Sex: Male
Education:
- Doctor of Philosophy in Applied Marine Biosciences, Tokyo University of Marine Science and Technology, 2008
- Master of Science in Aquatic Biosciences, Tokyo University of Marine Science and Technology, 2005
Field of Specialization:
Genetics
Biotechnology
Fisheries Science
Fisheries Management
Climate Change
Marine Biology
Fisheries
Sequencing
Marine Biodiversity
DNA
Researches:
Article title: Vulnerability drivers for small pelagics and milkfish aquaculture value chain determined through online participatory approach
Authors: Edison D. Macusi, Rollan C. Geronimo, Mudjekeewis D. Santos
Publication title: Marine Policy 133(5):104710, November 2021
Abstract:
Climate change impacts on the fisheries can be short-term or long-term, making them highly vulnerable. Fishers' vulnerability encompasses several factors and includes, among others, their sensitivity, exposure to the elements, and their adaptive capacity. The main aim of this study was to help develop a vulnerability assessment tool that can be applied in the various nodes of the fisheries and aquaculture value chains with a long-term view of enhancing the resilience of the fisheries and helping increase the adaptive capacity of the fishing communities. A participatory technique using online workshops was conducted together with various stakeholders (N = 214) who gave insights and suggested indicators that drive climate change impacts and vulnerability. Based on the online workshops conducted, the common hazards/drivers were increasing temperature, typhoons, flooding (sea-level rise), and the recent pandemic, which consequently destroy coral reef ecosystems, affect fisheries yield, increases fish mortality, damage boats, fishing gears, pens, cages, pond dikes, erode beach properties, and devastate houses. In association with these impacts, mobility, travel, processing, and logistic operations are severely reduced. In the human dimension, the fishers and fish farmers are directly affected in terms of income loss, destroyed fishing gears, nutritional deficiencies and health impacts, less fishing operations, early or reduced harvest yield, and low market value of products. In the adaptation options, the infrastructure, social, economic, awareness/knowledge, and relevant governance/policy dimensions are needed to address and help mitigate various climate change impacts.
Full text link https://tinyurl.com/e9zamnb8
Article title: Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria)
Authors: Dahiana Arcila, Lily C. Hughes, Bruce Meléndez-Vazquez, Carole C. Baldwin, et al.
Publication title: Systematic Biology, March 2021
Abstract:
The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a study of an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved elements and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was typically lower at inter- than intra-familial relationships regardless of the type of marker used. Several nodes that were highly supported with bootstrap had a very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths at the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic data sets.
Full text available upon request to the author
Article title: Genetic diversity, population structure and demographic history of the tropical eel Anguilla bicolor pacifica in Southeast Asia using mitochondrial DNA control region sequences
Authors: Melfa Marinia, Ivane R. Pedrosa-Gerasmioc, Mudjekeewis D. Santos,Takuro Shibuno, et al.
Publication title: Global Ecology and Conservation 26(3):e01493, February 2021
Abstract:
The tropical catadromous eel, Anguilla bicolor pacifica, an important fishery resource in Southeast Asia, is under threat due to overexploitation (especially of its glass eel phase) and the limited information on their current genetic status which is necessary for resource management. Mitochondrial DNA (mtDNA) control region sequences, a useful marker for population genetic studies in many aquatic organisms, were used to investigate the genetic diversity, population structure and demographic history of A. bicolor pacifica in the region. A total of 151 specimens were collected from three sites in Southeast Asia, namely: Phu Yen, Vietnam (n=48); General Santos, Philippines (n=52); and, Palu, Indonesia (n=51). A total of 138 haplotypes were identified using the mtDNA control region sequences. In spite of the lack of shared haplotypes, low and non-significant FST values, high haplotype diversity in concurrence with relatively low nucleotide diversity, a haplotype network with no phylogeographic structuring indicate no significant genetic population structuring among the eel samples from Vietnam, Philippines and Indonesia. Population expansion of A. bicolor pacifica was also suggested based on the results of the neutrality tests, mismatch distribution analysis and Bayesian skyline plot. Taken together, a joint management strategy for A. bicolor pacifica must involve countries in Southeast Asia particularly Vietnam, Philippines and Indonesia for its sustainable use.
Full text link https://tinyurl.com/h8raxv2z
Article title: A step forward to the joint management of the South China Sea fisheries resources: Joint works on catches, management measures and conservation issues
Authors: Shui-Ka iChang, Nien-Tsu, Alfred Hu, Samsudin Basir, Hai Vu Duyen, et al.
Publication title: Marine Policy 116:103716, October 2019
Abstract:
Degradation of the fishery resources in the SCS has been frequently reported, and calls for international cooperation through establishing an international or multilateral fisheries management organization were frequently made in recent years. However, little progress has been observed in this regard and most resources in the region are not subject to any regional cooperative management, mainly due to the disputes of sovereign rights on the SCS. In order to bypass such disputes and take a practical step forward towards reaching the goal of joint management for the SCS fisheries, a ‘bottom-up approach’ was undertaken through holding a “SCS Fisheries Resources and Management Workshop” in 2017 which is a non-political, depoliticized and non-State driven forum with key SCS fishing actors providing and exchanging substantive information on their individual fisheries for building up mutual understanding and confidence as the first step for further collaboration on the management of SCS fisheries resources. Based on information from the Workshop and substantial joint works afterwards, for the first time, this study have successfully compiled and presented basic information on (1) the fisheries statistics from key fishing actors of the region, (2) the management measures implemented by each fishing actor, and (3) subjective evaluations from managers/scientists of the key fishing actors through a questionnaire study on the causes of the stock depletion and/or the key issues that should be addressed for any potential stock recovery. Several statistical issues have been identified, and a further review of the existing statistical systems of the participating parties was recommended as an important topic for future meetings. Communication and mutual understanding of the management measures designed for and implemented in the region are considered crucial for the future construction of any regional collaborative management scheme. High priority issues that were emphasized by the respondents of the questionnaire study include insufficient control on fishing capacity and fishing efforts as well as weak law enforcement; which may relate to the issues of insufficient enforcement resources, low policy priority and institutional weakness.
Full text available upon request to the author
Article title: DNA barcoding cannot discriminate between Sardinella tawilis and S. hualiensis (Clupeiformes: Clupeidae)
Authors: Alison Faye O. Chan, Adrian U. Luczon, Ian Kendrich C. Fontanilla, Perry S.Ong, Mudjekeewis D. Santos, et al.
