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Reproductive biology, length-weight relationship and diet of co-occurring butterfly rays, Gymnura poecilura and Gymnura zonura, in Malaysian waters

Leung AJ, Then AY, Loh KH

J Fish Biol, 2023 Mar;102(3):564-574.
PMID: 36504128 DOI: 10.1111/jfb.15288

Recent IUCN assessments had resulted in up listing of the status of butterfly rays due to concerns of overfishing, but inadequate biological understanding of these rays prevents meaningful conservation and management measures. Therefore, this study was undertaken to address knowledge gaps in the reproductive biology and diet of longtail butterfly ray (Gymnura poecilura) and zone tail butterfly ray (Gymnura zonura) in Malaysian waters. From surveys of landing sites and fish markets from years 2017 to 2022, size (disc width, DW), weight and maturity were recorded, and stomachs were collected from 94 G. poecilura (N = 39 females and 55 males) and 20 G. zonura (N = 10 females and 10 males) specimens. The length-weight relationships were significantly different between sexes for G. poecilura. The size at maturity (DW50) was estimated to be 476.0 mm (females), 385.0 mm (males) for G. poecilura and 442.0 mm (combined) for G. zonura. The number of embryos ranged from 1 to 6, and the embryo size was between 73.90 to 130.44 mm DW. Dietary analysis of stomach contents revealed that fish prey was dominant in both G. poecilura [94.4% Index of Relative Importance (IRI)] and G. zonura (100% IRI). Ontogenetic shift was seen in G. poecilura that fed on more variety of prey items, including shrimps, squids and crabs with an increase in body size. Both species co-occur all along coastal Malaysia although G. zonura is rarely encountered from fisheries surveys along the Strait of Malacca. Given similar habitat associations and dietary habits, G. poecilura may be able to outcompete G. zonura across their shared habitat range. The validity of G. japonica and G. micrura records in Malaysia remains questionable and requires future investigation.
Fulltext Feeding ecology and reproductive biology of small coastal sharks in Malaysian waters

Lim KC, Then AY, Loh KH

PeerJ, 2023;11:e15849.
PMID: 37637173 DOI: 10.7717/peerj.15849

Small coastal demersal sharks form a major proportion of the sharks landed in Malaysia. However, little is known about their feeding ecology and reproduction. This study sought to elucidate the dietary patterns, role of ontogeny in prey consumption, and reproductive biology of four dominant small demersal shark species in Malaysian waters: the Hasselt's bamboo shark, Chiloscyllium hasseltii; brownbanded bamboo shark, C. punctatum; spadenose shark, Scoliodon laticaudus; and Pacific spadenose shark, S. macrorhynchos. Dietary analyses revealed a high overlap in prey taxa consumed; clear resource partitioning among co-occurring species based on the percentage Prey-specific Index of Relative Importance (%PSIRI), with higher fish %PSIRI for Chiloscyllium hasseltii, higher cephalopod %PSIRI for C. punctatum, and higher crustacean %PSIRI for both Scoliodon species; and an ontogenetic diet shift, seen through changes in prey size. Based on the examination of reproductive organs, the results showed larger sizes at maturity for males compared to females for all four species; no obvious reproductive cycles, based on hepatosomatic and gonadosomatic indices for all species; female bias in the sex ratio of the embryos of Scoliodon species; and increased reproductive output (number of eggs or embryos and size of eggs) with larger female size for C. hasseltii and Scoliodon species. The partitioning of food resources minimizes direct competition for food and supports coexistence within shared coastal habitats. The reproductive strategies of these small coastal sharks appear to be favorable for supporting short-term population productivity; although a reduction in fishing pressure, especially from bottom trawlers, is essential for the long-term sustainable use of these sharks.
Fulltext First record of the dotted grouper Epinephelusepistictus (Temminck & Schlegel, 1843) (Perciformes, Serranidae) in Malaysia

Du J, Loh KH, Then AY, Zheng X, Teguh Peristiwady, Rizman-Idid M, et al.

Zookeys, 2019;861:107-118.
PMID: 31333328 DOI: 10.3897/zookeys.861.34043

Five specimens of Epinephelusepistictus (Temminck & Schlegel, 1843) were collected from a major landing site located on the west coast of Peninsula Malaysia during a fish faunal survey on 23 August 2017. The present study extends the distribution range of E.epistictus southwards from Andaman Sea to the Strait of Malacca. Species identification was confirmed by colour pattern and DNA barcoding (567 bp of cytochrome C oxidase I) of all E.epistictus specimens and nine closely related Epinephelus species. The interspecies genetic distance ranged from 0.002-0.245. This study also presents, for the first time for Malaysia, data on length-weight relationships and otolith measurements. It contributes to a better understanding of taxonomy, and phylogenetic and genetic diversity of E.epistictus.
Fulltext Cephalopod species identification using integrated analysis of machine learning and deep learning approaches

