Diversity, extinction risk and conservation of Malaysian fishes

Hoven's carp Leptobarbus hoevenii strategized metabolism needs to cope with changing environment

Current water warming and freshwater acidification undoubtedly affect the life of aquatic animals especially ammonotelic teleost by altering their physiological responses. The effect of temperature (28 °C vs 32 °C) and pH (7 vs. 5) on the metabolic compromising strategies of Hoven's carp (Leptobarbus hoevenii) was investigated in this study. Fishes were conditioned to (i) 28 °C + pH 7 (N28°C); (ii) 32 °C + pH 7 (N32°C); (iii) 28 °C + pH 5 (L28°C) and (iv) 32 °C + pH 5 (L32°C) for 20 days followed by osmorespiration assay. Results showed that feeding performance of Hoven's carp was significantly depressed when exposed to low pH conditions (L28°C and L32°C). However, by exposed Hoven's carp to L32°C induced high metabolic oxygen intake and ammonia excretion to about 2x-folds higher compared to the control group. As for energy mobilization, Hoven's carp mobilized liver and muscle protein under L28°C condition. Whereas under high temperature in both pH, Hoven's carp had the tendency to reserve energy in both of liver and muscle. The findings of this study revealed that Hoven's carp is sensitive to lower water pH and high temperature, thereby they remodeled their physiological needs to cope with the environmental changes condition.

An integrative approach to assess the impact of disturbance on native fish in lakes

Freshwater fish are in a perilous state with more than 30% of species considered critically endangered. Yet significant ecological and methodological complexities constrain our ability to determine how disturbances are impacting native fish communities. We review current methods used to assess the responses of fish communities, especially native fish, to disturbances, with a focus on lakes. These methods include contemporary population surveys, manipulative experimental approaches, paleolimnological approaches and Indigenous Knowledge and social histories. We identify knowledge gaps, such as a lack of baseline data for native fish, an inability to assess the impact of historical disturbances, stressor response dynamics in contemporary multi-stressor environments, and natural disturbance regimes. Our assessment of the current methods highlights challenges to filling these knowledge gaps using the reviewed methods. We advocate strongly for the implementation of an integrative approach that combines emerging technologies (i.e. molecular-based techniques in contemporary surveys and paleolimnology) and underutilised knowledge streams (i.e. Indigenous Knowledge and social histories) which should be used in concert with conventional methods. This integrative approach will allow researchers to determine the key drivers of decline and the degree of change, which will enable more informed and successful management actions.

Impacts of tilapia aquaculture on native fish diversity at an ecologically important reservoir

Background

The Temengor Reservoir is the second largest reservoir in Peninsular Malaysia. Located in the northwestern state of Perak, it was selected to develop a large-scale tilapia (Oreochromis niloticus) aquaculture facility within the Aquaculture Industrial Zone (AIZ) in 2008 due to its favourable environmental conditions. No record of tilapia has ever been reported in the natural waters prior to this. However, a post-establishment study recorded tilapia sightings in the natural waters of this lake. The cultured tilapia was easily recognizable with the elongated mouth and body, and long caudal fin. It is postulated that these were escapees from the floating cages that had invaded the natural waters and would negatively impact the native fish species. To test our hypothesis, we investigated the impact of the aquaculture facility on native fish diversity through a spatial design.

Methods

The study was focused on assessing the impact of tilapia culture at sites nearer to the AIZ vs more distant sites, the former with a greater likelihood of receiving escapees. Two major sites were chosen; within 5 km (near-cage) and within 5-15 km (far-cage) radii from the AIZ. Fish sampling was conducted using multiple mesh sizes of gill nets (3.7, 5.1, 6.5, 7.6, and 10.2 cm) deployed at the littoral zone of the sampling points. Species diversity, abundance, dietary habits, and habitat preference were investigated.

Results

The CPUE (individual/hour) of native fish species at the far-cage site of the AIZ Reservoir was found to be significantly higher (p < 0.05) than that at the near-cage site. Principal component analysis (PCA) based on diet and habitat preferences showed that the tilapia, O. niloticus had almost overlapping diet resources and habitat with native fish species.

Conclusion

We conclude that there is a correlation between the reduced catches of native species (based on CPUE) and the high presence of tilapia. Thus, appropriate actions must be implemented for strategic and effective planning in terms of native fish conservation.

