Correcting widespread misidentifications of the highly abundant and commercially important sardine species Sardinella lemuru,Bleeker, 1853 in the Philippines

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.     

Molecular phylogeny of Philippine freshwater sardines based on mitochondrial DNA analysis

The commercially important Sardinella species (family Clupeidae or herrings) usually thrive in marine environments. An exception is Sardinella tawilis of Taal Lake, Batangas, Philippines, the only known freshwater sardine. This species is believed to have immigrated from Balayan Bay to the lake when it was formed in the course of volcanic eruptions some 240 years ago. To determine the relationship of S. tawilis to the marine species S. albella, S. fimbriata, and S. longiceps from the Balayan Bay we sequenced 358 bp of the cytochrome b gene and the mitochondrial control region. The cytochrome b gene was highly conserved and contained little phylogenetic information. The control region sequences, however, demonstrated two highly diversified main haplotypes grouping S. tawilis with S. albella, as shown by maximum parsimony and neighbor-joining analysis. The haplotypes are characterized by the presence of an 81 bp indel and up to eight 35 bp tandem repeat elements. The repeat copy number varied within individuals of S. tawilis and S. albella, thus showing heteroplasmy in these two species only. The analysis of two subpopulations of S. tawilis revealed restricted substitutions that may indicate the beginning of genetic differentiation of the two subpopulations.     

Hidden Diversity in Sardines: Genetic and Morphological Evidence for Cryptic Species in the Goldstripe Sardinella,Sardinella gibbosa (Bleeker, 1849)

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.     

Multivariate analyses of the biometric features from Philippine sardines – implications for the phylogenetic relationships of the freshwater Sardinella tawilis (Teleostei,Clupeomorpha)*

Philippine sardines are members of the commercially important Sardinella genus (Family Clupeidae). Sardines are mostly marine species with a very few exception like the Philippine freshwater sardine, Sardinella tawilis, of Lake Taal. This species is believed to have immigrated from Balayan Bay some 250 years ago. To determine the relationship of freshwater S. tawilis to the marine forms, 35 biometric features were investigated. The variables were subjected to univariate (mean, standard deviation and coefficient of variance) and multivariate analyses [Principal Component Analysis (PCA) and Hierarchical Cluster Analysis]. Results from univariate tests revealed that the number of ventral fin ray can discriminate Sardinella lemuru from the rest of the sardines. Multivariate PCA, on the other hand, showed discrete separation of the marine sardines. Sardinella tawilis, however, cannot be clearly separated from the marine species, Sardinella albella. The same clustering was recovered in HCA, thus providing evidence that S. albella is the closest marine relative of the freshwater S. tawilis.     

Genetic relationship of Sardinella lemuru from lombok strait with fish rich in omega-3 fatty acid

Lombok Strait has abundance of Sardine, Sardinella lemuru, which contains such high amount of omega-3 fatty acid (omega-3). However, the genetic relationship of S. lemuru with other commercial fish rich in omega-3 has not been widely studied yet. Studies on genetic proximity of S. lemuru with the other marine fish using 12S rRNA gene is very important in order to obtain genetic information of the Sardine to develop an appropriate strategy for future conservation of the fish in Lombok Strait. The aim of this study was to find out the genetic relationship of Sardinella lemuru living in Lombok Strait with the economically valuable fish and its correlation with omega-3 production. Sardinella lemuru were collected from Lombok Strait, the phylogenetic tree was done based on 12S rRNA gene through a neighbor-joining method to identify the relationship of Sardines and fish rich in omega-3 fatty acid. The phylogenetic tree showed that Sardinella lemuru is similar to Sardinella aurita and has a close similarity with Sardinella maderensis. However, the relationship did not correspond to omega-3 production. Based on the results of the study, it is suggested that the production of omega-3 is not specifically based on the proximity of the species, but it is more associated with conserved domain of Δ6-desaturase. Nevertheless, detailed mechanisms still need to be elucidated.     

