Kar-Hoe Loh

Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes).

Elucidating the phylogenetic relationships of the current but problematic Dasyatidae (Order Myliobatiformes) was the first priority of the current study. Here, we studied three molecular gene markers of 43 species (COI gene), 33 species (ND2 gene) and 34 species (RAG1 gene) of stingrays to draft out the phylogenetic tree of the order. Nine character states were identified and used to confirm the molecularly constructed phylogenetic trees. Eight or more clades (at different hierarchical level) were identified for COI, ND2 and RAG1 genes in the Myliobatiformes including four clades containing members of the present Dasyatidae, thus rendering the latter non-monophyletic. The uncorrected p-distance between these four ‘Dasytidae’ clades when compared to the distance between formally known families confirmed that these four clades should be elevated to four separate families. We suggest a revision of the present classification, retaining the Dasyatidae (Dasyatis and Taeniurops species) but adding three new families namely, Neotrygonidae (Neotrygon and Taeniura species), Himanturidae (Himantura species) and Pastinachidae (Pastinachus species). Our result indicated the need to further review the classification of Dasyatis microps. By resolving the non-monophyletic problem, the suite of nine character states enables the natural classification of the Myliobatiformes into at least thirteen families based on morphology.

Three decades of sea water abstraction by Kapar power plant (Malaysia): What impacts on tropical zooplankton community?

Zooplankton samples collected before (1985-86) and after (2013-14) the establishment of Kapar power station (KPS) were examined to test the hypothesis that increased sea surface temperature (SST) and other water quality changes have altered the zooplankton community structure. Elevated SST and reduced pH were detected between before and after impact pairs, with the greatest impact at the station closest to KPS. Present PAHs and heavy metal concentrations are unlikely causal factors. Water parameter changes did not affect diversity but community structure of the zooplankton. Tolerant small crustaceans, salps and larvaceans likely benefited from elevated temperature, reduced pH and shift to a more significant microbial loop exacerbated by eutrophication, while large crustaceans were more vulnerable to such changes. It is predicted that any further rise in SST will remove more large-bodied crustacean zooplankton, the preferred food for fish larvae and other meroplankton, with grave consequences to fishery production.

Annotated checklist of eels (orders Anguilliformes and Saccopharyngiformes) from Taiwan

An annotated checklist of eels, orders Anguilliformes and Saccopharyngiformes, occurring in Taiwanese waters is presented. The checklist is the result of a series of systematic studies conducted by the authors in the past few years. The eel fauna of Taiwan is one of the richest in the world with a total of 206 species in 74 genera and 13 families in Anguilliformes and a single species in Saccopharyngiformes. The most species-rich families are the Muraenidae with 71 species, followed by the Ophichthidae with 60 species, the Congridae with 29 species, and the Synaphobranchidae with 17 species. Moreover, three genera and 42 species have been described based on at least one type specimen collected from Taiwan. Of these, 36 species are recognized as valid and 23 species are known only from Taiwanese waters at present. Historical records of all Taiwanese eel species are reviewed by examining the original descriptions and figures, vouchers, as well as the recently collected specimens, where available. This represents the first detailed checklist of eels from Taiwanese waters.

Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA)

Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy. Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features. Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study. Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The model codes can be accessed at http://mybiodiversityontologies.um.edu.my/Otolith/ and https://peerj.com/preprints/1517/. The current model has flexibility to be used for more species and families in future studies.

Assessment of heavy metal pollution in surficial sediments from a tropical river-estuary-shelf system: A case study of Kelantan River, Malaysia

To understand the source-to-sink of pollutants in the Kelantan River estuary and the adjacent shelf area in Malaysia, a total of 42 surface sediment samples were collected in the Kelantan River-estuary-shelf system to analyze for grain size, total organic carbon (TOC) content, Al and heavy metals (Cr, Ni, Cu, Zn, Cd and Pb). The surficial sediments were mainly composed of clayey silt and the TOC content in sediments decreased from the river to the shelf. The surficial sediments experienced Pb pollution; Cr only showed a certain level of pollution in the coastal area of the estuary but not in other areas, and Ni, Cu, Zn, and Cd showed no pollution. The heavy metals mainly originated from natural weathering and erosion of rocks and soils in the catchment and enriched near the river mouth. Total organic carbon can promote the enrichment of heavy metals in sediments.

Automated otolith image classification with multiple views: an evaluation on Sciaenidae

Combined multiple 2D views (proximal, anterior and ventral aspects) of the sagittal otolith are proposed here as a method to capture shape information for fish classification. Classification performance of single view compared with combined 2D views show improved classification accuracy of the latter, for nine species of Sciaenidae. The effects of shape description methods (shape indices, Procrustes analysis and elliptical Fourier analysis) on classification performance were evaluated. Procrustes analysis and elliptical Fourier analysis perform better than shape indices when single view is considered, but all perform equally well with combined views. A generic content-based image retrieval (CBIR) system that ranks dissimilarity (Procrustes distance) of otolith images was built to search query images without the need for detailed information of side (left or right), aspect (proximal or distal) and direction (positive or negative) of the otolith. Methods for the development of this automated classification system are discussed.

A new species of the worm-eel genus Neenchelys (Anguilliformes: Ophichthidae) from southern Taiwan

A new ophichthid worm-eel, Neenchelys gracilis sp. nov., is described from a specimen collected from southwestern Taiwan. It differs from its congeners by having: a minute pectoral fin, many filamentous cirri on the anterior nostril rim; a very slender body; a very small gill opening; and a vertebral formula of 30-78-200.

ADDITIONS TO THE TAIWAN EEL FAUNA WITH FIVE NEWLY RECORDED SPECIES OF MORAY EELS (ANGUILLIFORMES: MURAENIDAE), AND REDESCRIPTION OF A RARE SPECIES GYMNOTHORAX SAGMACEPHALUS

Five rare moray species: ＂Anarchias cantonensis＂ (Schultz), ＂Gymnothorax dorsalis＂ Seale, G. ＂intesi＂ (Fourmanoir and Rivaton), ＂G. phasmatodes＂ (Smith) and ＂G. sagmacephalus＂ (Bohlke) belonging to subfamilies Uropterygiinae and Muraeninae are reported for the first time off Taiwan. Diagnoses of these five species of moray eels including their fresh coloration and dentitions are provided. A redescription of ＂G. sagmacephalus＂ is provided since its description was based on the unique holotype was incomplete, especially due to its damaged tail tip. We add twelve additional specimens, give the statistics of morphological measurements and vertebral formulae for this species, and expand its geographical distribution from Japan to Taiwan.

Next generation sequencing yields the complete mitochondrial genome of the Zebra moray, Gymnomuraena zebra (Anguilliformes: Muraenidae)

Abstract In this study, the complete mitogenome sequence of the Zebra moray, Gymnomuraena zebra (Anguilliformes: Muraenidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,576 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Zebra moray is 30.2% for A, 26.8% for C, 17.2% for G, and 25.8% for T and show 80% identities to Kidako moray, Gymnothorax kidako. The complete mitogenome of the Zebra moray provides an essential and important DNA molecular data for further phylogeography and evolutionary analysis for moray eel phylogeny.

Next generation sequencing yields the complete mitochondrial genome of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae)

Abstract In this study, the complete mitogenome sequence of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae) has been sequenced by next-generation sequencing method. The length of the assembled mitogenome is 16,615 bp, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Clarion angelfish is 28.3% for A, 29.3% for C, 16.5% for G, 25.9% for T and show 85% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Clarion angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.