Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmars.2024.1396016/full#supplementary-materialThe 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.The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Australian Centre for International Agriculture Research (ACIAR) project FIS/2016/122: “Increasing technical skills supporting community-based sea cucumber production in Vietnam and the Philippines”. Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development of the Department of Science and Technology (DOST-PCAARRD: Project Numbers QSR-MR-CUC.02.01 and QSR-MR-CUC.02.02)

Nursery culture of sandfish Holothuria scabra in sea-based floating hapa nets: Effects of initial stocking density, size grading and net replacement frequency

Sea-based culture of early juvenile sandfish Holothuria scabra up to fingerling size (>2 g) using floating hapa nets has been confirmed as a viable nursery system in tropical countries such as the Philippines. However, production can be further optimized through more efficient rearing practices. In this study, we demonstrate the effects of initial stocking density, size grading and net replacement frequency during the culture of early juvenile sandfish in sea-based floating hapa nets (2 × 1 × 1 m). Testing different initial stocking density treatments ranging from 150 to 2000 early juveniles (4–10 mm; 0.02–0.06 g) per hapa net, we confirmed significantly faster growth (0.06–0.08 g d−1) and higher survival (72–97%) in low densities (≤500 hapa−1), compared to high densities (≥700 hapa−1: 0.02–0.04 g d−1; 67–80%). Low density culture can produce 2 g sandfish in about a month, while higher densities will require a 2–3 mo culture period to reach this size. Culture performance following size grading was also compared using three initial size classes (small, 0.05–0.99 g; medium, 1–1.99 g; and large, 2–3 g) and a mixed group (0.05–3.00 g). At 45 d, juveniles in pooled size-graded groups grew significantly faster (0.11–0.13 g d−1) than those in the mixed group (0.01 g d−1). Survival was significantly higher in the medium (85.3%) and large (84.7%) groups, than those in the small (54.4%) and mixed (45.6%) groups. However, size variation was not significantly mitigated by grading during the 45-d culture. Culture performance of sandfish was not significantly enhanced by more frequent net replacement for short-term rearing (30–45 d). Optimal results were gained from an initial stocking density of ≤500 early juveniles (5–10 mm) per floating hapa net which may be cultured in a month, without requiring net replacement and size grading to produce ≥2 g sandfish. However, in cases of high hatchery production, it is also feasible to adopt higher density stocking (e.g. >1000 hapa−1), but will require longer culture duration (60–85 d), monthly net replacement and size-grading to attain the same size. Results of this study can help fine-tune management practices for nursery culture of sandfish in sea-based floating hapa net nurseries in order to boost production of fingerlings needed for aquaculture and restocking.This study was funded by the Australian Centre for International Agriculture Research (ACIAR) through the project FIS/2010/042 “Expansion and Diversification of Production and Management Systems for Sea Cucumbers in the Philippines, Vietnam and Northern Australia” with counterpart funding support by SEAFDEC/AQD through study code FS-03-Y2014T. Special thanks to MRB Altamirano for valuable help in developing the manuscript in the early stages. We also appreciate the useful suggestions from M Lal and P Southgate, as well as the constructive comments from anonymous reviewers, all contributed in improving this paper. We are grateful to CP Recente, JC Rodriguez, Jr., H Figurado, and N Tibubos for the assistance in sandfish hatchery production, experimental setup and monitoring