Sexual dimorphism and reproductive biology of Cephalocassis borneensis (Siluriformes: Ariidae), a paternal mouth-brooding fish in the Mekong River

Information on the reproductive biology of fish species is essential for fisheries management, conservation and culture potential assessment. Therefore, this study aimed to understand the sex-based morphological differences and reproductive characteristics of Cephalocassis borneensis, an ariid species with a rapid decline of wild populations. Fish samples were collected monthly from local fishermen (n = 1092) in the Vietnamese Mekong River over a year. Morphological analyses revealed that sexual dimorphism was observed in mature, but not immature, fish. The length at first maturity (L_m ) was smaller for males (11.5 cm) than for females (12.5 cm). Mature males had larger head length and pre-pectoral distance than mature females, increasing the space for oral incubation of fertilized eggs and larvae in males. Conversely, females were larger in three head parameters (head angle, head width and head depth) and three abdomen parameters (body deep, ventral fin length and distance between pectoral and ventral fin) involved in ovary development. Paternal mouth-brooding behaviour is an important reproductive strategy in C. borneensis to increase offspring survival. Monthly variations in gonado-somatic index and condition factor (K) and the presence of maturation stages indicated that C. borneensis spawns year-round, mainly in the rainy season from June to October. This species' fecundity was relatively low, from 10 to 31 eggs per female of quite large sizes (about 7.30 ± 0.68 mm in diameter). Besides, non-functional oocytes (hyaline eggs) of smaller size (<3 mm) were found in the females' ovaries. Low fecundity with large eggs and paternal care indicated that the species is an equilibrium strategist. These characteristics are critical in developing ariid species conservation plans, such as setting the time and mesh-size for fishing, and domestication programmes in artificial conditions.

First insight into freshwater fish assemblages in the western part of the Endau-Rompin landscape, Malaysia

In Malaysia, our knowledge of freshwater ecosystem and its aquatic inhabitants, particularly freshwater fish, remains inadequate, even in protected regions. It is essential to understand the composition of freshwater fish, their distribution along river gradients, and their interactions between environmental variables to develop and strategize effective conservation and management plans. Consequently, an investigation into freshwater fish assemblages in three rivers draining off from the western part of Endau-Rompin Landscape was conducted in 12 established substations. Sampling sessions were conducted from September to December 2021 in the Labis district of Johor, using multiple sampling methods along 200 meters for each substation. The environmental variables were measured using water quality parameters. A total of 66 species were collected. The family Cyprinidae presented the highest species diversity (17 species), constituting 52% of total capture. Crossocheilus obscurus was the most dominant species, and the highest species richness was recorded in the Segamat River (45 species), followed by Juaseh (36 species) and Labis River (34 species). It was discerned that the composition of fish varied between the substations. The knowledge presented here is the first documentation on the freshwater fish from these rivers. It would serve as a baseline information for key authorities and stakeholders to conserve the biodiversity inhabiting freshwater ecosystems in Malaysia.

Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding

Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.

Scleractinian coral (Cnidaria, Hexacorallia, Scleractinia) diversity of the Mersing Islands, Peninsular Malaysia

We present a comprehensive checklist of scleractinian (hard) corals for the Mersing Islands, Malaysia based on surveys conducted at 24 reefs across protected and unprotected marine areas. A total of 261 species of corals from 16 families and one incertae sedis (Pachyseris spp.) were recorded, along with ten records that are new for the east coast of Peninsular Malaysia. Compared against the IUCN Red List, 46.7% of coral species found in the Mersing Islands were of Least Concern (LC), 29.5% as Near Threatened (NT) and 16.4% Vulnerable (V). Only one recorded species, Pectiniamaxima (Moll & Best, 1984), was listed as Endangered (EN). Baseline species diversity data are essential for the monitoring and management of marine biodiversity, especially within marine protected areas. With both protected and unprotected coral reef areas in the vicinity of the widely scattered Mersing Islands, the diversity and distribution of coral species can be used as the basis for area-based conservation and management strategies. The diversity and abundance of scleractinian corals of each island or area should be surveyed periodically to ensure the appropriate level of protection is afforded to retain scleractinian biodiversity in this region.

Invasion Risk and Potential Impact of Alien Freshwater Fishes on Native Counterparts in Klang Valley, Malaysia

Simple Summary

The mechanisms on how alien species naturally affect the native species in the real aquatic environment are infrequently studied. This study explores the potential effects of alien fishes on the native fish community, well-being, and trophic preferences in selected rivers of Klang Valley, Malaysia. We found that alien fishes benefited from the impacts of anthropogenic activities in their surrounding habitats, while their plasticity in feeding habits might help them to invade, survive, and dominate. This study revealed the natural mechanisms on the establishment of alien fish species and their potential ecological impacts on native fishes in the rivers of Klang Valley, Malaysia.

