DNA barcoding cannot discriminate between Sardinella tawilis and S. hualiensis (Clupeiformes: Clupeidae)

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

Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

Twelve cDNA libraries from two species of catfish have been sequenced, resulting in the generation of nearly 500,000 ESTs

DNA barcoding of common freshwater eleotrids (Gobiiformes: Eleotridae) in the Philippines, with a global comparison and notes on their conservation and management

Eleotrids, also known as gudgeons or sleeper gobies, are found mostly in freshwater and mangrove habitats of tropical and subtropical regions. Some eleotrids exhibit minimal morphological variation at the species level. In this study, DNA barcoding was used to assess the molecular diversity of common freshwater eleotrids in the Philippines in relation to other eleotrid species from other countries with available DNA sequences in public databases. A total of 422 mitochondrial DNA cytochrome c oxidase I (COI) gene sequences were analyzed: 107 of which were generated from this study, while the remaining 315 sequences were mined from Barcode of Life Data System and GenBank. Both the neighbor-joining and maximum likelihood trees constructed based on the COI sequences clustered most of the species in concordance with their taxonomic classification. The mean Kimura 2-parameter genetic distances within species and genera were 1.31% and 11.60%, respectively. As expected, the mean interspecific distance was higher than the mean intraspecific distance except in some species. This study revealed the presence of nine distinct eleotrid species belonging to five genera in the Philippines. These species include Giuris laglaizei, G. tolsoni, Eleotris acanthopomus, E. fusca, E. melanosoma, Belobranchus sp., Belobranchus belobranchus, Butis butis, and Ophiocara ophicephalus. This study also revealed the presence of possibly undescribed Belobranchus species in the Philippines. This undescribed Belobranchus species differs by a high percentage of genetic divergence from the other species of Belobranchus (3.00% from B. segura and 13.40% from B. belobranchus). Furthermore, high genetic distance (2.62%) was also observed between G. laglaizei species of Laguna de Bay and Mindanao. This study strongly recommends a taxonomic review of the Laguna de Bay G. laglaizei and the Philippine Belobranchus spp., as these species may harbor species complexes that require closer examination so that proper conservation and management measures can be implemented for each species

DNA barcoding of fishes from Lake Lanao, Philippines

Lake Lanao, the second largest lake in the Philippines and one of the 15 ancient lakes in the world, used to contain 20 endemic cyprinid species, which had attracted the attention of evolutionary biologists in the past. Over the years, there has been a steady decline in the abundance and diversity of endemic fishes in the lake because of overfishing and introduction of non-native species. This study represents the first molecular survey of the ichthyofauna of Lake Lanao. A total of 75 specimens of 12 different species belonging to nine genera, eight families, and five orders were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Average Kimura 2-parameter genetic distances were 0.24% (within species), 8.31% (between species), 9.69% (within family), and 24.86% (between families). Possible hybrids between Oreochromis species were detected. Glossogobius spp. was highlighted for further taxonomic investigation because barcoding indicated unidentified species of this genus. The partial sequence of mitochondrial COI gene was found to be a good DNA barcode for fast and accurate species identification of fishes in Lake Lanao and for tagging species that warrant further taxonomic investigation

Low genetic diversity in Clarias macrocephalus Günther, 1864 (Siluriformes: Clariidae) populations in the Philippines and its implications for conservation and management

Clarias macrocephalus Günther, 1864 is a Near Threatened freshwater catfish found in the Philippines and other Southeast Asian countries.  Its numbers have dwindled over the past few years because of habitat loss and competition.  This study examined the genetic diversity of the remaining viable populations of C. macrocephalus in the Philippines.  Primers were designed to amplify via polymerase chain reaction (PCR) the complete mitochondrial DNA (mtDNA) control region (870-bp) in 120 specimens collected from three sites: (1) Buguey, Cagayan; (2) Camalaniugan, Cagayan; and (3) Agusan del Sur.  Of the 120 sequences generated, only three haplotypes and two polymorphic sites were found. Overall haplotype and nucleotide diversity (h=0.479, π=0.00058) were alarmingly low, consistent with populations of other freshwater fishes that have experienced a genetic bottleneck.  The overall FST value was 0.80050, indicative of large genetic differentiation between populations.  The very low genetic variation found in all three C. macrocephalus populations calls for conservation and management efforts for the protection of the remaining populations of this economically important species.</p

Low isozyme variation in native and transplanted populations of the endemic Philippine silver perch, Leiopotherapon plumbeus (Kner, 1864) from three lakes in the Philippines

The silver perch, Leiopotherapon plumbeus (Kner, 1864), is an endemic and economically important fish in the Philippines. A native species of Laguna de Bay, the silver perch was transplanted from this lake to Sampaloc Lake in the late 1950s and Taal Lake in the early 1970s. Morphological variation has been observed among the native and transplanted populations of the silver perch. In this study, genetic variation within and between the native and transplanted populations was examined using isozyme electrophoresis. Four sites were sampled: two in Laguna de Bay (Binangonan and Tanay) and one each in Sampaloc Lake and Taal Lake. Twenty-two (22) loci were scored but only one locus (PGM*) was polymorphic by the 95% criterion and only two loci (ADH* and PGM*) were polymorphic by the 99% criterion. The average heterozygosities, genetic distances and FST values of specimens from the four sites were very low, suggesting that the native and transplanted populations had very low genetic variation and that they were genetically homogeneous despite the presence of morphological varia- tion. The low genetic variation could possibly be due to a population bottleneck in the native population in Laguna de Bay in the past and to the low genetic variation of the founders in the transplanted populations

Status Assessment of Clarias Species in the Philippines: Insights from DNA Barcodes

Catfishes of the genus Clarias are important food fishes in aquaculture. In the Philippines, six species are documented but only three, namely C. batrachus, C. macrocephalus, and C. gariepinus, are found in the market today. Of these, C. macrocephalus is both native and near threatened. In this study, the cytochrome c oxidase I (COI) gene was amplified for 20 Agusan Marsh, Agusan del Sur specimens provisionally identif ied as C. macrocephalus. These specimens have a different morphology compared to other C. macrocephalus specimens previously obtained elsewhere. The COI sequences all matched the Philippine COI sequences of C. macrocephalus, thus confirming its identity. Reanalysis of barcode sequences was also conducted to resolve the conflicting claims regarding the status of some Clarias species. A total of 179 COI sequences from Clarias species present in GenBank were included in the analyses. The average intraspecif ic and interspecif ic Kimura-2-Parameter distances were 2.99% and 13.26%, respectively. There was very little sequence diversity observed in the Philippine samples of C. macrocephalus. Philippine samples of C. batrachus and C. macrocephalus formed distinct clades, while Philippine C. gariepinus specimens clustered with those of other countries, supporting the claim that the former two species are native and the latter was introduced to the country. The status of the other Clarias species in the Philippines is also discussed