Search

Aquaculture is growing rapidly as a food-producing sector and in recent years, fishmeal prices have climbed by more than twofold on a global scale. This review of previous studies was performed to contribute to the extant literature on the aquaculture sector to aid cost reduction of aquafeeds by identifying substitute protein that can replace fishmeal. The review followed the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) using the SCOPUS and WOS (Web of Science), DOAJ (Directory of Open Access Journals), Academia, and Pubmed Central databases with the following search terms: “fishmeal,” “alternative protein source” and “aquafeeds.” This resulted in 5,331 articles from the SCOPUS and WOS databases. Finally, the titles and abstracts of the articles were screened, giving a total of 162 articles that were used in the study; another 58 articles came from open databases. Results have shown that 100% replacement of fishmeal with blood meal did not affect the growth of fish as well as 75% to 100% combination of poultry-by-product (PBM), feather meal (FEM), and blood meal (BM). Moreover, a 10% replacement of fishmeal using seaweed (Gracilaria arcuata) has no adverse effect on feed efficiency and growth performance of tilapia, a 50% replacement of fishmeal using black soldier fly (Hermetia illucens), and 25% replacement using soybean (Glycine max) also showed better results for fish growth. With that, this review shows that alternative protein can be a great alternative to the aquaculture sector in reducing the cost of aquafeeds since alternative proteins are much cheaper than the usual fishmeal.

An uncharacterized protein from Lindgomyces ingoldianus was initially annotated to contain various domains with promising biotechnological applications. Thus, this study was conducted to determine the structural characteristics, classification, and potential function of this protein through in silico methods. Results revealed that this protein has a neutral charge and is unstable and non-polar. It is predicted to have a signal peptide, glycoside hydrolase family 114 (GH114) domain, low complexity region, and fungal type cellulose-binding domain (fCBD) or type 1 carbohydrate-binding module (CBM1) region. Structural characterization and phylogenetic analysis revealed that this protein is an endo-α-1,4-polygalactosaminidase enzyme. This protein was also predicted to contain 36 active sites and is extracellularly secreted. Molecular docking analysis showed that it could bind galactosaminogalactan (GAG), a key virulence factor for Aspergillus fumigatus chronic infections. The binding of this protein to GAG was much better than Ega3, which could be attributed to the presence of the fCBD region that is unique to this protein. It is hypothesized that the fCBD domain helps in carbohydrate recognition and holds them in place for maximum catalysis in the GH114 domain. Finally, this protein is found to be related to its orthologue from the plant pathogenic fungus Zopfia rhizophila.

Cetaceans, including dolphins, serve as definitive hosts of zoonotic anisakid nematodes, which are important etiological agents for human anisakiasis and allergy-associated health risks. With limited knowledge of these zoonotic parasites from the marine environment in the Philippine waters, the stranding of a Fraser’s dolphin (Lagenodelphis hosei Fraser, 1956) off the central Philippines made it possible to identify the worm species isolated from its gut. Parasitological examinations were carried out using morphological and molecular tools. Morphologically, the SEM and LM data revealed that the specimens belong to the genus Anisakis of the Type 1 group. Molecularly, PCR-RFLP results of the ITS region generated only a single fragment pattern on all worm samples corresponding to the reported molecular keys for A. typica. Further sequence and phylogenetic analyses of both ITS rDNA and mtDNA COX2 genes confirmed the anisakid nematodes’ identity as A. typica. The molecular data obtained in this study support previous findings on the possible existence of local variants of A. typica in this region.

Aquaculture production is under pressure to increase its production to meet the growing demand for food from a growing population. In the Philippines, aquaculture has experienced the shift from milkfish to prawn with its attractive marketable price. Its intensification has led to negative and positive impacts making its collapse inevitable in the mid-1990s and raised a range of environmental and socioeconomic problems. This paper reviewed the environmental impacts, challenges, and disease outbreaks that overtook the industry using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) method. We examined gaps and changes required to revitalize the industry to properly take-off. It considers and gives details on the impacts of shrimp culture on the environment e.g. shrimp farm management, marine pollution, disease outbreaks, climate change impacts, and socioeconomic impacts. Moreover, the presence of viral diseases such as White Spot Syndrome Virus (WSSV), Monodon Baculovirus (MBV), Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV), Hepatopancreatic Parvovirus (HPV), and Yellow Head Virus (YHV), have caused socioeconomic impacts with approximate losses of 40,080 mt in 1997 to 51,000 mt in 2014 in the shrimp industry. Recommended strategies were considered to improve the environmental management of shrimp aquaculture, including disease management, and priorities that were highlighted for future research. This management relates to adopting good aquaculture practices on shrimp culture, proper environmental monitoring and sustainable practices at the farm level.

