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Journal article
Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management
Frontiers in Marine Science, Vol.11, pp.1-24
2024
Abstract
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.
Details
- Title
- Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management
- Authors
- Monal Lal (Corresponding Author) - University of the Sunshine Coast, Queensland, Australian Centre for Pacific Islands ResearchDeo A S Macahig - University of the Philippines DilimanMarie Antonette Juinio-Menez - University of the Philippines DilimanJon P AltamiranoRoselyn Noran-BaylonMargarita dela Torre-dela Cruz - Guiuan Development Foundation Inc.Janine L Villamor - Guiuan Development Foundation Inc.John Ray Gacura - Guiuan Development Foundation Inc.Wildfredo H Uy - Mindanao State University NaawanHanzel Mira-Honghong - Mindanao State University NaawanPaul C Southgate - University of the Sunshine Coast, Queensland, Australian Centre for Pacific Islands ResearchRachel Ravago-Gotanco - University of the Philippines Diliman
- Publication details
- Frontiers in Marine Science, Vol.11, pp.1-24
- Publisher
- Frontiers Research Foundation
- Date published
- 2024
- DOI
- 10.3389/fmars.2024.1396016
- ISSN
- 2296-7745
- Copyright note
- © 2024 Lal, Macahig, Juinio-Meñez, Altamirano, Noran-Baylon, de la Torre-de la Cruz, Villamor, Gacura, Uy, Mira-Honghong, Southgate and Ravago-Gotanco. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
- Data Availability
- Genotypic data for sandfish sampled and sequenced during this study are available as Supplementary Data files 2, 3 for selectively neutral and putatively adaptive markers, respectively. Data have been deposited in the OSF repository, available at https://doi.org/10.17605/OSF.IO/BZ98K.
- Organisation Unit
- Australian Centre for Pacific Islands Research; School of Science, Technology and Engineering
- Language
- English
- Record Identifier
- 991036698302621
- Output Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web Of Science research areas
- Environmental Sciences
- Marine & Freshwater Biology
- Oceanography