Publication title: Mitochondrial DNA Part B 4(2): 2499-2503, July 2019
Abstract:
Sardinella tawilis, the only known freshwater sardinella in the world, is endemic to Taal Lake, Philippines. Previous studies found the Taiwan sardinella, S. hualiensis, to be morphologically very similar to S. tawilis and identified it as the marine sister species of S. tawilis. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was carried out to analyze species demarcation in the Sardinella genus, focusing primarily on the relationship between S. tawilis and S. hualiensis. The neighbour-joining (NJ) tree that was constructed using Kimura 2-parameter (K2P) model showed a single clade for the two species with 100% bootstrap support. K2P interspecific genetic divergence ranged from 0% to 0.522%, which is clearly below the suggested 3–3.5% cutoff for species discrimination. Recombination activating gene 1 (RAG1), mitochondrial control region (CR), cytochrome b, 16S rRNA, and S7 markers were used to further validate the results. Sardinella tawilis and S. hualiensis clustered together with a bootstrap support of 99–100% in each of the NJ trees. Low interspecific genetic distances between S. tawilis and S. hualiensis for all the markers except CR could be attributed to incipient allopatric speciation.
Full text link https://tinyurl.com/4sbw9np7
Article title: Identification of Fish Prey of an Irrawaddy Dolphin (Orcaella brevirostris) using Mitochondrial Cytochrome c Oxidase 1 Sequence Analysis
Authors: John François L. Postrado, Katrina Ma. Antonia J. Jover, Hannah Jezreel D. Mabulac, John Simon B. Velasco, et al.
Publication title: The Philippine Journal of Fisheries 26(1): 1-7, June 2019
Abstract:
A new species of the genus Acropoma, A. arafurensis sp. nov., is described based on two specimens (57.3–76.2 mm standard length: SL) collected from the Arafura Sea. The present species is distinguished from other congeners by a combination of the following characters: luminous gland U-shaped extending from throat to posterior tip of pectoral fin; luminous-gland length 29.5–32.0% SL; symphysis of lower jaw not sharply protruded; proximal radial of first anal-fin pterygiophore with concavity on anterior surface; anus situated closer to pelvic-fin insertion than to origin of anal fin; cycloid scales on lateral side of posterior half of body; vertical line on cheek absent; scales between first dorsal-fin base and lateral line 4; pectoral-fin rays 15; and gill rakers 20–21. Acropoma leobergi is redescribed based on 60 specimens (38.6–143.5 mm SL) from Taiwan, Philippines, and northern and west coast of Australia. Additionally, two specimens (94.9–103.1 mm SL) of A. boholensis collected from Luzon, Philippines, represent the first record of this species from the South China Sea.
Full text available upon request to the author
Article title: First report of the Non-native Midas Cichlid, Amphilophus citrinellus (Gunther, 1864), in Laguna de Bay, Philippines
Authors: Jennifer A. Poniente, John T. Dela Peña, Romualdo M. Pol, Levita H. Zapanta and Mudjekeewis D. Santos
Publication title: The Philippine Journal of Fisheries 26(2): 55-60, December 2019
Abstract:
In recent years, increasing global trade, travel, and transport had rapidly increased the rate of introduction and diversity of non-native sh species. Once established, some introduced sh species can become aggressive and dangerously invasive. Here, we provide the rst report of the occurrence of a non-native Midas cichlid Amphilophus citrinellus in Laguna de Bay using morphological analysis and genetic marker, specically the mitochondrial gene cytochrome c oxidase subunit 1 (CO1). e results provide important information on the presence of another invasive species in Laguna de Bay that needs to be addressed since this species can competitively exclude, predate, and displace native species.
Full text link https://tinyurl.com/hex72v2w
Article title: Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current
Authors: Amanda S. Ackiss, Christopher E. Bird, Yuichi Akita, Mudjekeewis D. Santos, Katsunori Tachihara, et al.
Publication title: Ecology and Evolution 8(3), November 2018
Abstract:
Aim Mayr's central‐peripheral population model (CCPM) describes the marked differences between central and peripheral populations in genetic diversity, gene flow, and census size. When isolation leads to genetic divergence, these peripheral populations have high evolutionary value and can influence biogeographic patterns. In tropical marine species with pelagic larvae, powerful western‐boundary currents have great potential to shape the genetic characteristics of peripheral populations at latitudinal extremes. We tested for the genetic patterns expected by the CCPM in peripheral populations that are located within the Kuroshio Current for the Indo‐Pacific reef fish, Caesio cuning. Methods We used a panel of 2,677 SNPs generated from restriction site‐associated DNA (RAD) sequencing to investigate genetic diversity, relatedness, effective population size, and spatial patterns of population connectivity from central to peripheral populations of C. cuning along the Kuroshio Current. Results Principal component and cluster analyses indicated a genetically distinct lineage at the periphery of the C. cuning species range and examination of SNPs putatively under divergent selection suggested potential for local adaptation in this region. We found signatures of isolation‐by‐distance and significant genetic differences between nearly all sites. Sites closest to the periphery exhibited increased within‐population relatedness and decreased effective population size. Main Conclusions Despite the potential for homogenizing gene flow along the Kuroshio Current, peripheral populations in C. cuning conform to the predictions of the CCPM. While oceanography, habitat availability, and dispersal ability are all likely to shape the patterns found in C. cuning across this central‐peripheral junction, the impacts of genetic drift and natural selection in increasing smaller peripheral populations appear to be probable influences on the lineage divergence found in the Ryukyu Islands.
Full text link https://tinyurl.com/22rebv6u
Article title: Mapping Fishing Activities and Suitable Fishing Grounds Using Nighttime Satellite Images and Maximum Entropy Modelling
Authors: Rollan C. Geronimo , Erik C. Franklin, Russell E. Brainard, Christopher D. Elvidge, et al.
Publication title: Remote Sensing 10(10):1604, October 2018
Abstract:
Fisheries surveys over broad spatial areas are crucial in defining and delineating appropriate fisheries management areas. Yet accurate mapping and tracking of fishing activities remain largely restricted to developed countries with sufficient resources to use automated identification systems and vessel monitoring systems. For many countries, the spatial extent and boundaries of fishing grounds are not completely known. We used satellite images at night to detect fishing grounds in the Philippines for fishing gears that use powerful lights to attract coastal pelagic fishes. We used nightly boat detection data, extracted by U.S. NOAA from the Visible Infrared Imaging Radiometer Suite (VIIRS), for the Philippines from 2012 to 2016, covering 1713 nights, to examine spatio-temporal patterns of fishing activities in the country. Using density-based clustering, we identified 134 core fishing areas (CFAs) ranging in size from 6 to 23,215 km 2 within the Philippines' contiguous maritime zone. The CFAs had different seasonal patterns and range of intensities in total light output, possibly reflecting differences in multi-gear and multi-species signatures of fishing activities in each fishing ground. Using maximum entropy modeling, we identified bathymetry and chlorophyll as the main environmental predictors of spatial occurrence of these CFAs when analyzed together, highlighting the multi-gear nature of the CFAs. Applications of the model to specific CFAs identified different environmental drivers of fishing distribution, coinciding with known oceanographic associations for a CFA's dominant target species. This case study highlights nighttime satellite images as a useful source of spatial fishing effort information for fisheries, especially in Southeast Asia.