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.

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.

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.[Concatenation; exons; introns; phylogenomics; species-tree methods; target capture.]

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.

In recent years, increasing global trade, travel, and transport had rapidly increased the rate of introduction and diversity of non-native fish species. Once established, some introduced fish species can become aggressive and dangerously invasive. Here, we provide the first report of the occurrence of a non-native Midas cichlid Amphilophus citrinellus in Laguna de Bay using morphological analysis and genetic marker, specifically the mitochondrial gene cytochrome c oxidase subunit 1 (CO1). The 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

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.

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.

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.

Summary 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.

Understanding the extinction risk of taxonomic groups increases our ability to prioritize efforts to address biodiversity loss. Over 400 species of herrings, shads, sardines, anchovies, menhadens, and relatives belong to the Order Clupeiformes and include many of the most important forage fishes. These small, schooling fishes are ecologically, economically, and culturally significant. However, despite their global contribution to fisheries and our increasing reliance on them for food and modern commodities, we lack critical information regarding basic biology and population trends for most species. We applied the IUCN Red List methodology, a comprehensive and systematic approach to assess extinction risk, to all clupeiform species. The best estimate suggests nearly 11% of species are of elevated conservation concern, although this could be as high as 36%. Two regions, the Caribbean and the Indo-Malay-Philippine Archipelago have high concentrations of threatened and Data Deficient species and are areas of conservation concern. Major threats include overexploitation, pollution, and habitat modification. Immediate conservation priorities include: 1) increasing research and mitigative action directed toward species assessed as threatened or Data Deficient; 2) improving fisheries management regulations for the understudied but heavily exploited species, and 3) promoting local, intensive habitat restoration to reduce pollution and remove dams. These extinction risk assessments and subsequent analyses should be used as an informative tool for fisheries and conservation managers and to monitor conservation progress.

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.

This study used mitochondrial cytochrome c oxidase 1 in the identification of the fish prey from the gut samples collected from a stranding of a dead Irrawaddy dolphin in Pulupandan, Negros Occidental. Obtained consensus sequences were searched against the nucleotide database of NCBI and reference sequences, and sample sequences were used for generating the dendrogram and the pairwise genetic distances between species. Results showed that most of the sample sequences were 99% identical to the reference sequences.Eubleekeria splendens and Conger japonicus were the identified species in the stomach contents. E. splendens is a demersal and coastal species while C. japonicus is a demersal species and has not been previously recorded in the Philippines. Conflict in the taxonomy of the Conger genus may suggest that this may be identified as C. jordani. This study reports the first record of fish prey identification of the Irrawaddy dolphin in the country. Continuous monitoring of the Irrawaddy dolphin in the Guimaras Strait, including their feeding ecology, is needed to understand the population further and to improve their conservation.

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 km2 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.

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 (Lacepede, 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 F ST 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.

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.

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.

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.

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.

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.

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. In 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. The 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

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.

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.

Summary Morphology, meristics, and molecular genetics tools were used to determine the species level identification of the most commonly landed sardine species in the Philippines. Results from this study indicated that the historical and widely applied nomenclature of the Indian oil sardine, Sardinella longiceps, is incorrect and that this species is instead the Bali sardinella Sardinella lemuru. Developing an effective strategy for managing one of the Philippines most important commodity sardine species first requires accurate identification of this species. Results of this study provide needed information that is now being applied to emerging management policies.