Abstract

This study explores the potential effects of alien fishes on the native fish community, well-being, and tropic preferences in selected rivers of Klang Valley, Malaysia. Following the Aquatic Species Invasiveness Screening Kit assessment, most of the alien fishes (80%) are invasive. The alien species occurrences correlated positively (p < 0.05) with poor water quality, such as rivers with high ammonia-nitrogen and nitrite, but negatively with phosphate and dissolved oxygen. Anthropogenic characteristics, such as rivers with high pollution levels and ease of accessibility to the fish habitat, are mainly associated positively (p < 0.05) with the occurrences of alien fish species. In general, the results of fish stomach contents analyses and their associated indices, together with stable carbon and nitrogen isotopes, revealed domination by alien fishes or diet overlaps between both alien and native fish species. This finding indicates that alien fishes benefited from the impacts of the anthropogenic activities in their surrounding habitats, while their plasticity in feeding habits might help them to invade, survive, and dominate in the rivers of Klang Valley, Malaysia.

Biometric indices and population parameters of three polynemid fishes from Batang Lassa Estuary of East Malaysia

The length-weight relationships (LWRs), condition factor (Kn), growth, mortality and exploitation status of three polynemid fishes, i.e., Filimanus xanthonema (Valenciennes, 1831), Polynemus melanochir (Valenciennes, 1831) and Polynemus paradiseus (Linnaeus, 1758) from Batang Lassa River estuary were estimated. Fish samples were caught during April 2019 to September 2020 using the ESBN (locally called Gnian) having 1.25 to 4.00 cm mesh size. The total length (TL) and body weight of each individual fish was measured to the nearest 0.1 cm and 0.01 g respectively. The growth coefficients (b) for F. xanthonema, P. melanochir and P. paradiseus, were 2.880, 2.717 and 2.724 with the R² values 0.956, 0.972 and 0.936 respectively. Estimated growth coefficients indicated a negative allometric growth pattern for all three threadfin fishes. To date, information regarding length-weight relationships for F. xanthonema and P. melanochir is insufficient whereas the information is available for P. paradiseus. About 40–48% of fishes exhibited flat or thin body shape (Kn < 1), 48–50% were rounded or fat (Kn > 1) and only 1–3% of fishes showed proportional body shape (Kn = 1). The growth parameters L_∞, K and ϕ’ were estimated at 15.75 cm, 0.95 yr⁻¹ and 2.37 for F. xanthonema; 27.61 cm 0.87 yr⁻¹ and 2.82 for P. melanochir; and 27.30 cm, 0.58 yr⁻¹ and 2.64 for P. paradiseus; respectively. The estimated natural mortality (M) included 2.10, 1.69 and 1.30 yr⁻¹; the fishing mortality (F) 0.57, 0.67 and 0.60 yr⁻¹; and exploitation ratio (E) 0.21, 0.28 and 0.31 for F. xanthonema, P. melanochir and P. paradiseus respectively. The study concluded that the stocks are still under exploitation (E < 0.5) condition. However, the studied Batang Lassa estuary could be a potential nursery ground considering the minimum lengths of 5.0, 3.8 and 4.0 cm for F. xanthonema, P. melanochir and P. paradiseus respectively. Therefore, management initiatives are needed to escape juvenile catches.

DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia

The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.

Biology and ecology of sea catfish (Ariidae) of estuarine, lagoon and coastal ecosystems in West Africa

The family Ariidae, sea catfish of the order Siluriformes, is widely distributed throughout the world, particularly in tropical and subtropical areas. The three species of Ariidae found on the coasts and estuaries of West Africa are the smoothmouth catfish Carlarius heudelotii (Valenciennes 1840), the rough-head catfish Carlarius latiscutatus (Günther 1864) and the Guinean sea catfish Carlarius parkii (Günther 1864). They have been increasingly exploited by artisanal and industrial coastal fisheries in recent decades, but there is still little information available on their ecology and biology. The aim of this study was to deepen our knowledge of these three West African Ariidae species based on a dataset collected between 1980 and 2013 during experimental fishing programmes. They were carried out in Mauritania in the Banc d'Arguin National Park, in Senegal in the Sine Saloum estuary including the Bamboung Marine Protected Area (MPA), in The Gambia in the Gambia estuary, in Guinea-Bissau in the Urok Islands MPA in the Bijagos archipelago, in Guinea in the Fatala estuary and Dangara inlet, and in Côte d'Ivoire in the Ebrié Lagoon. C. latiscutatus accounted for 65%, C. parkii for 29% and C. heudelotii for 6% of total number of Ariidae sampled. C. latiscutatus was abundant in the Sine Saloum and Gambia estuaries as well as in Guinea and Guinea-Bissau and was the only species present in the Ebrié Lagoon. C. parkii was in the majority in Mauritania. The three species were recorded in a salinity range of 0 to 50, a temperature range of 19 to 34°C, in areas 1.7 to 15 m depth, and transparency ranging from 0.1 to 4 m (Secchi disk depth). C. heudelotii was present in less saline (25 vs. 32-34), less warm (27 vs. 29°C) and less transparent (0.8 m vs. 1.6 m) waters than the two other species. The maximum sizes (453 mm, 614 mm and 525 mm for, respectively, C. heudelotii, C. latiscutatus and C. parkii) were comparable to those recorded at sea. Length-weight relationships calculated for each species showed b coefficients greater than 3. Sex ratios were always in favour of females. The number of mature individuals and their smallest size at maturity were calculated per species, sex and study area. A size of 27-28 cm at first maturity was estimated for females of C. latiscutatus. A few dozen records made it possible to describe fecundity and cases of oral incubation by females. The diet of the three species was composed of crustaceans, fish and molluscs, confirming their classification as generalist predators. Thanks to their high environmental tolerance, these sea catfish populations are able to occupy both the continental shelf and adjacent estuaries throughout their life cycle, with the exception of spawning, which generally takes place at sea.