Full text link https://tinyurl.com/v5aza8fw
Article title: Climate-induced vulnerability of fisheries in the Coral Triangle: Skipjack Tuna thermal spawning habitats
Authors: Roberto Venegas, Thomas Oliver, Russell E. Brainard, Mudjekeewis Santos, et al.
Publication title: Fisheries Oceanography 28(2), September 2018
Abstract:
We investigated projected changes in sea surface temperature (SST) and the associated impacts on spawning habitat for skipjack tuna (Katsuwonus pelamis) in the Coral Triangle region (CT). A multimodel aggregate of SST CMIP5 models for the CT region, based on a comprehensive skill validation assessment, was used to identify the five best performing of 36 models tested for inclusion in a regional multimodel ensemble. Monthly 1° SST multimodel aggregate projections for the CT region under RCP8.5 show that increases in SST, as high as 2.8°C (mean value), will likely occur by the end of this century. Using these estimates of SST change, we applied three parameterizations of skipjack tuna spawning temperatures to assess the potential for change in spawning habitat within the CT region. The three spawning temperature parameterizations were as follows: (a) a square‐wave function derived from catch data with boundaries at 26 and 30°C; (b) a symmetric Gaussian function derived from the SEAPODYM models; and (c) an asymmetric Gaussian function that modifies the SEAPODYM curve in (b) to include the results of relevant physiological experiments. All three parameterizations show similar geographic patterns, with the amount of favourable spawning habitat decreasing throughout the central, equatorial CT region and increasing at higher latitudes. However, the three parameterizations show marked differences in the modelled magnitude of change, with an asymmetric Gaussian function (ASGF) showing a regionwide average of 66.1% decline in favourable spawning habitat between 2015 and 2099. These projected changes in tuna spawning habitats are likely to have important consequences on local and regional fisheries management in the CT region.
Full text link https://tinyurl.com/354wb3m9
Article title: Not fish in fish balls: fraud in some processed seafood products detected by using DNA barcoding
Authors: Katreena P. Sarmiento, Jacqueline Marjorie R. Pereda, Minerva Fatimae H. Ventolero, and Mudjekeewis D. Santos
Publication title: Philippine Science Letters 11(01), 2018
Abstract:
One of the most popular processed seafood products in the Southeast Asian region, “fishball” is a round, white food containing fish meat and other ingredients such as salt, starch, and sugar cooked in oil and sold as street food. Fish products are among the leading food categories with reported cases of food fraud— fish samples purchased at grocery stores, restaurants, and sushi bars are mislabeled. Fishballs are anecdotally known as being made up of shark meat. To identify the animal species used in commercially processed seafood products, we utilized DNA barcoding by analyzing cytochrome c oxidase I gene, which was further validated by cytochrome b gene. Twelve seafood products, including fish balls, fish nuggets, squid balls, and shrimp balls, were collected from supermarkets, street vendors, and commercial stalls in Iloilo City, Marikina City, and Quezon City, Philippines. Results revealed that processed seafood products manufactured and/or sold by well-established companies conform to some extent with their respective labels: fish balls contained meat from Chinese herring, Ilisha elongata, and broad club cuttlefish, Sepia latimanus; fish nuggets were composed of blue grenadier, Macruronus novaezelandiae; squid balls came from Humboldt squid Dosidicus gigas. Products sold by unknown companies or those with no labels—the products sold mostly as street food—showed an entirely different composition. Samples labeled squid and shrimp ball came from domestic pig, Sus scrofa, and chicken, Gallus gallus, suggesting that some seafood products being sold are mislabeled and misdeclared. We highlight the need for increasing quality control and inspection on lesser-known processed seafood product sources for consumer welfare and safety. DNA barcoding is an effective tool in assessing food identity and traceability in commercial fishery products even for those already processed.
Full text link https://tinyurl.com/56mancfb
Article title: Quorum quenching activity of lysates from bioluminescent bacteria isolated from selected Philippine marine and freshwater organisms
Authors: Roja G. Angeles-Gumban, Mudjekeewis D. Santos, Minerva Fatimae H. Ventolero, Janice A. Ragaza, Ronie J. Calugay
Publication title: AACL Bioflux 10(3):525-533, June 2017
Abstract:
Pathogens use cell density dependent gene expression known as Quorum Sensing (QS) to launch virulent factors. Targeting the QS circuit without killing the pathogens is a very promising alternative to using antibiotics which generate antibiotic resistance. The identity and diversity of bioluminescent bacteria associated with Philippine aquatic organisms, and their potential as sources of anti-QS or quorum quenching (QQ) molecules remain unknown. In this study, out of 43 organisms, 30 were observed to harbor bioluminescent bacteria with 26 from marine and four from freshwater sources. Purified bioluminescent bacterial cultures were screened for QQ activity using motility assay and the membrane fractions (MF) of 5 isolates from marine organisms namely Johnius sp. (croaker), Sillago sp. (golden-lined sillago), Variola louti (yellow-edged lyretail), Strombus variabilis (variable conch), Cistopus indicus (octopus), and one from a freshwater host, Chanos chanos (milkfish), inhibited the QS-mediated swarming of Pseudomonas aeruginosa strain NSRI based on statistical analysis using Paired t-test and Univariate Analysis of Variance (p < 0.05). Despite the host differences, the bacterial isolates shared evolutionary relationship with commonly known bioluminescent genera based on 16S rRNA gene sequence analysis with five strains belonging to the genus Photobacterium (P. leiognathi and P. mandapamensis, 99-100% identity), and two to the genus Vibrio (V. harveyi and V. campbellii, with 99% identity).
