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National Committee on Marine Sciences (NCMS)

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AGROVOC Keyword: search.filters.agrovoc.genetic diversity (resource)Ocean Decade Challenge: search.filters.odc.Challenge 4: Develop a sustainable and equitable ocean economy

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Now showing 1 - 4 of 4
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    Two hidden mtDNA-clades of crown-of-thorns starfish in the Pacific Ocean
    Yasuda, Nina; Inoue, Jun; Hall, Michael R.; Nair, Manoj R.; Adjeroud, Mehdi; Fortes, Miguel D.; Nishida, Mutsumi; Tuivavalagi, Nat; Ravago-Gotanco, Rachel; Forsman, Zac H.; Soliman, Taha; Koyanagi, Ryo; Hisata, Kanako; Motti, Cherie A.; Satoh, Noriyuki (Frontiers Media SA, 2022-04-27)
    Recurring outbreaks of crown-of-thorns starfish (COTS) severely damage healthy corals, especially in the Western Pacific Ocean. To obtain a better understanding of population genetics of COTS and historical colonization across the Pacific Ocean, complete mitochondrial genomes were sequenced from 243 individuals collected in 11 reef regions. Our results indicate that Pacific COTS (Acanthaster cf. solaris) comprise two major clades, an East-Central Pacific (ECP) clade and a Pan-Pacific (PP) clade, separation of which was supported by high bootstrap value. The ECP clade consists of COTS from French Polynesia, Fiji, Vanuatu and the Great Barrier Reef (GBR). The Hawaii population is unique within this clade, while California COTS are included in EPC clade. On the other hand, the PP clade comprises multiple lineages that contain COTS from Vietnam, the Philippines, Japan, Papua New Guinea, Micronesia, the Marshall Islands, GBR, Vanuatu, Fiji and French Polynesia. For example, a lineage of the PP clade, which has the largest geographic distribution, includes COTS from all of these locations. These results suggest two alternative histories of current geographic distributions of COTS in the Pacific Ocean, an ECP clade ancestry or Western Pacific clade ancestry. Although further questions remain to be explored, this discovery provides an evolutionary context for the interpretation of COTS population structure which will aid future coral reef research in the Pacific Ocean, and ultimately improve reef management of COTS.
    We thank the following people for their help with sample collection: Dr. Hugh Sweatman and the AIMS Bioresources Library for GBR samples, Dr. Molly Timmers for Hawaiian samples, Geoff Jones and Jeff Kinch for Papua New Guinean samples, Monal Lal for Fijian samples, Christina Shaw for Vanuatu samples, Hoang Dinh Chieu for Vietnamese samples, and Hiromitsu Ueno for Japanese samples. The DNA Sequencing Section and IT section of OIST are acknowledged for its expert help with genome sequencing and bioinfomatic analysis. Last, but not least, we acknowledge the traditional owners of the lands and sea country on which this research took place.
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    Strong genetic structure and limited gene flow among populations of the tropical seagrass Thalassia hemprichii in the Philippines
    Nakajima, Yuichi; Matsuki, Yu; Fortes, Miguel D.; Uy, Wilfredo H.; Campos, Wilfredo L.; Nadaoka, Kazuo; Lian, Chunlan (MDPI AG, 2023-02-05)
    Seagrasses are marine angiosperms, and seagrass beds maintain the species diversity of tropical and subtropical coastal ecosystems. For proper understanding, management and conservation of coastal ecosystems, it is essential to understand seagrass population dynamics. Population genetic studies can cover large geographic scales and contribute to a comprehensive understanding of reproductive dynamics and potential dispersal among locations. The clonal and genetic diversity and genetic connectivity of Thalassia hemprichii in the Philippines were estimated by a population genetics approach. The geographic scale of this study has a direct distance of approximately 1600 km. Although high clonal diversity was found in some sites (R = 0.07–1.00), both sexual and asexual reproduction generally maintains separate populations. Genetic diversity is not definitely correlated with latitude, and genetic differentiation is significant in all pairs of sites (FST = 0.026–0.744). Complex genetic structure was found in some regions, even at a fine geographic scale. The migration of fruits and seedlings was elucidated as an infrequent and stochastic event. These results suggest the necessity for the conservation of this species due to a deficiency in migrants from external regions.
    We thank members of CECAM project.
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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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    Genetic diversity of Kappaphycus malesianus (Solieriaceae, Rhodophyta) from the Philippines
    Dumilag, Richard V.; Crisostomo, Bea A.; Aguinaldo, Zae-Zae A.; Lluisma, Arturo O.; Gachon, Claire M.M.; Roleda, Michael Y. (Elsevier, 2023-07)
    Kappaphycus farming for carrageenan production is characterized by a strong selective pressure at the genetic level. Traits of agronomic importance are compromised due to domestication bottlenecks and the subsequent events of possible selective breeding of founding cultivars. Kappaphycus malesianus is farmed in Malaysia and the Philippines, and is distributed within the Malesian region. While the majority of genetically characterized specimens of this species are from Malaysia, those from the Philippines are poorly explored. Here, we assessed the genetic diversity of K. malesianus from the Philippines based on cox1 sequences. Of the 15 identified haplotypes, 14 specimens represent three novel haplotypes (wild specimens) that form a group distinct from the main clade comprising most K. malesianus haplotypes known to date. An additional haplotype from a cultivated specimen was identical to that of the most widely distributed haplotype. Our findings demonstrate that the K. malesianus is genetically more diverse than previously recognized. It is expected that higher genetic diversity may be revealed through additional sampling from a wider geographic range and careful application of integrative approaches. Future selective breeding programs in Kappaphycus would benefit from the incorporation of the genetic resources, as provided in this study.