Pattern of genetic structure of the common stream fish, Neolissochilus soroides (Pisces: Cyprinidae), addresses the importance of protected areas in eastern Thailand

The well-known presence of mahseers, Neolissochilus soroides (Cyprinidae), in forested streams in eastern Thailand has attracted many visitors to protected areas for several decades. Because of its historical high abundance, this species was never considered of conservation concern. In this study, the authors revealed that mahseers are very limited to upstream areas in mountains facing the Gulf of Thailand and are now solely confined to habitats within protected areas. The fish were sampled below seven waterfalls in four national parks. All individuals were analysed using a fragment of the mitochondrial DNA cytochrome b gene and eight nuclear microsatellite DNA loci to uncover spatial genetic patterns. Cytochrome b data showed very low genetic diversity but indicated strong genetic differentiation between the most distant Klong Kaeo (KK) population and the other populations. The more variable microsatellite DNA markers showed moderate level of genetic diversity compared to other mahseers but revealed limited gene flow among all locations (overall F_ST  = 0.25, P < 0.05). In addition, significant correlation was found between genetic and geographic distances (P < 0.05). Genetic bottleneck analyses provided an insight into evolutionary history in N. soroides that may have experienced past reduction in population size. As eastern Thailand is a relatively heavily populated region, habitat modification in lowland areas is inevitable, and it will have consequences for species that prefer fast-flowing and clear water. Protected areas therefore provide valuable sanctuaries for N. soroides in headwater streams.

High environmental temperature and low pH stress alter the gill phenotypic plasticity of Hoven's carp Leptobarbus hoevenii

Climate warming and low pH environment are known to negatively impact all levels of aquatic organism from cellular to organism and population levels. For ammonotelic freshwater species, any abiotic factor fluctuation will cause disturbance to the fish, specifically at the gills which act as a multifunctional organ to support all biological processes. Therefore, this study was designed to investigate the effect of temperature (28 vs. 32°C) and pH (7.0 vs. 5.0) stress on the gill plasticity of Hoven's carp after 20 days of continuous exposure. The results demonstrated that high temperature and low pH caused severe changes on the primary and secondary lamellae as well as the cells within lamellae. An increasing trend of the proportion available for gas exchange was noticed at high temperature in both pH exposures, which resulted from a reduction of the primary lamellae width with elongated and thinner secondary lamellae compared to fishes at ambient temperature. Following exposure to high temperature and acidic pH, Hoven's carp experienced gill modifications including aneurysm, oedema, hypertrophy, curling of secondary lamellae, epithelial lifting, hyperplasia and lamellae fusion. These modifications are indicators of the coping mechanism of Hoven's carp to the changing environment in order to survive.

Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)

Benthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490-0.900, nucleotide diversity, π = 0.0010-0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118-0.216; π = 0.0004-0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.