Full text link https://tinyurl.com/cttbcf3k
Article title: Larvae Identification and Development of the Only Freshwater Sardinella, Sardinella tawilis Endemic to Taal Lake, Philippines
Authors: Maria Theresa M. Mutia, Katreena P. Sarmiento, Myla C. Muyot, Michael John R. Mendiola, Benjie D. Tordecilla, Mudjekeewis D. Santos
Publication title: Philippine Journal of Science 146(3): 257-265, September 2017
Abstract:
The only freshwater Sardinella, Sardinella tawilis (Herre 1927), endemic to Taal Lake, Philippines, continues to be an important food commodity and serves as a piece of cultural heritage within the country. However, the early life history of this species is unknown. In the present study, identification of the S. tawilis larvae has been finally confirmed through the utilization of the DNA barcode marker cytochrome c oxidase I (CO1) gene and the Kimura 2-parameter (K2P) distance model. Results showed 100% identity of three larvae samples with S. tawilis GenBank reference sequences based on clustering analysis, which was supported by mean genetic distance of 1%, suggesting accurate identification of the larvae samples. Subsequently, the larval developmental stages in pre-flexion, flexion, post-flexion and juvenile stage of S. tawilis were described and illustrated. Morphological analyses revealed that the larvae had elongated and straight gut with budding pectoral fin during pre-flexion stage, disappearance of fin-fold on the flexion stage, growth of fin rays during post-flexion stage and well developed fins in juvenile stage. This study serves as the first report on the identification of S. tawilis larvae as well as its morphological description during larval development.
Full text link https://tinyurl.com/2s6c3eyw
Article title: Acanthurus albimento, a new species of surgeonfish (Acanthuriformes: Acanthuridae) from northeastern Luzon, Philippines, with comments on zoogeography
Authors: Kent E Carpenter, Jeffrey T. Williams, Mudjekeewis Dalisay Santos
Publication title: Journal of the Ocean Science Foundation
Abstract:
Acanthurus albimento is described as a new surgeonfish from northeastern Luzon from six specimens collected during extensive fish-market surveys in the Philippines. The new species is characterized by a distinctive white band below the lower jaw; many irregular, wavy, thin, blue lines on the head; a brown-orange pectoral fin with a bluish tinge on the outer membrane of the rays and a dark band on the posterior margin; a narrow rust-orange stripe along the base of the dorsal fin; and a large blackish caudal spine and sheath with the socket broadly edged in black. An analysis using the mitochondrial cytochrome c oxidase subunit 1 (COI), supported by an independent multi-locus analysis, suggests phylogenetic affinities with an Acanthurus clade that includes A. auranticavus, A. bariene, A. blochii, A. dussumieri, A. gahhm, A. leucocheilus, A. maculiceps, A. mata, A. nigricauda, and A. xanthopterus; a clade that shares a suite of color characteristics. Based on the sampling history in the region, the new species may be a limited-range endemic in the westernmost Pacific Ocean, which is unusual for members of this genus. This raises potential questions about drivers of dispersal and long-held assumptions about zoogeographic patterns along the Kuroshio Current.
Full text link https://tinyurl.com/5cx3vhk9
Article title: First DNA evidence on the occurrence of Pacific bluefin tuna, Thunnus orientalis in northern Philippine waters
Authors: Katreena P. Sarmiento, Minerva Fatimae H. Ventolero, Rafael V. Ramiscal, William S. Dela Cruz, Mudjekeewis D. Santos
Publication title: Marine Biodiversity Records 9(1), December 2016
Abstract:
Background Pacific bluefin tuna (Thunnus orientalis) spawning adults, juveniles and larvae are all reported to occur in areas between Philippine Sea and Japan Sea. However, no DNA evidence has been generated to support this. Context and purpose of the studyIn this study, Pacific bluefin tuna caught North of Polilio Island in the Philippine Pacific Seaboard, was identified through DNA barcoding using mitochondrial DNA D-loop region and cytochrome oxidase 1 gene. FindingsThe results show clustering of Philippine-caught bluefin tuna D-loop and CO1 sequences with published reference sequences for T. orientalis and supported by pairwise distances <0.034. Conclusion This study provides the first DNA evidence on the occurrence of T. orientalis in Philippine waters.
Full text link https://tinyurl.com/ekc5mzy2
Article title: Characteristics of a previously undescribed fishery and habitat for Manta alfredi in the Philippines
Authors: Jo Marie V. Acebes, Yotam Barr, Jacqueline Marjorie R. Pereda & Mudjekeewis D. Santos
Publication title: Marine Biodiversity Records 9(97), November 2016
Abstract:
Seven species of mobulid rays occur in the Philippines, six of which, including the Giant Manta Ray (Manta birostris) are caught directly or indirectly. In the Bohol Sea, mobulids have been fished since at least the nineteenth century yet the extent is not well-understood. A second species of manta, Manta alfredi was taxonomically resurrected in 2009 and also only recently been confirmed to occur in the Philippines. This study aimed to identify and describe the presence of and fishery for M. alfredi in a previously unknown area of occurrence in the Philippines. Key informant interviews, observation of catch landings, and tissue sample collection were conducted in a fishing village off Dinagat Island. Based on morphological examination and through DNA barcoding using the mitochondrial DNA CO1 gene of tissue samples it was verified that the species targeted in this area is the reef manta ray, Manta alfredi. Local ecological knowledge of the fishers provided important information on the extent and characteristics of the fishery. This relatively recent ray fishery in the Surigao Strait is the source of mobulids during the off-fishing season in Bohol with fishers from this area transporting and selling their processed catches to Bohol. The description of this fishery and habitat for the reef manta ray in the Surigao Strait is important in the understanding of the status of the species in the Philippines and in designing a management framework.
Full text available upon request to the author
Article title: Possible Effects of El Niño on Some Philippine Marine Fisheries Resources
Authors: Amor M. Damatac II and Mudjekeewis D. Santos
Publication title: Philippine Journal of Science 145(3):283-295, October 2016
Abstract:
El Niño is the warm phase of extreme climatic phenomenon observed in the equatorial Pacific. Over the past decades, frequent El Niño events have been observed and pose great threat to biodiversity. Reporting mostly the effects from 1982-1983 and 1997-1998 events, El Niño affected factors involved in ocean-atmospheric interactions such as sea surface temperature, salinity, nutrient availability, precipitation rate, ocean currents, and tropical typhoons. The changes in these factors influenced marine organisms leading to an increased phytoplankton biomass and widespread coral bleaching, and possibly resulting to fish kills, occurrence of seaweed diseases and threats to marine mammals. It affected pelagic fishes leading to migration or change in catch production. The data in this paper raise concerns on the predicted impact of El Niño on food security. Considering our susceptibility, key researchable areas must be implemented to support management strategies that will mitigate the possible effects of El Niño in the country.