Pattern recognition receptors (PRRs) are involved in the effective innate defense against several microbes. Here, we identified a nucleotide-oligomerization domain (NOD)-like receptor subfamily C (NLRC) from Japanese flounder (Paralichthys olivaceus). Full-length transcript of JfNLRC is composed of 3976 bp encoding a protein of 1175 deduced amino acid residues. The presence of a signature nucleotide-binding domain (NACHT) and leucine-rich repeated domain (LRR) suggested that the protein is a member of the NLR family. Interestingly, its C-terminus presents an extra PRY/SPRY (B30.2) domain similar to fish in the Trim (finTrim) family. A phylogenic tree of JfNLRC revealed that full-length JfNLRC diverged from the NOD1 and NOD2 clusters, and the NACHT domain in JfNLRC was clustered within the NLRC3 group. Stimulation by formalin-killed Edwardsiella tarda, Streptococcus iniae, and lipopolysaccharide (LPS) showed that the JfNLRC expression was raised a few hours after stimulation, suggesting this novel protein is involved in the immediate response against both Gram-positive and Gram-negative bacteria. Furthermore, the IL-1β mRNA expression level in JfNLRC-over-expressing HINAE cells was significantly increased, when compared to a control, after LPS-stimulation and E. tarda infection. These results suggested that JfNLRC probably induced IL-1β gene expression mediated by LPS-stimulation.

Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Triangle pose challenges to biogeographers and resource managers. Comparative phylogeography provides a powerful tool to test biogeographic hypotheses evoked to explain species richness in the Coral Triangle. It can also be used to delineate management units for marine resources. After about a decade of phylogeographical studies, patterns for the Coral Triangle are emerging. Broad connectivity in some species support the notion that larvae have maintained gene flow among distant populations for long periods. Other phylogeographic patterns suggest vicariant events resulting from Pleistocene sea level fluctuations, which have, at least occasionally, resulted in speciation. Divergence dates ranging back to the Miocene suggest that changing land configurations may have precipitated an explosion of species diversification. A synthesis of the marine phylogeographic studies reveals repeated patterns that corroborate hypothesized biogeographic processes and suggest improved management schemes for marine resources.

The Alaska pollock, Theragra chalcogramma (Pallas), is an important raw source for surimi and other food products in Japan. However, Alaska pollock caught in the Atlantic and Mediterranean regions has been reported to harbor Anisakis species that pose considerable food safety problems. Here, we identified the third-stage (L3) Anisakis spp. sampled from Alaska pollock caught in northern Japan using a combination of morphological and molecular analyses which included PCR-RFLP and sequencing of the ITS (ITS1-5.8S rDNA-ITS2) region and mtDNA cox2 gene markers. Four Anisakis spp. were confirmed, namely Anisakis simplex (sensu stricto [s.s.]), A. pegreffii, A. brevispiculata, and an Anisakis sp. belonging to the Anisakis Type II group. The identification of 4 different Anisakis spp. occurring in Alaska Pollock, and the identification of A. brevispiculata and an Anisakis sp. (Anisakis Type II) in the northwest Pacific region, are first reports. Anisakis simplex (s.s.) composed the majority of Anisakis spp. in Alaska pollock at 91.0%, followed by A. pegreffii (5.2%), Anisakis sp. (Anisakis Type II) (2.4%), and A. brevispiculata (1.4%).

Interleukin 11 is a class-1 helical cytokine, having the four-helix bundle structure, possessing pleiotropic characteristics involved in physiological processes including blood production, bone formation and placentation. The interleukin 11 paralogues (IL11a and IL11b) have been identified in fish with only IL11a from carp and trout have been characterized and analyzed for its expression thus far. Here, we cloned and studied the structure and expression of IL11b in Japanese flounder (Paralichthys olivaceus), and compared this with the existing information on fish IL11 paralogues. Japanese flounder IL11b (poIL11b) cDNA is composed of 1536 bp encoding for 201 aa residues with a 23 aa leader peptide, three cysteine residues (C12, C183 and C198) and four potential N-linked glycosylation sites. poIL11b does not show constitutive expression in tissues of adult fish except for the very slight expression in kidney and spleen, and the very high expression in peripheral blood leukocytes (PBLs). poIL11b is transiently up-regulated by bacterial lipopolysaccharide (LPS) and increasingly stimulated by the IFN inducer poly I:C in kidney, spleen and peripheral blood leukocytes of adult fish in vitro. It is likewise slightly stimulated by Edwardsiella tarda infection but is highly expressed after hirame rhabdovirus (HIRRV) infection in kidney of juvenile fish. The stimulation studies suggest that poIL11b, aside from its role in bacterial infection, is well involved in antiviral responses. Moreover, poIL11b structure and expression pattern appears to be slightly distinct and opposite to IL11a, respectively, suggesting a complementation of function of the duplicate fish IL11 genes.