Equilibrium reproductive strategy of the peacock bass Cichla kelberi facilitates invasion into a Neotropical reservoir

The reproductive strategy of the non-native predator cichlid Cichla kelberi was determined to explain its success after more than 60 years of being introduced into an isolated reservoir in southeastern Brazil. This was one of the first-known translocations of the genus Cichla out of its natural range. Macro- and microscopy characteristics of the gonadal development stages and the maturation phases, along with the reproductive features (size at first maturation size, gonado-somatic index and sex ratio), were described. It was hypothesized that the stable conditions of the reservoir, with low connectivity, weakly defined spatial gradient and slight seasonal changes in environmental variables, favour the equilibrium strategy that enables predators to have high offspring survivorship because of great parental investment in individual progeny. Sex ratio was well balanced, with males and females reaching first maturity between 30.0 and 28.6 cm total length (L_T ), respectively. The stages of oocyte (primary and secondary growth, vitellogenic and atresia) and spermatocyte (spermatogonia, spermatocytes, spermatids and spermatozoa) development were identified. Five phases of gonadal development (immature, developing, spawning capable, regressing and regenerating) were described for both sexes. A long reproductive season was found, with spawning peaks in August/September and, to a lesser extent, in April/May. Parental care and spawns in parcels (batch spawns) corroborated the raised equilibrium strategy that was effective in this isolated reservoir. This species developed reproductive mechanisms that fit to different environmental conditions, with multiple spawning being associated with lentic environments and asynchronous development of oocytes, which are released over long periods. The reproductive plasticity in reservoirs may be one of the main factors inherent to the successful of colonization and establishment of the peacock bass in the environments in which they were introduced.

A Semi-Analytical Optical Remote Sensing Model to Estimate Suspended Sediment and Dissolved Organic Carbon in Tropical Coastal Waters Influenced by Peatland-Draining River Discharges off Sarawak, Borneo

Coastal water quality degradation is a global challenge. Marine pollution due to suspended sediments and dissolved matter impacts water colour, biogeochemistry, benthic habitats and eventually human populations that depend on marine resources. In Sarawak (Malaysian Borneo), peatland-draining river discharges containing suspended sediments and dissolved organic carbon influence coastal water quality at multiple locations along the coast. Optical remote sensing is an effective tool to monitor coastal waters over large areas and across remote geographic locations. However, the lack of regional optical measurements and inversion models limits the use of remote sensing observations for water quality monitoring in Sarawak. To overcome this limitation, we have (1) compiled a regional spectral optical library for Sarawak coastal waters, (2) developed a new semi-analytical remote sensing model to estimate suspended sediment and dissolved organic carbon in coastal waters, and (3) demonstrated the application of our remote sensing inversion model on satellite data over Sarawak. Bio-optical data analysis revealed that there is a clear spatial variability in the inherent optical properties of particulate and dissolved matter in Sarawak. Our optical inversion model coupled with the Sarawak spectral optical library performed well in retrieving suspended sediment (bias = 3% and MAE = 5%) and dissolved organic carbon (bias = 3% and MAE = 8%) concentrations. Demonstration products using MODIS Aqua data clearly showed the influence of large rivers such as the Rajang and Lupar in discharging suspended sediments and dissolved organic carbon into coastal waters. The bio-optical parameterisation, optical model, and remote sensing inversion approach detailed here can now help improve monitoring and management of coastal water quality in Sarawak.

Species composition and invasion risks of alien ornamental freshwater fishes from pet stores in Klang Valley, Malaysia

The ornamental fish trade has been considered as one of the most important routes of invasive alien fish introduction into native freshwater ecosystems. Therefore, the species composition and invasion risks of fish species from 60 freshwater fish pet stores in Klang Valley, Malaysia were studied. A checklist of taxa belonging to 18 orders, 53 families, and 251 species of alien fishes was documented. Fish Invasiveness Screening Test (FIST) showed that seven (30.43%), eight (34.78%) and eight (34.78%) species were considered to be high, medium and low invasion risks, respectively. After the calibration of the Fish Invasiveness Screening Kit (FISK) v2 using the Receiver Operating Characteristics, a threshold value of 17 for distinguishing between invasive and non-invasive fishes was identified. As a result, nine species (39.13%) were of high invasion risk. In this study, we found that non-native fishes dominated (85.66%) the freshwater ornamental trade in Klang Valley, while FISK is a more robust tool in assessing the risk of invasion, and for the most part, its outcome was commensurate with FIST. This study, for the first time, revealed the number of high-risk ornamental fish species that give an awareness of possible future invasion if unmonitored in Klang Valley, Malaysia.

