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Glass‐perchlets of the genus Ambassis (Teleostei; Ambassidae) form an important component of the brackish and marine coastal fish communities of tropical Asia. However, their species‐level diversity is still poorly documented because of the absence of recent taxonomic revisions in this region and the limited availability of specimens for research. In addition, long‐standing taxonomic and nomenclatural issues complicate the studies of this genus. Herein, we examine the diversity of Ambassis in Peninsular Malaysia using an integrative taxonomic approach and a large set of recently collected specimens from this region. Our initial morphological observations of 260 specimens revealed the presence of eight species, identified as Ambassis dussumieri, Ambassis interrupta, Ambassis kopsii, Ambassis macracanthus, Ambassis nalua, Ambassis octava, Ambassis urotaenia and Ambassis vachellii. We then sequenced the barcode fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene for 122 of our specimens, representing all eight morpho‐species. Automatic species delimitation methods recovered nine Molecular Operational Taxonomic Units (MOTUs) because A. interrupta is made of two MOTUs. Morphological re‐examination within A. interrupta detected variation at one character, congruent with molecular delimitation. Overall, our integrative approach unveiled rich species‐level diversity within the genus Ambassis in Peninsular Malaysia, with the presence of nine species. Further comparisons between our COI dataset and the COI sequences archived in the Barcode of Life Data System (BOLD) from specimens of Ambassis broadly collected in tropical Asian regions, indicated regional‐scale hidden diversity and identification conflicts, triggering the need for a complete taxonomic revision of this genus. [ABSTRACT FROM AUTHOR]

Ambassis octava sp. nov. (Teleostei: Ambassidae) is described on the basis of eight specimens collected from the west and east coasts of Peninsular Malaysia. The new species closely resembles Ambassis nalua (Hamilton 1822), both species having body about twice as long as deep, continuous lateral line, no nasal spine and two transverse scale rows on cheek. However, the new species is distinguishable from A. nalua by having second anal-fin ray shorter than third one (vs. equal or longer), 15–17 gill rakers on lower limb of first branchial arch (vs. 19–21), more predorsal scale count (13 or 14) (vs. 11 or 12, modally 12), and interopercle lower margin and preorbital ridge smooth (vs. serrate). In addition, A. nalua and the new species are separated by 14.5% mean uncorrected p-distance in the mitochondrial cytochrome oxidase subunit I (COI) gene. The description of A. octava is only the second description of a new species of Ambassis in Southeast Asia in the last 100 years. [ABSTRACT FROM AUTHOR]

The taxonomic diversity of penaeid shrimps from the northwest coast of Peninsular Malaysia was investigated based on morphometric and molecular approaches. For geometric morphometrics (GM) approach, eighteen homologous landmarks were analyzed with principal component analysis (PCA) and canonical variate analysis (CVA) in Morpho J software. The morphological variations among species were attributed to body shape, rostrum, carapace head, and telson. The first four components accounted for 87.27% in the PCA, while for CVA, the first three components contributed to 78.47%. Although not absolute, there is a tendency for closely related species to cluster together. The CVA analyses clearly differentiated Metapenaeopsis stridulans, Megokris sedili, Metapenaeus brevicornis and Mierspenaeopsis sculptilis into discrete clusters, and highlighted the closeness of the groups; Mierspenaeopsis sculptilis - M. hardwickii, Penaeus merguiensis - P. semisulcatus, Metapenaeus affinis - M. dobsoni - M. ensis, and Penaeus monodon - P. pulchricaudatus. Molecular phylogeny among these species of penaeid shrimp were examined using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Geometric morphometric analyses revealed shape overlap among the 12 shrimp species, yet significant differences were also detected. The morphometric and molecular multispecies analyses were largely in agreement. The phylogenetic signal was assessed by mapping the morphometric data onto three phylogenetic trees (Neighbour Joining-NJ, Maximum Likelihood-ML, and Bayesian Inference-BI) generated from the partial mitochondrial COI on the same 12 species. Results revealed non-significance (no phylogenetic signal) for NJ but significant phylogenetic signals (evolutionary significance) for ML and BI, suggesting that the shape difference among the penaeid shrimp species investigated was related to their evolutionary history. The NJ tree is prone to errors when dealing with deeper divergence times, whereas ML and BI trees are ideal for phylogeny tree reconstruction, which applies a model of sequence evolution on the data. [ABSTRACT FROM AUTHOR]

Next-generation DNA sequencing (NGS) technology advancements provide new insight into the level of variation in killer immunoglobulin-like receptor (KIR) genes. High resolution allele genotyping of seven KIR genes was conducted among 94 unrelated Malay and Orang Asli (OA) individuals of Peninsular Malaysia. A manual bioinformatics analysis is performed and optimised by Sanger sequencing method. The Malays expressed a total of 22 alleles, as compared to only 15 alleles in the OA population. In total, 12 centromeric and 9 telomeric allelic haplotypes were identified in the Malays, whereas 8 centromeric and 5 telomeric allelic haplotypes were identified in the OA. The KIR2DL1 , KIR2DL3 , and KIR2DS4 genes exhibited a high degree of variation and balanced distribution in the Malay and OA populations. On the other hand, KIR2DL4 , KIR3DL1, KIR3DL2 and KIR3DL3 genes exhibited a high degree of conservation, with less number of alleles identified and the dominance of a single allele at high frequency. High-resolution KIR allele genotyping has revealed unique sequence variations and allelic haplotypes between individuals and populations. The distributions of KIR alleles and haplotypes are useful for genetic population studies and serve as a baseline for future transplantation matching and disease association research. [ABSTRACT FROM AUTHOR]