DNA barcoding of the ichthyofauna of Taal Lake, Philippines

This study represents the first molecular survey of the ichthyofauna of Taal Lake and the first DNA barcoding attempt in Philippine fishes. Taal Lake, the third largest lake in the Philippines, is considered a very important fisheries resource and is home to the world's only freshwater sardine, Sardinella tawilis. However, overexploitation and introduction of exotic fishes have caused a massive decline in the diversity of native species as well as in overall productivity of the lake. In this study, 118 individuals of 23 native, endemic and introduced fishes of Taal Lake were barcoded using the partial DNA sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene. These species belong to 21 genera, 17 families and 9 orders. Divergence of sequences within and between species was determined using Kimura 2-parameter (K2P) distance model, and a neighbour-joining tree was generated with 1000 bootstrap replications using the K2P model. All COI sequences for each of the 23 species were clearly discriminated among genera. The average within species, within genus, within family and within order percent genetic divergence was 0.60%, 11.07%, 17.67% and 24.08%, respectively. Our results provide evidence that COI DNA barcodes are effective for the rapid and accurate identification of fishes and for identifying certain species that need further taxonomic investigation.     

Reproductive patterns of Sardinella maderensis (Lowe, 1841) off Cameroon

The gonadosomatic index and gonad mean weight of Sardinella maderensis off the west coast of Cameroon were used to assess their reproductive patterns. Results showed that first maturity is at about 17 cm total length, and is the same for both males and females. S. maderensis breeds continuously but with two spawning peaks, a major one from April to July and a minor one from December to January.
Réumé
Reproduction des Sardinella maderensis sur la côte ouest du Cameroun
L'indice gonadosomatique et le poids moyen des gonades ont été utilisés pour évaluer les schimas de reproduction des Sardinella maderensis (Clupeidés) dans une étude menée sur la côte ouest du Cameroun. Dapres les risultats obtenus, la taille de premiére maturité est identique chez les msàles et chez les femelles (de l'ordre de 17 cm de longueur totale). S. maderensis se reproduit continuellement avec deux piriodes de grande ponte, I'une d'avril sà juillet et l'autre, moins importante, de décembre sà janvier.

Zusammenfassung

Reproduktionsmodus von Sardinella maderensis an der Westküste won Kamerun
Der gonado-somatische Index und das mittlere Gonadengewicht wurden zur Beurteilung des Repro-duktionsmodus von Sardinella maderensis an der Westküste von Kamerun herangezogen. Die Ergeb-nisse zeigen, daß die Länge der Erstlaicher sowohl für Weibchen als auch für Männchen bei etwa 17 cm Totallänge liegt. S. maderensis laicht kontinuierlich, mit zwei ausgeprägten Spitzen: eine Hauptlaichpe-riode zwischen April und Juli und eine schwächer ausgeprägte zwischen Dezember und Januar.     

Population structure of the Brazilian sardine (Sardinella brasiliensis) in the Southwest Atlantic inferred from body morphology and otolith shape signatures

Hydrobiologia - The Brazilian sardine (Sardinella brasiliensis) sustains the most important pelagic fishery off Brazilian waters. The present study evaluated the existence of distinct...     

Human exposures and potential health hazard assessment of Hg and Pb in some major imported frozen fish species in Nigeria

The levels of mercury and lead in three major species of imported frozen fish—Atlantic mackerel (Scomber scombrus), sardine (Sardinella sindesis), and scumbera (Scumbria spp)—were determined and potential health hazard resulting from their ingestion by Nigerians was assessed. Sample digestion was carried out as prescribed in the Food and Agricultural Organisation/Swedish International Development Agency wet digestion method. Quantitation of the Hg and Pb content of the digested samples and blanks was carried out spectrophotometrically using thiozone as the ligand. The ranges of level of Hg in the samples in mg/Kg were: 0.03–0.42 for Scomber scombrus and 0.03–0.37 and 0.020–0.31 for Scumbria and Sardinella sindesis, respectively. Also, Pb had value ranges in mg/Kg of 0.20–0.28, 0.24–0.32, and 0.15–0.32 in Scomber scombrus, Scumbria, and Sardinella sindesis, respectively. Potential health hazard assessment that was carried out showed no risk status for children and adults consuming Sardinella sindesis and scumbera and adults consuming Scomber scombrus (HQ < 1). The results further showed a risk (HQ = 1.022 and THI = 1.036) for children taking Scomber scombrus.     

Genetic analysis of rabies virus isolates in the Philippines

To determine the genetic characteristics of the rabies virus in the Philippines, 59 rabies virus isolates were obtained from domestic rabid dogs and their partial nucleotide sequences of nucleoprotein (N) gene were compared. Based on comparison with reported sequences, phylogenetic analysis revealed that all isolates from the Philippines had close genetic relations and formed two subgroups. The Philippines isolates belonged to a different lineage from other Asian isolates but were closer to them than to terrestrial isolates and laboratory strains. Several specific nucleotide and amino acid substitutions were observed among the Philippines isolates. Our results suggest that rabies viruses in the Philippines might have a characteristic evolution.     