Comparative genetic stock structure in three species of commercially exploited Indo-Malay Carangidae (Teleosteii, Perciformes)

We examine genetic structuring in three commercially important species of the teleost family Carangidae from Malaysian waters: yellowtail scad Atule mate, bigeye scad Selar crumenophthalmus and yellowstripe scad Selaroides leptolepis, from the Indo-Malay Archipelago. In view of their distribution across contrasting habitats, we tested the hypothesis that pelagic species display less genetic divergence compared with demersal species, due to their potential to undertake long-distance migrations in oceanic waters. To evaluate population genetic structure, we sequenced two mitochondrial (mt)DNA [650 bp of cytochrome oxidase I (coI), 450 bp of control region (CR)] and one nuclear gene (910 bp of rag1) in each species. One hundred and eighty samples from four geographical regions within the Indo-Malay Archipelago including a population of yellowtail from Kuwait were examined. Findings revealed that the extent of genetic structuring among populations in the semi-pelagic and pelagic, yellowtail and bigeye were lower than demersal yellowstripe, consistent with the hypothesis that pelagic species display less genetic divergence compared with demersal species. The yellowtail phylogeny identified three distinct clades with bootstrap values of 86%-99% in mtDNA and 63%-67% in rag1. However, in bigeye, three clades were also observed from mtDNA data while only one clade was identified in rag1 dataset. In yellowstripe, the mtDNA tree was split into three closely related clades and two clades in rag1 tree with bootstraps value of 73%-99% and 56% respectively. However, no geographic structure appears in both mtDNA and rag1 datasets. Hierarchical molecular variance analysis (AMOVA), pair wise F_ST comparisons and the nearest-neighbour statistic (S_nn ) showed significant genetic differences among Kuwait and Indo-Malay yellowtail. Within the Indo-Malay Archipelago itself, two distinct mitochondrial lineages were detected in yellowtail suggesting potential cryptic species. Findings suggests varying degrees of genetic structuring, key information relevant to management of exploited stocks, though more rapidly evolving genetic markers should be used in future to better delimit the nature and dynamics of putative stock boundaries.

First development of the Malaysian River Integrity Index (MyRII) based on biological, chemical and physical multi-metrics

Anthropogenic pressures are causing substantial degradation to the freshwater ecosystems globally and Malaysia has not escaped such a bleak scenario. Prompted by the predicament, this study's objective was to pioneer a river assessment system that can be readily adopted to monitor, manage and drive improvement in a wholesome manner. Three sets of a priori metrics were selected to form the Ichthyofaunal Quality Index (IQI: biological), Water Quality Index (WQI: chemical) and River Physical Quality Index (RPQI: physical). These indices were further integrated on equal weighting to construct a novel Malaysian River Integrity Index (MyRII). To test its robustness, the MyRII protocol was field tested in four eco-hydrological zones located in the Kampar River water basin for 18 months to reveal its strengths, weaknesses, and establish the "excellent", "good", "average", "poor" and "impaired" thresholds based on the "best performer" reference site in an empirical manner. The resultant MyRII showed a clear trend that corresponded with different levels of river impairment. Test site zone A which was a reference site with minimal disturbance achieved the highest MyRII (88.95 ± 4.29), followed by partially disturbed zone B (61.95 ± 5.90) and heavily disturbed zone C (50.00 ± 4.29). However, the MyRII in zone D (59.9 ± 6.39), which was a heavily disturbed wetland that was disjointed from the river, did not conform to such trend. Also unveiled and recognized, however, are some unexpected nuances, limitations and challenges that emerged from this study. These are critically discussed as precautions when interpreting and implementing the MyRII protocol. This study adds to the mounting body of evidence that water resource stakeholders and policymakers must look at the big picture and adopt the "balanced ecosystem" mind-set when assessing, restoring and managing the rivers as a freshwater resource.

Using DNA Barcodes to Aid the Identification of Larval Fishes in Tropical Estuarine Waters (Malacca Straits, Malaysia)

Larval descriptions of tropical marine and coastal fishes are very few, and this taxonomic problem is further exacerbated by the high diversity of fish species in these waters. Nonetheless, accurate larval identification in ecological and early life history studies of larval fishes is crucial for fishery management and habitat protection. The present study aimed to evaluate the usefulness of DNA barcodes to support larval fish identification since conventional dichotomous keys based on morphological traits are not efficient due to the lack of larval traits and the rapid morphological changes during ontogeny. Our molecular analysis uncovered a total of 48 taxa (21 families) from the larval samples collected from the Klang Strait waters encompassing both spawning and nursery grounds of marine and estuarine fishes. Thirty-two (67%) of the larval taxa were identified at the species level, two taxa (4%) at the genus level, and 14 taxa (29%) at family level. The relatively low rate of species-level identification is not necessarily due to the DNA barcoding method per se, but a general lack of reference sequences for speciose and non- commercial fish families such as Gobiidae, Blenniidae, and Callionymidae. Larval morphology remains important in species diagnoses when molecular matches are ambiguous. A lower ethanol percentage (50%) for larva preservation is also useful to keep the body of larvae intact for morphological identification, and to preserve DNA for subsequent molecular analyses. The 10% Chelex resin used to extract DNA is also cost- effective for long term monitoring of larval fishes. Hence, the DNA barcoding method is an effective and easy way to aid the identification of estuarine larval fishes at the species level.