Tan HY, Goh ZY, Loh KH, Then AY, Omar H, Chang SW

PeerJ, 2021;9:e11825.
PMID: 34434645 DOI: 10.7717/peerj.11825

Background: Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images.
Methods: A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance.
Results: The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of the developed model.
Fish Ontology framework for taxonomy-based fish recognition

Ali NM, Khan HA, Then AY, Ving Ching C, Gaur M, Dhillon SK

PeerJ, 2017;5:e3811.
PMID: 28929028 DOI: 10.7717/peerj.3811

Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users.
Fulltext Brown banded bamboo shark (Chiloscyllium punctatum) shows high genetic diversity and differentiation in Malaysian waters

Lim KC, Then AY, Wee AKS, Sade A, Rumpet R, Loh KH

Sci Rep, 2021 Jul 21;11(1):14874.
PMID: 34290296 DOI: 10.1038/s41598-021-94257-7

The demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.
Fulltext A Review of Published Literature Regarding Health Issues of Coastal Communities in Sabah, Malaysia

Azzeri A, Ching GH, Jaafar H, Mohd Noor MI, Razi NA, Then AY, et al.

Int J Environ Res Public Health, 2020 Feb 27;17(5).
PMID: 32120949 DOI: 10.3390/ijerph17051533

Several of the coastal zones in Sabah, Malaysia, are isolated and inaccessible. This study aimed to review the published literature on the health status of the coastal communities in Sabah. The following four main health issues were found: (i) malaria, (ii) tuberculosis (TB), (iii) seafood poisoning, and (iv) antenatal problems. Factors associated with the risk of acquiring malarial infection in the studied coastal area were advanced age, male sex, farming as an occupation, history of travel outside the village, and rainy seasons. TB infection was primarily observed in adult men. Seafood poisoning was significantly common in Sabah. Studies have reported that tetrodotoxin and paralytic shellfish poisoning were commonly reported (30-60 cases annually). Several pregnant women in the coastal community had insufficient knowledge of the national antenatal care programme. Nonetheless, 99% of them received antenatal care at public healthcare facilities with 92% of them undergoing safe delivery. Nevertheless, a majority of the pregnant women had iodine deficiency due to low iodised salt intake. Findings from this review highlighted that the coastal communities in Sabah are experiencing significant health problems. Specific attention is required to significantly enhance the health and well-being of the individuals living in the coastal communities in Sabah.
Complete mitogenome of two moray eels of Gymnothorax formosus and Scuticaria tigrina (Anguilliformes: Muraenidae)

Loh KH, Shao KT, Chen CH, Chen HM, Then AY, Loo PL, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 Jul;27(4):2651-2.
PMID: 26029876 DOI: 10.3109/19401736.2015.1043530

In this study, the complete mitogenome sequence of two moray eels of Gymnothorax formosus and Scuticaria tigrina (Anguilliformes: Muraenidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome, with the length of 16,558 bp for G. formosus and 16,521 bp for S. tigrina, shows 78% identity to each other. Both mitogenomes follow the typical vertebrate arrangement, including 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region of D-loop. The length of D-loop is 927 bp (G. formosus) and 850 bp (S. tigrina), which is located between tRNA-Pro and tRNA-Phe. The overall GC content is 45.5% for G. formosus and 47.9% for S. tigrina. Complete mitogenomes of G. formosus and S. tigrina provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for moray eel.
Fulltext Advancing DNA Barcoding to Elucidate Elasmobranch Biodiversity in Malaysian Waters

Loh KH, Lim KC, Then AY, Adam S, Leung AJ, Hu W, et al.

Animals (Basel), 2023 Mar 09;13(6).
PMID: 36978544 DOI: 10.3390/ani13061002

The data provided in this article are partial fragments of the Cytochrome c oxidase subunit 1 mitochondrial gene (CO1) sequences of 175 tissues sampled from sharks and batoids collected from Malaysian waters, from June 2015 to June 2022. The barcoding was done randomly for six specimens from each species, so as to authenticate the code. We generated barcodes for 67 different species in 20 families and 11 orders. DNA was extracted from the tissue samples following the Chelex protocols and amplified by polymerase chain reaction (PCR) using the barcoding universal primers FishF2 and FishR2. A total of 654 base pairs (bp) of barcode CO1 gene from 175 samples were sequenced and analysed. The genetic sequences were blasted into the NCBI GenBank and Barcode of Life Data System (BOLD). A review of the blast search confirmed that there were 68 valid species of sharks and batoids that occurred in Malaysian waters. We provided the data of the COI gene mid-point rooting phylogenetic relation trees and analysed the genetic distances among infra-class and order, intra-species, inter-specific, inter-genus, inter-familiar, and inter-order. We confirmed the addition of Squalus edmundsi, Carcharhinus amboinensis, Alopias superciliosus, and Myliobatis hamlyni as new records for Malaysia. The establishment of a comprehensive CO1 database for sharks and batoids will help facilitate the rapid monitoring and assessment of elasmobranch fisheries using environmental DNA methods.