Multiplex 16S rRNA haplotype-specific PCR, a rapid and convenient method for fish species identification: an application to West African Clupeiform larvae

A multiplex haplotype-specific polymerase chain reaction (MHS-PCR) method was developed, which identified seven Clupeiform species living in the tropical Eastern Atlantic region: Sardinella aurita, Sardinella maderensis, Ethmalosa fimbriata, Sardina pilchardus, Engraulis encrasicholus, Pellonula leonensis and Ilisha africana. 16S rRNA fragments were amplified using a species-specific set of primers, yielding species-specific size fragments, and then separated using agarose gel electrophoresis, enabling direct visual identification of targeted species. This method provides an accurate, easy and rapid tool for identifying species within large Clupeiform samples. It is suitable for investigations on early Clupeiform stages, species and identification in fishery management in the tropical Eastern Atlantic area.     

Incidence of histoplasmin hypersensitivity in the Philippines

Long-term residents of the Philippines were skin tested with histoplasmin skin test material. This study was conducted with 143 electric company (MERALCO) employees from Manila, Philippines. We found that 37 (26 %) of the subjects were skin test positive. Characteristics of the positive group were: average age of 37 years; all except one were lifelong inhabitants of Metro Manila; 25 were male and 12 were female; one-half of the subjects reported extended contact with chickens. Despite these findings, histoplasmosis is considered to be a very rare disease in the Philippines. This survey indicates that Histoplasma capsulatum is sufficiently present in the Philippines to come in contact withone-fourth of the test population. This reinforces the hypothesis that histoplasmosis is present in the Philippines and is probably being misdiagnosed as granulomatous-inducing diseases such as tuberculosis, e.g., so-called “drug resistant” tuberculosis. We recommend larger surveys of this type and attempts to culture the etiologic agent from natural sources such as chicken and bat droppings. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the asian and Australian faunal zones

The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas, and the Moluccas). Studies of this region by Wallace marked the genesis of the field of biogeography, yet few workers have used molecular methods to investigate the biogeography of taxa whose distribution spans this interface. Some taxa, such as the fanged frogs of the ranid genus Limnonectes, have distributions on either side of the zoogeographical lines of Wallace and Huxley, offering an opportunity to ask how frequently these purported barriers were crossed and by what paths. To examine diversification of Limnonectes in Southeast Asia, the Philippines, and Wallacea, we estimated a phylogeny from mitochondrial DNA sequences obtained from a robust geographic sample. Our analyses suggest that these frogs dispersed from Borneo to the Philippines at least twice, from Borneo to Sulawesi once or twice, from Sulawesi to the Philippines once, and from the Philippines to Sulawesi once. Dispersal to the Moluccas occurred from Sulawesi and to the Lesser Sundas from Java/Bali. Species distributions are generally concordant with Pleistocene aggregate island complexes of the Philippines and with areas of endemism on Sulawesi. We conclude that the recognition of zoogeographic lines, though insightful, may oversimplify the biogeography of widespread taxa in this region.     

Mass mortality of Sardinella aurita Valenciennes (Pisces, Clupeidae) in Thessaloniki Bay (Macedonia, Greece)

Mass mortality of Sardinella aurita was observed in Thessaloniki Bay during an abrupt temperature fall in February 1991. The mass of dead fish was estimated to be about 79.4 tonnes.     

Molecular analyses confirm the coexistence of Fasciola gigantica and parthenogenetic Fasciola in the Philippines

Fasciola flukes collected from domestic buffalos and cattle in the Philippines were confirmed as Fasciola gigantica and parthenogenetic Fasciola based on DNA analyses of nuclear pepck and pold genes, and the mitochondrial ND1 gene. This study is the first to elucidate that F. gigantica and parthenogenetic Fasciola coexist in the Philippines with prevalences of 90.6% and 9.4%, respectively. The F. gigantica population showed a high genetic diversity with 25 ND1 haplotypes, suggesting that F. gigantica has existed in the Philippines for a long time. In contrast, parthenogenetic Fasciola flukes showed a single ND1 haplotype (Fsp-ND1-P1), which was identical to the founder haplotype, Fg-C2 of parthenogenetic Fasciola in China. These results indicate that parthenogenetic Fasciola in the Philippines is a recently introduced population from a neighboring continent.     