Full text link https://tinyurl.com/bv9une
Article title: Identification of prohibited red piranha, Pygocentrus nattereri (Kner 1858) from confiscated juvenile fish in Manila, Philippines
Authors: Katreena P. Sarmiento, Minerva Fatimae H. Ventolero, and Mudjekeewis D. Santos
Publication title: International Journal of Philippine Science and Technology 9(1), 2016
Abstract:
Trade has significantly influenced marine and freshwater biodiversity because of overexploitation, habitat degradation, and invasive species introduction. Despite the developed international control measures, cases of illegal trade were proven to be rampant by reported cases of wildlife trafficking. In this regard, species authentication in traded fishery products through DNA barcoding is considered to be a more efficient technique in the confirmation of species identity since morphological characterization is difficult in juvenile species. In this study, confiscated live fish fingerlings, declared as " pacu " , were brought to the Genetic Fingerprinting Laboratory (GFL) by the Manila Police District-District Special Operations Unit (MPD-DSOU) for species identification. Three random samples were subjected to DNA barcoding by the amplification of cytochrome oxidase I (COI) gene and alignment of generated sequence with reference sequences for Pygocentrus nattereri and Piaractus brachypomus in the GenBank database. The Kimura 2-parameter (K2P) distance model was used to compute genetic distances and to generate Neighbour-Joining (NJ) tree. The results confirm that the three samples are P. nattereri as shown by a monophyletic cluster of sample sequences with reference sequences for P. nattereri. The mean genetic distance between the samples and P. nattereri was 1.1%. This report shows that the trade of prohibited red piranha is still happening in spite of the ban. This study aims to emphasize the significance of species authentication in strengthening law implementation and the capability of DNA barcoding to support it.
Full text link https://tinyurl.com/kxd6xwp9
Article title: Molecular cloningand expression of chitin deacetylase 1 gene from the gills of Penaeus monodon (black tiger shrimp)
Authors: Katreena P.Sarmiento, Vivian A. Panes, Mudjekeewis D.Santos
Publication title: Fish & Shellfish Immunology 55: 484-489, August 2016
Abstract:
Chitin deacetylases have been identified and studied in several fungi and insects but not in crustaceans. These glycoproteins function in catalyzing the conversion of chitin to chitosan by the hydrolysis of N-acetamido bonds of chitin. Here, for the first time, the full length cDNA of chitin deacetylase (CDA) gene from crustaceans was fully cloned using a partial fragment obtained from a transcriptome database of the gills of black tiger shrimp Penaeus monodon that survived White Spot Syndrome Virus (WSSV) infection employing Rapid Amplification of cDNA Ends (RACE) PCR. The shrimp CDA, named PmCDA1, was further characterized by in silico analysis, and its constitutive expression determined in apparently healthy shrimp through reverse transcription PCR (RT-PCR). Results revealed that the P. monodon chitin deacetylase (PmCDA1) is 2176 bp-long gene with an open reading frame (ORF) of 1596 bp encoding for 532 amino acids. Phylogenetic analysis revealed that PmCDA1 belongs to Group I CDAs together with CDA1 and CDA2 proteins found in insects. Moreover, PmCDA1 is composed of a conserved chitin-binding peritrophin-A domain (CBD), a low-density lipoprotein receptor class A domain (LDL-A) and a catalytic domain that is part of CE4 superfamily, all found in group I CDAs, which are known to serve critical immune function against WSSV. Finally, high expression of PmCDA1 gene in the gills of apparently healthy P. monodon was observed suggesting important basal function of the gene in this tissue. Taken together, this is a first report of the full chitin deacetylase 1 (CDA1) gene in crustaceans particularly in shrimp that exhibits putative immune function against WSSV and is distinctly highly expressed in the gills of shrimp.
Full text available upon request to the author
Article title: Maternal mismatches in farmed tilapia strains ( Oreochromis spp.) in the Philippines as revealed by mitochondrial COI gene
Authors: June Ordoñez, Minerva Fatimae Ventolero, Mudjekeewis Dalisay Santos
Publication title: Mitochondrial DNA Part A 28(4):1-10, March 2016
Abstract:
The introduction of genetically enhanced tilapia has significantly boosted the performance of Philippine aquaculture industry. While enhanced strains contribute to the increase in tilapia production, genetic characterization of present tilapia stocks is critical to maintain their quality and to ensure the genetic gains are sustained. To understand and determine the genetic relationship of the genetically enhanced strains produced in the Philippines, mitochondrial cytochrome oxidase subunit I (COI) gene using DNA barcoding approach was analyzed. Specimens representing 10 genetically enhanced strains (GIFT, FaST, GET-EXCEL, GST, SST, COLD, YY-male, GMT, Molobicus, and BEST), three red tilapia (Taiwan red, Florida red, and FAC-red), and two pure lines (initially identified as O. aureus and O. spilurus) were collected, sequenced, and identified using DNA barcoding. Results revealed that farmed tilapias consisted of four different Oreochromis species. As expected, COI could not distinguish individuals at the strain level but surprisingly, mismatch between the species of maternal origin and present-day offspring was observed. This particular result may pose a question on the genetic purity and integrity of the strains being distributed to farmers and suggests a re-evaluation of the effectiveness of major tilapia breeding centers in maintaining their stocks.
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Article title: Longtail tuna Thunnus tonggol (Bleeker, 1851) shows genetic partitioning across, but not within, basins of the Indo-Pacific based on mitochondrial DNA
Authors: D. A. Willette, M. D. Santos, D. Leadbitter
Publication title: Journal of Applied Ichthyology 32(2), February 2016
Abstract:
Genetic stock structure is atypical in tuna species, with most species demonstrating geographically-broad, panmictic populations. Here, genetic data suggest a distinct pattern for Thunnus tonggol across the Indo-Pacific region. The genetic variation in the coastal tuna T. tonggol sampled from across the South China Sea was examined using the highly variable mitochondrial DNA displacement loop (D-loop) gene region. One hundred and thirty-nine specimens were sampled from four locations in Indonesia, Vietnam and the Philippines. Phylogenetic reconstruction of genetic relationships revealed no significant ɸST statistics and hence no population structure within the South China Sea. However, subsequent analysis with sequence data from coastal northwest India infers discrete genetic stocks between the Indian Ocean and the South China Sea. Consistent with previous genetic analyses of tuna species in the Indo-Pacific, the findings in this study infer no population structure within each basin, but rather show a significant partitioning across the wider region. Furthermore, these results have implications for the management of the commercially valuable Thunnus tonggol across national boundaries, and thus requiring collaboration among countries to ensure its sustainable use.