First record of the dotted grouper Epinephelusepistictus (Temminck & Schlegel, 1843) (Perciformes, Serranidae) in Malaysia

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.

Fish Assemblages, Growth Pattern and Environmental Factors in Upper Baleh River, Kapit, Sarawak

A survey of the freshwater fish composition in the upper Baleh River, Sarawak was conducted in 2015. A total of 1,538 specimens, comprising 45 species from nine families were collected using electrofishing devices and cast nets. The family Cyprinidae was the most dominant (62.9%) as well as diverse (42.2%) family, followed by the Balitoridae (31.0%; 31.1%) in the river. The three most dominant species were Tor tambra (18.1%), Lobocheilos ovalis (12.9%), and Parhomaloptera microstoma (11.3%). Shannon’s diversity index, Margalef’s richness index, and Pielou’s evenness index were 2.9, 6.0, and 0.8, respectively, an indication of moderate species diversity. Canonical Correspondence Analysis demonstrate that elevation, stream order and sedimentation were the most significant factors related to fish assemblages in the river, particularly for members of the families Cyprinidae and Balitoridae. The coefficient ‘n’ value in length-weight relationship for T. tambra, L. ovalis, and P. microstoma were determined as 2.92, 2.72, and 3.15, respectively. T. tambra and L. ovalis exhibited a negative allometric growth pattern which could be due to food competition whereas P. microstoma exhibited a positive allometric growth pattern as mountainous forest stream habitat offers favourable environmental conditions. The Fulton’s condition factor of each species indicates that T. tambra and L. ovalis were in poor condition, whereas P. microstoma was in extremely poor condition. It is hypothesized that environmental degradation caused by logging activities have affected the health of the most dominant fish species in the upper Baleh River. Further study should be conducted to determine the underlying factors that are affecting the fish diversity.

DNA barcoding of Malaysian commercial snapper reveals an unrecognized species of the yellow-lined Lutjanus (Pisces:Lutjanidae)

Management of wild fisheries resources requires accurate knowledge on which species are being routinely exploited, but it can be hard to identify fishes to species level, especially in speciose fish groups where colour patterns vary with age. Snappers of the genus Lutjanus represent one such group, where fishes can be hard to identify and as a result fisheries statistics fail to capture species-level taxonomic information. This study employs traditional morphological and DNA barcoding approaches to identify adult and juvenile Lutjanus species harvested in Malaysian waters. Our results reveal a suite of species that differs markedly from those that have previously been considered important in the Malaysian wild-capture fishery and show that official fisheries statistics do not relate to exploitation at the species level. Furthermore, DNA barcoding uncovered two divergent groups of bigeye snapper ('Lutjanus lutjanus') distributed on either side of the Malay Peninsula, displaying a biogeographical pattern similar to distributions observed for many co-occurring reef-distributed fish groups. One of these bigeye snapper groups almost certainly represents an unrecognized species in need of taxonomic description. The study demonstrates the utility of DNA barcoding in uncovering overlooked diversity and for assessing species catch composition in a complicated but economically important taxonomic group.

Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding

Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.

A review of length-weight relationships of freshwater fishes in Malaysia

This manuscript reviews the length-weight relationships (LWRs) of freshwater fishes in Malaysia. A total of 102 LWRs of fishes gathered from literature pertaining to 64 freshwater fish species were analysed. A meta-analysis from 13 previous reports showed that the b values was ranged from 2.19 (Clarias batrachus) to 4.106 (Barbodes binotatus). Out of 64 observed species, 47 species (11 families) experienced positive allometric growth, while another 23 species (eight families) and 31 species (12 families) were recorded under isometric and negative allometric growth, respectively. The fish LWRs observed can be used as an indicator of environmental changes and fish ecological health for freshwater fishes in Malaysia.

Fish Ontology framework for taxonomy-based fish recognition

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.

Fish Composition and Diversity in Perak, Galas and Kelantan Rivers (Malaysia) after the Major Flood of 2014

Fish from three major rivers, namely the Kelantan River (KR) and the Galas River (GR) in Kelantan, and the Perak River (PR) in Perak, Malaysia, were caught using gill nets with different mesh sizes, cast nets, and the electroshock method. There were 14 fishes representing five families and five fish species were collected from the Kelantan systems in February 2015. While the Galas system holds more fish, 48 individual fishes comprising of four families and 10 fish species were found there. A total of 213 fish specimens representing 10 families and 22 species were captured in PR in May 2015. For diversity index, PR had the highest value due to the catchment area and the environmental condition: Shannon-Weiner index (H’) (2.54), Species Evenness (J’) (0.73) and Simpson’s Dominance (D’) (8.93), compared to GR (H’) (2.09) (J’) (0.603) (D’) (6.52) and KR (H’) (1.62) (J’) (0.47) (D’) (5.62).