Colonization of the Philippines from Taiwan: a multi‐locus test of the biogeographic and phylogenetic relationships of isolated populations of shrews

Aim Colonization of the Philippines from Taiwan or neighbouring areas of the Asian mainland has been proposed as an important source of diversity for some plant and animal groups in the northern Philippines. Previous inferences, however, were based on taxonomic groupings, which sometimes fail to reflect phylogenetic history. Here, we test for colonization of the Philippines from the north in a group of shrews (Soricomorpha: Crocidura) using explicit inferences of evolutionary history. Location Southeast Asia. Methods We estimate the phylogenetic relationships of populations of shrews from Batan and Sabtang islands in the northern Philippines using DNA sequences from two mitochondrial genes and three nuclear loci. We employ topology tests to evaluate the possible relationships of these shrews to species from throughout Southeast Asia. Results We find conclusive evidence that shrews from Batan and Sabtang are closely related to Crocidura tanakae from Taiwan and additional specimens from the Asian mainland. Bayesian and frequentist topology tests using alignments of individual loci strongly reject any notion that shrews from Batan and Sabtang are part of the main Philippine radiation of Crocidura, indicating that the northernmost Philippine islands were almost certainly colonized by shrews from Taiwan or mainland Asia. Main conclusions Our results provide the first compelling evidence for colonization of the Philippine archipelago by a terrestrial vertebrate via a northern route. Invasion of the northern Philippines by shrews, however, did not lead to further range expansion to more southerly parts of the Philippines. This study, combined with previous results, documents that Crocidura colonized the Philippines at least three times. However, only one of these invasions led to in situ speciation and ubiquity across the archipelago. Our findings are part of a growing body of literature suggesting that oceanic archipelagos are often colonized multiple times by groups of closely related species, and occasionally from multiple sources.     

Karyotypes and cellular DNA contents of three species of the subfamily Clupeinae

Karyotypes of three species of the subfamily Clupeinae collected from northern Japan were analyzed by in vitro methods and their cellular DNA contents were measured using an integrating microdensitometer.Sardinella zunasi andSardinops melanostictus show very similar karyotypes: 2n = 48, consisting of acrocentric or subtelocentric chromosomes with a gradual decrease in chromosome size, but with differences in cellular DNA of 2.32 and 2.69pg/cell respectively.Clupea pallasii differs from the aforementioned species in karyotype: 2n = 52, consisting of 6 metacentric or submetacentric chromosomes and 46 acrocentric or subtelocentric chromosomes, with a cellular DNA content of 1.96 pg/cell. The results showed two different modes in karyological evolution within the subfamily Clupeinae, i.e. an increase of cellular DNA content without apparent change in karyotype, as shown bySardinella zunasi andSardinops melanostictus, and less change in cellular DNA content but with marked change in karyotype, as shown byClupea pallasii.     

Genetic diversity of JC virus in the modern Filipino population: implications for the peopling of the Philippines

The Philippines is generally believed to have been established by various peoples who migrated from neighboring areas. To gain new insights into the peopling of the Philippines, we used the JC virus (JCV) genotyping approach. We collected about 50 urine samples on each of two representative islands of the Philippines, Luzon and Cebu. DNA was extracted from the urine samples and used to amplify the 610-bp region (IG region) of the viral genome. For each island, we determined about 20 IG sequences, from which a neighbor-joining phylogenetic tree was constructed to classify the JCV isolates detected into distinct genotypes. The predominant genotype detected was SC, the Southeast Asian genotype. Minor JCV genotypes were SC/Phi, B1-a, and B3. SC/Phi was a subcluster of SC and has not been detected in areas other than the Philippines. B1-a was detected previously in mainland China, Pamalican Island (Palawan, Philippines), and Taiwan (an aboriginal tribe). B3 was classified in this study into two subgroups, one (B3-a) containing three Luzon isolates and several Chinese, Thai, and Uzbek isolates, the other (B3-b) containing two Luzon, one Cebu, and one Indonesian isolate. These findings suggest that the modern Filipino population was formed not only by Southeast Asians carrying SC but also by a few distinct ethnic groups carrying SC/Phi, B1-a, and B3-a or -b.     

Preparation and testing of Sardinella peptones: application to lipase production by Staphylococcus sp

Production of lipase by Staphylococcus sp. in media containing fish peptones from sardinelle (Sardinella aurita) prepared in the laboratory was studied. Lipase production is strongly affected by lipids present in fish flours. Fish peptones prepared from dIgresed whole flesh was an excellent substrate for lipase production. A comparison of lipase production in media containing fish peptones or high quality commercial peptones indicated that fish peptones enhanced enzyme formation.