lack of comprehensive genome or transcriptome resources. The present study developed and evaluated the use of gene-associated single nucleotide polymorphism (SNP) markers to assign sandfish to three locations in the Philippines, in the proximity of existing and emerging hatchery production centers. In silico SNP discovery pipeline using pooled RNA-Seq libraries and medium-throughput genotyping approach generated a dataset comprising 115 individuals genotyped at 88 SNPs. Population assignment using machine-learning analysis and Bayesian approach revealed that the 88 transcriptome-derived SNPs allowed the assignment of sandfish individuals to population of origin, with an overall assignment accuracy of >80%. The novel SNPs developed could find their utility in facilitating the development of geographic traceability tools applicable in the context of sandfish aquaculture, fisheries management and conservation.