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.

Diverse and abundant multi-drug resistant E. coli in Matang mangrove estuaries, Malaysia

E.coli, an important vector distributing antimicrobial resistance in the environment, was found to be multi-drug resistant, abundant, and genetically diverse in the Matang mangrove estuaries, Malaysia. One-third (34%) of the estuarine E. coli was multi-drug resistant. The highest antibiotic resistance prevalence was observed for aminoglycosides (83%) and beta-lactams (37%). Phylogenetic groups A and B1, being the most predominant E. coli, demonstrated the highest antibiotic resistant level and prevalence of integrons (integron I, 21%; integron II, 3%). Detection of phylogenetic group B23 downstream of fishing villages indicates human fecal contamination as a source of E. coli pollution. Enteroaggregative E. coli (1%) were also detected immediately downstream of the fishing village. The results indicated multi-drug resistance among E. coli circulating in Matang estuaries, which could be reflective of anthropogenic activities and aggravated by bacterial and antibiotic discharges from village lack of a sewerage system, aquaculture farms and upstream animal husbandry.

Variation in fatty acid composition of the bigeye snapper Lutjanus lutjanus collected in coral reef habitats of the Malaysian South China Sea

Background

In order to understand trophic ecology, habitat use and migration of coral reef fish, fatty acid composition and levels were examined in the bigeye snapper Lutjanus lutjanus collected in the Malaysian South China Sea.

Results

Proportions of saturated fatty acids (SAFA) ranged from 55.0% to 66.5%, with the highest proportions in fatty acids, the second highest was monounsaturated fatty acids (MUFA) ranged from 30.7% to 40.2% while the proportion of polyunsaturated fatty acids (PUFA) was the lowest ranged from 2.8% to 4.8%. Palmitic acid (16:0) was the most common in SAFA, oleic acid (C18:1ω9c) was the dominant in MUFA and linolenic acid (C18:3n3) showed the highest value in PUFA. Fatty acid concentrations, especially in SAFA and MUFA, increased with fish growth, suggesting diet and habitat shifts during the fish life history. Most of the fish had more than 1 of EPA: DHA ratio, which suggested that diets of L. lutjanus tended to be higher trophic organisms such as zooplankton and crustacean in coral ecosystem.

Conclusions

The diet shift revealed by the composition and levels of the fatty acid profile revealed potential pattern in the habitat use and migration scale in coral reef environment of L. lutjanus.

Fatty acid composition indicating diverse habitat use in coral reef fishes in the Malaysian South China Sea

Background

In order to understand feeding ecology and habitat use of coral reef fish, fatty acid composition was examined in five coral reef fishes, Thalassoma lunare, Lutjanus lutjanus, Abudefduf bengalensis, Scarus rivulatus and Scolopsis affinis collected in the Bidong Island of Malaysian South China Sea.

Results

Proportions of saturated fatty acids (SAFA) ranged 57.2% 74.2%, with the highest proportions in fatty acids, the second highest was monounsaturated fatty acids (MUFA) ranged from 21.4% to 39.0% and the proportion of polyunsaturated fatty acids (PUFA) was the lowest ranged from 2.8% to 14.1%. Each fatty acid composition differed among fishes, suggesting diverse feeding ecology, habitat use and migration during the fishes’ life history in the coral reef habitats.

Conclusions

Diets of the coral fish species might vary among species in spite of that each species are living sympatrically. Differences in fatty acid profiles might not just be considered with respect to the diets, but might be based on the habitat and migration.

Detection of multiple potentially pathogenic bacteria in Matang mangrove estuaries, Malaysia

The deltaic estuarine system of the Matang Mangrove Forest Reserve of Malaysia is a site where several human settlements and brackish water aquaculture have been established. Here, we evaluated the level of fecal indicator bacteria (FIB) and the presence of potentially pathogenic bacteria in the surface water and sediments. Higher levels of FIB were detected at downstream sampling sites from the fishing village, indicating it as a possible source of anthropogenic pollution to the estuary. Enterococci levels in the estuarine sediments were higher than in the surface water, while total coliforms and E. coli in the estuarine sediments were not detected in all samples. Also, various types of potentially pathogenic bacteria, including Klebsiella pneumoniae, Serratia marcescens and Enterobacter cloacae were isolated. The results indicate that the Matang estuarine system is contaminated with various types of potential human bacterial pathogens which might pose a health risk to the public.