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Article title: Distinct Yellowfin Tuna (Thunnus albacares) Stocks Detected in Western and Central Pacific Ocean (WCPO) Using DNA Microsatellites
Authors: Roselyn D. Aguila, Sweedy Kay L. Perez, Billy Joel N. Catacutan, Grace V. Lopez, NoelC. Barut, Mudjekeewis D. Santos
Publication title: PLoS ONE 10(9):e0138292, September 2015
Abstract:
The yellowfin tuna, Thunnus albacares (Bonnaterre, 1788), covers majority of the Philippines’ tuna catch, one of the major fisheries commodities in the country. Due to its high economic importance sustainable management of these tunas has become an imperative measure to prevent stock depletion. Currently, the Philippine yellowfin tuna is believed to be part of a single stock of the greater WCPO though some reports suggest otherwise. This study therefore aims to establish the genetic stock structure of the said species in the Philippines as compared to Bismarck Sea, Papua New Guinea using nine (9) DNA microsatellite markers. DNA microsatellite data revealed significant genetic differentiation between the Philippine and Bismarck Sea, Papua New Guinea yellowfin tuna samples. (FST = 0.034, P = 0.016), which is further supported by multilocus distance matrix testing (PCoA) and model-based clustering (STRUCTURE 2.2).With these findings, this study posits that the yellowfin tuna population in the Philippines is a separate stock from the Bismarck Sea population. These findings add evidence to the alternative hypothesis of having at least 2 subpopulations of yellowfin tuna in the WCPO and calls for additional scientific studies using other parameters to investigate this. Accurate population information is necessary in formulating a more appropriate management strategy for the sustainability of the yellowfin tuna not only in the Philippines but also in the WCPO.
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Article title: First record of a rare beaked whale Mesoplodon hotaula in the Philippines
Authors: Joanne Krisha M. Lacsamana, Minerva Fatimae H. Ventolero, Darrell Blatchley and Mudjekeewis D. Santos
Publication title: Marine Biodiversity Records 8, May 2015
Abstract:
Beaked whales of the Family Ziphiidae are the least known of all cetacean families. Here, using mitochondrial DNA Control Region and Cytochrome B, and supported by morphological comparisons of skull and teeth, we identified a 4.6 m female beaked whale, stranded in Maco, Compostela Valley, Philippines on December 19 2012, as the Deranayigala's beaked whale, Mesoplodon hotaula. This is the first record of M. hotaula in the Philippines and only the eighth specimen in the world.
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Article title: Genetic diversity, population genetic structure, and demographic history of Auxis thazard (Perciformes), Selar crumenophthalmus (Perciformes), Rastrelliger kanagurta (Perciformes) and Sardinella lemuru (Clupeiformes) in Sulu-Celebes Sea inferred by mitochondrial DNA sequences
Authors: Ivane R. Pedrosa-Gerasmio, Altair B. Agmata, Mudjekeewis D. Santos
Publication title: Fisheries Research 162:64-74, February 2015
Abstract:
Aside from having an important ecological role in the ocean food web, small pelagic fishes have become the major food source in the Sulu-Celebes Sea (SCS) which is bordered by Indonesia, Malaysia and the Philippines. Conservation and management of these fishes are of prime importance because the people living around the SCS are highly dependent on these resources. Nevertheless, basic biological information, especially relating to genetic diversity, population genetic structure, and demographic patterns, are often deficient. In this study, population genetic methods were used to investigate the genetic structure and diversity as well as historical demography of four ecologically and economically important small pelagic fishes in the SCS: Auxis thazard (Lacepède, 1800); Bali sardine, Sardinella lemuru (Bleeker, 1853); Indian mackerel, Rastrelliger kanagurta (Cuvier, 1816); and bigeye scad, Selar crumenophthalmus (Bloch, 1793). Fish samples were collected from 5 geographic locations: (Philippines: Zamboanga, Tawi-Tawi and Palawan; Indonesia: Manado; and Malaysia: Kudat) around the SCS and muscle tissues were sequenced for the mitochondrial DNA (D-loop) control region (n = 150, 231, 169 and 224 for AT, SL, RK, and SC, respectively). Low overall FST values, high haplotype diversity but low genetic differentiation among haplotypes, and highly mixed clusters from BAPS analysis indicate no distinct genetic population structuring among the samples. Furthermore, neutrality tests, mismatch analysis and Bayesian skyline plots suggest population expansion for all species. Generally, these results indicate that the four marine pelagic species are very resilient over evolutionary time scales; yet, proper management is very necessary, especially because overexploitation of small pelagic fishes has already been reported in the SCS region.
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Article title: Development and application of the fisheries vulnerability assessment tool (Fish Vool) to tuna and sardine sectors in the Philippines
Authors: Melchor R. Jacinto, Al Jayson G.Songcuan, Graceous Von Yip, Mudjekeewis D. Santos
Publication title: Fisheries Research 161: 174-181, January 2015
Abstract:
Climate change studies in the Philippines are emerging fast, focusing on different fields of sciences. However, studies that address the fisheries sector remain insufficient. Here, we described a sector-based fisheries vulnerability assessment tool (Fish Vool) to evaluate the vulnerability of primary fishery commodities. Tool demonstration and validation were conducted in General Santos and Zamboanga City, which are the primary producers of tuna and sardine, respectively. Fish Vool revealed an overall medium vulnerability (low exposure, medium sensitivity, and low adaptive capacity) for both sectors. The vulnerability assessment of the tuna and sardine sectors emphasizes the potential of Fish Vool to assess climate change vulnerability for primary commodities and other fishery sectors.
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Article title: Zooplankton Composition and Abundance and its Relationship with Physico-chemical Parameters in Manila Bay
Authors: Ellaine C. Jose, Elsa F. Furio, Valeriano M. Borja, Norvida C. Gatdula and Mudjekeewis D. Santos
Publication title: Biosafety 03(01), January 2015
Abstract:
Anthropogenic activities affect water quality and biological resources in bays such as zooplankton community. A survey on the zooplankton in Manila Bay was done from January to December 2013 in relation to physico-chemical parameters.Temperature and salinity in the bay showed uniform spatial patterns. Mean DO concentrations in the bay ranges from 2.79-6.25 mg/L, the lowest value was recorded in station 14 in the month of July with a value of 1.01 mg/L. Mean concentrations of nitrate, phosphate, nitrite, silicate ranges from 0.0265-8.3902 μM, 0.0135-0.2573 μM, 0.1385- 0.8396 μM, and 5.4887-53.2027 μM respectively. Arthropods, consist mainly of copepods, dominated the zooplankton community in the bay. High concentrations were observed in the eastern and southern part of the bay. Copepod nauplii, calanids and Oithona sp. were among the dominant species. Redundancy Analysis revealed that salinity, temperature, dissolved oxygen, phosphate and nitrate have positive correlation with zooplankton.
