00. Ocean Decade - Philippines
Permanent URI for this communityhttps://repository.unesco.gov.ph/handle/123456789/7
The UNACOM Online and Digital Enabling Library and Index is developed to support the alignment of research, investments, and community initiatives toward contributing to a well-functioning, productive, resilient, sustainable, and inspiring ocean. The goal is to enable the government, partner agencies, and UNESCO to develop more robust Science-Informed Policies and facilitate a stronger Science-Policy Interface through the gathered data, information, and knowledge related to the Ocean Decade in the Philippines.
Particularly, it aims to:
Particularly, it aims to:
- Gather and index all publications, reports, policies, laws, legislations, articles, and other documents of the Philippine National Committee on Marine Sciences (NCMS) related to the Ocean Decade.
- Disseminate and promote these publications, reports, policies, and other documents on the initiatives and actions to address the Ocean Decade challenges.
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- Two hidden mtDNA-clades of crown-of-thorns starfish in the Pacific OceanYasuda, 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.
- Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery managementLal, 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.
- Genetic diversity and population connectivity of the greenblotch parrotfish (Scarus quoyi Valenciennes, 1840) within southern Mindanao inferred from mitochondrial 16S rRNALabrador, Kevin; Fortaleza, Maybelle; Cabasan, Joey; Elumba, Merlene; Nañola, Cleto (Science and Technology Information Institute, 2022-10-03)A genetic assessment was done on the greenblotch parrotfish (Scarus quoyi Valenciennes, 1840) in three bays within southern Mindanao, Philippines. Mitochondrial 16S rRNA recovered 12 haplotypes, one of which was dominant in all sites. Despite the reported phenotypic variation from previous assessments, there was neither evidence of genetic structure (global Φst = 0.012, p = 0.13) nor isolation by distance (r = 0.05, p = 0.50). Genetic diversity was also low (Hglobal = 0.472; πglobal = 0.13%), with ~ 77% of haplotype diversity accounted for with just 69 samples. While connectivity suggests continuous larval exchange within southern Mindanao owing to the species’ high dispersal potential, low genetic diversity implies reduced effective population size, probably due to recent bottlenecks (e.g. overfishing, habitat destruction). Although this study provides baseline genetic information on the local population, inferences are considerably limited by the genetic marker used and the spatial scale under investigation. A thorough understanding of the population will be possible if the entire habitat range of the species is assessed using markers with high resolving power, such as the hypervariable mitochondrial control region, microsatellites, or genome-wide single nucleotide polymorphisms (SNPs).This project was funded by the DOST-PCAARRD (Department of Science and Technology–Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development) through the projects titled “DNA Barcoding and Genetic Diversity of Selected Marine Fishes along the North Bifurcation of the North Equatorial Current (NEC)” and “DNA Barcoding of Selected Marine Fishes in Davao and Sulu Archipelago (MINDA).” Sample collection was covered by the DARETO (Discovery-Applied Research and Extension for Trans/Inter-disciplinary Opportunities) research grant under CHED (Commission on Higher Education) through the project entitled “Bioeconomic Assessment and Modelling of Reef Fisheries and Sustainable Harvest Project”. We would like to thank Junissa M. Consuegra, Joemarie J. Lanutan, and Jodi Eugenia Lourdes F. del Fierro for their assistance in sample collection and laboratory work.
- Genetic connectivity and diversity between tropical and subtropical populations of the tropical horned sea star Protoreaster nodosus in the northwest PacificNakajima, Yuichi; Yasuda, Nina; Matsuki, Yu; Arriesgado, Dan M.; Fortes, Miguel D.; Uy, Wilfredo H.; Campos, Wilfredo L.; Nadaoka, Kazuo; Lian, Chunlan (Springer, 2024-06-01)Seagrass beds are ecologically and economically important coastal ecosystems, and seagrass-associated organisms are a key part of their biodiversity. Marine organisms that reproduce through broadcast spawning are likely to have less genetic differentiation among populations than those that use other modes of reproduction, but this has not been well studied. Here, we investigated the genetic diversity, genetic differentiation, and migration patterns of the seagrass-associated sea star Protoreaster nodosus across 12 sites spanning approximately 2500 km from the Ryukyu Archipelago, Japan, to the Philippines. We genotyped 405 individuals by using seven microsatellite loci and analyzed allelic richness and expected heterozygosity as indices of genetic diversity. Of these two indices, only expected heterozygosity decreased slightly with increasing latitude. These results suggest that genetic diversity has not clearly decreased, even in the isolated Ryukyu Archipelago populations. Geographic distance was significantly correlated with genetic differentiation (pairwise FST: − 0.005 to 0.049). However, populations in the Ryukyu Archipelago and the Philippines showed relatively low genetic structuring and the pairwise genetic differentiation between these regions was often non-significant. Analysis of historical migration rates showed bidirectional north–south migration, which appears to be influenced by the Kuroshio Current and its countercurrents.We thank members of the project ‘Coastal Ecosystem Conservation and Adaptive Management under Local and Global Environmental Impacts in the Philippines’ (CECAM project: https://sites.google.com/view/cecam-project).
- Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabraOrdoñez, 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.