Members of the interleukin 6 (IL6)-cytokine subfamily of proteins are involved in numerous physiological processes including cellular development, inflammatory function, and acute phase and immune responses. Previously, a cytokine-like gene named M17, which is closely associated with the IL6 subfamily, has been identified in fish with no apparent orthologue in higher vertebrates. Here, we cloned a novel cDNA from Japanese flounder, Paralichthys olivaceus, which had significant identity but exhibited contrasting expression with fish M17s, named here as M17 Homologue (MSH). With subsequent in silico search and full annotation of the M17 orthologue in zebrafish (Danio rerio), MSH orthologues in tiger puffer (Takifugu rubripes), green spotted pufferfish (Tetraodon nigroviridis) and stickleback (Gastorosteus aculeatus), as well as structural, synteny comparisons and phylogenetic analysis with known IL6-cytokines, we determined the novelty of the fish MSH. Japanese flounder MSH was observed to be highly expressed in immune-related tissues and are induced by immune stimulants, lipopolysaccharide (LPS), polyI:C and peptidoglycan (PG) in vitro suggesting that it is involved in fish immunity particularly against viral and bacterial agents, a functional feature exhibited by previously reported fish cytokines.

South and Southeast Asian countries have undertaken demersal trawl surveys to measure the fisheries potential of their waters throughout the 20th century. However, ensuring full use of, and easy access to the resulting data is a challenge in developing countries. The “Fisheries Resource Information System and Tools” (FiRST) was developed through a regional collaborative effort across eight South and Southeast Asian counties to meet these needs. FiRST is a data management system for scientific trawl survey data and includes data summary and visualization tools, an analytical routine to estimate biomass, and data import/export modules. The FiRST software has also facilitated the establishment of a regional database, ‘TrawlBase’, which contains more than 20,000 hauls or stations from scientific trawl surveys in 10 countries conducted between 1926 and 1995. The regional database is an important regional resource for coastal fisheries management complementing national fisheries catch statistics. This article describes the refined version of FiRST (version 2004) and provides examples on how the database (‘TrawlBase’) has been used to date for analyses aimed at establishing historic resource baselines and examining the status of coastal fishery resources. The results show a severe decline of resource biomass to an average of 22% of pre-exploitation levels, with cases as low

Granulocyte colony-stimulating factor (CSF3) is a glycoprotein cytokine, which influences the hematopoiesis of the phagocytic neutrophils and its precursors and was used extensively in cancer therapy and for the treatment of neutropenia in mammals. However, CSF3 is yet to be identified in nonmammalian species mainly because of its rapid mutation. Here, we report the first CSF3 genes from three teleost fishes: Japanese flounder (Paralichthys olivaceus), fugu (Takifugu rubripes), and green-spotted pufferfish (Tetraodon nigroviridis) and present evidence that the chicken (Gallus gallus) myelomonocytic growth factor is in fact the chicken CSF3 orthologue. We support this by showing significant conservation of the CSF3 genes' structure, domains, regulatory motifs, and synteny across species and by phylogenetic analysis. CSF3 orthologues are indeed evolving rapidly and appears to be undergoing purifying selection in mammals but positive selection in fish and chicken. Furthermore, the paralogous fugu and pufferfish CSF3-1s and CSF3-2s are shown to be the ancestral and duplicate genes, respectively. Finally, we demonstrate that the Japanese flounder CSF3 gene is at least involved in immunity based on its basal expression in immune-related tissues and its upregulation in kidney and peripheral blood leukocytes after in vitro stimulation with lipopolysaccharide and a combination of concanavalin A/phorbol myristate acetate.

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.

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 ofM. hotaulain the Philippines and only the eighth specimen in the world.