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Article title: First report on the occurrence of invasive black-chin tilapia Sarotherodon melanotheron (Ruppell, 1852) in Manila Bay and of Mayan cichlid Cichlasoma urophthalmus (Gunther, 1892) in the Philippines
Authors: June Feliciano F. Ordoñez, Angelli Marie Jacynth M. Asis, Billy Joel Catacutan, John dela Pena and Mudjekeewis D. Santos
Publication title: BioInvasions Records 4, December 2014
Abstract:
We report the presence of blackchin tilapia, Sarotherodon melanotheron, in the coastal waters of Manila Bay and in the river tributary of Hagonoy, Bulacan, suggesting its possible range expansion. The occurrence of the native Central American Mayan cichlid, Cichlosoma urophthalmus, is also putatively confirmed for the first time in Hagonoy, Bulacan. While morphological features, morphometric characters, and meristic counts of the current populations match those reported elsewhere for these species, further genetic work is required to confirm their identification and possibly provide information on their source. Negative impacts of the existence of the two species due to competitive interactions have already been anecdotally reported, however, no empirical scientific evidence is available to provide verification. Therefore, studies on the potential ecological impacts should be done, especially because the two species were already reported as notoriously invasive.
Full text link https://tinyurl.com/a365wx26
Article title: Species composition of by-catch from milkfish ( Chanos chanos ) fry fishery in selected sites in the Philippines as determined by DNA barcodes
Authors: Angelli Marie Jacynth Asis-Egar, Irma Destura, Mudjekeewis Dalisay Santos
Publication title: Mitochondrial DNA 27(3):1-5, October 2014
Abstract:
Abstract Milkfish fry fishery, an important industry in the Philippines, uses non-selective fishing gears and push nets in coastal areas which lead to the capture of other non-targeted juvenile aquatic species. Unfortunately, information on the amount and the identity of by-catch species is lacking thus the extent of impact of the fry fishery is not known. In this study, the species composition of milkfish fry fishery by-catch sampled from selected coastal areas that are known to be fry collection sites in the country were identified and assessed through the use of DNA barcoding. Analyses revealed that by-catch fish species of the milkfish fry industry included Black Tiger shrimp (Peneaus monodon), Tarpon (Megalops cyprinoides), Glass perchlets (Ambasis gymnocephalus and Ambasis buruensis), Ladyfish (Elops hawaiensis), Snapper (Lutjanus fulviflamma), Cardinal fishes (Apogon hyalosoma and Sphaeramia orbicularis), Whipfin siver biddy (Gerres filamentosus), Mullet (Liza sp.), Anchovy (Encrasicholina heteroloba), and Tiger perch (Terapon jarbua), almost all of which are potential marketable food fish and culture species. The results of the study provide preliminary information, as well as awareness, on the species composition of milkfish fry by-catch.
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Article title: Utilization of loop-mediated isothermal amplification (LAMP) technology for detecting White Spot Syndrome Virus (WSSV) and Vibrio spp. in Litopenaeus vannamei in selected sites in the Philippines
Authors: Amalea Dulcene Nicolasora, D Nicolasora, Benedict Arias Maralit, Christopher Marlowe, et al.
Publication title: Philippine Science Letters 7(2), 2014
Abstract:
Shrimp disease outbreaks in the Philippines remain to be uncontrollable. This is compounded by the inac-cessibility of disease diagnostics to most shrimp farmers. The loop-mediated isothermal amplification (LAMP) is a new technology that is used as a practi-cal alternative for rapid detection of viral and bacterial patho-gens. The method proves to be rapid, highly sensitive, and cost-effective compared to other detection assays. In this study, LAMP protocols for the detection of the two most common shrimp pathogens, white spot syndrome virus (WSSV) and Vi-brio spp., in the Philippines were developed. A temperature range of 55⁰C to 68⁰C for WSSV detection and 59⁰C to 67⁰C for Vibrio spp., and incubation periods of 45 minutes to 1 hour, were proven to be the suitable conditions for the LAMP assay. Using 309 Vol. 7 | No. 2 | 2014 Philippine Science Letters Editor-in-charge: Eduardo A. Padlan these conditions, asymptomatic Litopenaeus vannamei samples from selected sites (Iloilo, Batangas, Bulacan, Laoag, and Leyte) were tested for WSSV. Samples which indicated WSSV infec-tion were from Iloilo (89.47%), Batangas (30.00%), Bulacan (43.33%), and Leyte (75.00%), while shrimps from Laoag City (0.00%) tested negative. Likewise, the occurrence of Vibrio spp. was determined in shrimps sampled in Pangasinan and six bacte-rial DNA isolates of Vibrio spp. were identified. Moreover, con-ventional PCR and microbiological methods were performed along with the LAMP reaction for comparison and further con-firmation. The results showed that the LAMP assay was faster and 10 times more sensitive than polymerase chain reaction in detecting WSSV and was more efficient than the traditional microbiological method in diagnosing vibriosis. Overall, the results indicated that a LAMP protocol, which is more conven-ient, highly sensitive, faster, and more practical, has been effec-tively utilized to detect WSSV and vibriosis in selected Philip-pine shrimp farms. KEYWORDS loop-mediated isothermal amplification, polymerase chain reac-tion, white spot syndrome virus, Vibrio spp., shrimps INTRODUCTION
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Article title: Updates on the status of giant clams Tridacna spp. and Hippopus hippopus in the Philippines using mitochondrial CO1 and 16S rRNA genes
Authors: Apollo Marco D. Lizano and Mudjekeewis D. Santos
Publication title: Philippine Science Letters 7(1), 2014
Abstract:
The CO1 and 16S rRNA genes of six of the possible eight species of giant clams (Hippopus hippopus, Tridacna gigas, T. crocea, T. squamosa, T. derasa, and Tridacna sp.YCT-2005) under the Tridacnidae family found in the Philippines were sequenced for molecular approach-based species identification. We first report-ed here the CO1 sequence of H. hippopus and made it available online through GenBank. We also reported the first sighting of Tridacna sp. YCT-2005 in Philippine waters, an undescribed species of giant clam, which has initially been reported to be a potentially new species that was thought to be found only in Tai-wan. Phylogenetic trees of CO1 and 16S rRNA gene sequences of giant clam samples from the Philippines were constructed using both the Neighbor-Joining approach and the Maximum-Likelihood approach. Both trees showed similar topology in which Tridacna and Hippopus formed two distinct clades. T. crocea, T. squamosa, T. maxima, T. costata, and Tridacna sp. YCT-2005 showed monophyletic grouping under subgenus Chametrachea confirming the recognized groupings of giant clams based on morphology. On the other hand, restriction site mapping based on the 16S rRNA gene showed a unique recogni-187 Vol. 7 | No. 1 | 2014 Philippine Science Letters tion site at 367-370 bp (5'AGCT3') for the species of T. maxima as opposed to the species of Tridacna sp. YCT-2005. Alu I re-striction endonuclease was identified as a candidate diagnostic enzyme to differentiate between these species. This study con-firmed the identity of giant clams found in the Philippines using molecular techniques. The use of DNA barcoding can be a useful tool to identify different species of giant clams which is needed for their proper management and conservation in the Philippines, since they are all declared as endangered.
Full text link https://tinyurl.com/sdruz28z
Article title: Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding
Authors: Angelli Marie Jacynth M. Asis, Joanne Krisha M. Lacsamana, Mudjekeewis D. Santos
Publication title: Mitochondrial DNA 27(1):1-8, May 2014
Abstract:
Illegal trade has greatly affected marine fish stocks, decreasing fish populations worldwide. Despite having a number of aquatic species being regulated, illegal trade still persists through the transport of dried or processed products and juvenile species trafficking. In this regard, accurate species identification of illegally traded marine fish stocks by DNA barcoding is deemed to be a more efficient method in regulating and monitoring trade than by morphological means which is very difficult due to the absence of key morphological characters in juveniles and processed products. Here, live juvenile eels (elvers) and dried products of sharks and rays confiscated for illegal trade were identified. Twenty out of 23 (87%) randomly selected "elvers" were identified as Anguilla bicolor pacifica and 3 (13%) samples as Anguilla marmorata. On the other hand, 4 out of 11 (36%) of the randomly selected dried samples of sharks and rays were Manta birostris. The rest of the samples were identified as Alopias pelagicus, Taeniura meyeni, Carcharhinus falciformis, Himantura fai and Mobula japonica. These results confirm that wild juvenile eels and species of manta rays are still being caught in the country regardless of its protected status under Philippine and international laws. It is evident that the illegal trade of protected aquatic species is happening in the guise of dried or processed products thus the need to put emphasis on strengthening conservation measures. This study aims to underscore the importance of accurate species identification in such cases of illegal trade and the effectivity of DNA barcoding as a tool to do this.
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Article title: Subtracted Transcriptome Profile of Tiger Shrimp (Penaeus monodon) That Survived WSSV Challenge
Authors: Benedict A. Maralit, Minerva Fatimae H. Ventolero, Mary Beth B. Maningas, Edgar C. Amar, and Mudjekeewis D. Santos
Publication title: Dataset Papers in Science 2014(10), May 2014
Abstract:
There is increased interest in the development of virus-resistant or improved shrimp stock because production is currently hindered by outbreaks and limited understanding of shrimp defense. Recent advancement now allows for high-throughput molecular studies on shrimp immunity. We used next-generation sequencing (NGS) coupled with suppression subtractive hybridization (SSH) to generate a transcriptome database of genes from tiger shrimp that survived White spot syndrome virus (WSSV) challenge. A total of 9,597 unique sequences were uploaded to NCBI Sequence Read Archive with accession number SRR577080. Sixty-five unique sequences, 6% of the total, were homologous to genes of Penaeus monodon. Genes that were initially related to bacterial infection and environmental stress such as 14-3-3 gene, heat shock protein 90, and calreticulin were also found including a few full-length gene sequences. Initial analysis of the expression of some genes was done. Hemocyanin, ferritin, and fortilin-binding protein exhibited differential expression between survivor and control tiger shrimps. Furthermore, candidate microsatellite markers for brood stock selection were mined and tested. Four trinucleotide and one dinucleotide microsatellites were successfully amplified. The study highlights the advantage of the NGS platform coupled with SSH in terms of gene discovery and marker generation.
Full text link https://tinyurl.com/2wp4x7n5
Article title: Gene pool and population structure in larval Herklotsichthys quadrimaculatus (Rüppell, 1837)
Authors: R. C. Thomas Jr., P. D. Beldia III, W. L. Campos, M. D. Santos
Publication title: Journal of Applied Ichthyology 30(5), April 2014
Abstract:
No available
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Article title: Taxonomic identification of "Ludong" fish from the Cagayan River (Philippines)
Authors: Minerva Fatimae Ventolero, Evelyn Ame, Billy Joel N. Catacutan, Mudjekeewis D. Santos
Publication title: Philippine Science Letter 7(1), 2014
Abstract:
"Ludong”, also known as the President’s fish, is a mullet fish belonging to the Mugilidae family that is indigenous to Cagayan River and its tributaries. Because of its rarity and apparent threatened status, it has been the subject of intense research, conservation and management. To date, its accurate taxonomic identification is unclear and only based on conflicting published reports. In this study, we established the identity of “Ludong” using morphological analysis and comparison with pictures of holotypes from the Museum National d’Histoire Naturelle collection-Paris and National Museum of Natural History of the Smithsonian Institution, USA. Results revealed that “Ludong” was confirmed to belong to the genus Cestraeus of the Mugilidae family. Furthermore, there were at least two species found in Cagayan River, namely Cestraeus oxyrhynchus and Cestraeus goldiei. These results established the identity of “Ludong” species which can now be used as baseline information for further studies and conservation.
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Article title: Hidden Diversity in Sardines: Genetic and Morphological Evidence for Cryptic Species in the Goldstripe Sardinella, Sardinella gibbosa (Bleeker, 1849)
Authors: Rey C. Thomas Jr., Demian A. Willette, Kent E. Carpenter, Mudjekeewis D. Santos
Publication title: PLoS ONE 9(1):e84719, January 2014
Abstract:
Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while Clade 2 is limited to the northernmost sampling site. In addition, morphometric analyses revealed a unique head shape that characterized each genetic clade. Hence, both genetic and morphological evidence strongly suggests a hidden diversity within this common and commercially-important sardine.
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Article title: Evolution of the freshwater sardinella, Sardinella tawilis (Clupeiformes: Clupeidae), in Taal Lake, Philippines and identification of its marine sister-species, Sardinella hualiensis
Authors: Willette, Demian A; Carpenter, Kent E; Santos, Mudjekeewis D.
Publication title: Bulletin of Marine Science -Miami- 90(1), January 2014
Abstract:
We identify the sister species of the world's only freshwater sardinella, Sardinella tawilis (Herre, 1927) of Taal Lake, Philippines as the morphologically-similar marine Taiwanese sardinella Sardinella hualiensis (Chu and Tsai, 1958). Evidence of incomplete lineage sorting and a species tree derived from three mitochondrial genes and one nuclear gene indicate that S. tawilis diverged from S. hualiensis in the late Pleistocene. Neutrality tests, mismatch distribution analysis, sequence diversity indices, and species tree analysis indicate populations of both species have long been stable and that the divergence between these two lineages occurred prior to the putative 18th century formation of Taal Lake.
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Article title: So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute
Authors: DA Willette, FW Allendorf, PH Barber, DJ Barshis, KE Carpenter, ED Crandall
Publication title: Bulletin of Marine Science -Miami- 90(1):79-122, January 2014
Abstract:
The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to. marine biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled "Genomic Applications to Marine Science and Resource Management in Southeast Asia" was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions.
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