The island of Penang lying off the northwestern coast of Peninsular Malaysia, is one of the historical places for ichthyological exploration in Southeast Asia and the type locality of three freshwater species and one euryhaline species. Freshwater ecosystems on the island are currently threatened by multiple causes. To facilitate further environmental-oriented monitoring actions, we reexamined the fish diversity by surveying several freshwater localities across the island. All collected specimens were vouchered, morphologically identified and then genetically characterized using the "Barcode" fragment of the cytochrome oxidase I gene. We collected a total of 52 fish species, including 37 (21 native + 16 introduced) strictly-adapted freshwater species. Five native and 10 introduced species represent new records for the island. Genetic analyses revealed low cryptic diversity within morphologically identified species. Combining our results with those of previous surveys, a total of 63 fish species are now known from Penang freshwaters, however, five native species were not collected in the last 60 years and their conservation status is certainly at risk on the island. Overall, the presence of many introduced species along with the general degradation of freshwater habitats of Penang Island threaten its native fish diversity. [ABSTRACT FROM AUTHOR]

Objectives: Killer cell immunoglobulin‐like receptor (KIR) genes with high polymorphism at genotypic levels are important in providing immune defense and have been expanded towards human population genetics. The aim of this study is to provide supporting information from this new biomarker to strengthen the comprehension of genetic history of the complex Malay population. Methods: KIR genotyping for 213 unadmixed Malay individuals from six subethnic groups (Acheh, Bugis, Champa, Mandailing, Minang and Kedah) was carried out using PCR‐SSP (sequence specific primers) method in 16 independent reactions. Results: The most frequent KIR genotype observed is AA1, followed by AB4 and AB5. Five genotypes; AA1, AB4, AB5, AB7 and AB8 were shared among all Malay subethnic groups. The highest frequency of KIR haplotype A was observed in Minang Malays, whereas Acheh and Kedah Malays carry a balanced distribution of A and B KIR haplotypes. PCA for the KIR genes clearly illustrated six ethnogeographical population clusters; Africans, Amerindian, Northeast Asian, South Asian, Oceania and Southeast Asian populations. All six Malay subethnic groups fell within the Southeast Asian cluster. Conclusions: The complex array of KIR genotypes observed in the Malays indicates their historical interactions with various populations, especially with the Chinese, Indians and Orang Asli. This study has demonstrated the potential of KIR genes as a genetic marker for deducing population structure and genetic relationship between populations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The Asian elephant has been listed as an endangered species on the International Union for Conservation of Nature Red List since 1986. In Peninsular Malaysia, the elephant population continues to decline, threatened by habitat degradation. Distinguishing their potential habitats is important in mitigating the impacts of forest fragmentation. This study aimed to predict the potential habitats of elephants in the fragmented forest landscape of Ulu Jelai Forest Reserve and to identify its characteristics. Habitat suitability was evaluated using several environmental variables––elevation, slope, land use, lithology, distance to river and distance from urban areas. The results showed that the distribution of suitable habitats mainly occurred in the eastern region of the study area. Elephant habitat prediction, using maximum entropy modelling, indicated that their most suitable habitat was located in a forested area that was greatly influenced by altitude and river proximity, while urban and agricultural areas cause forest fragmentation and restricted suitability. The prediction of wildlife habitats using maximum entropy modelling is a favourable and effective tool for improving the management and conservation planning of wildlife in the region. [ABSTRACT FROM AUTHOR]

The taxonomic status of the Southeast Asian spotted barb, Barbodes binotatus (Teleostei: Cyprinidae), has puzzled researchers because of large but inconsistent geographic variation of its body melanin marking pattern. In this study, the authors appraise the differentiation of B. binotatus and two closely related species, Barbodes rhombeus and saddle barb, Barbodes banksi, in Peninsular Malaysia using mitochondrial and nuclear markers. The results of this study reveal that the Peninsular Malaysia populations of each of the three species form largely reciprocal monophyletic lineages that differ from each other by a minimum of 2.3% p‐genetic distance using COI gene. Nonetheless, specimens of B. binotatus in Peninsular Malaysia are only distantly related to specimens of B. binotatus in Java (type locality). The monophyly of B. banksi is not refuted although specimens of Peninsular Malaysia are genetically distinct from those of Sarawak (type locality). The authors discuss alternative hypotheses whether each of these three valid species is a single species or each of the main five genetic lineages revealed in this study represents a distinct species. Preliminary investigations reveal a mito‐nuclear discordance at one locality in Peninsular Malaysia where B. binotatus and B. banksi co‐occur. Further studies should inform on the extent of reproductive porousness between these two lineages and others. [ABSTRACT FROM AUTHOR]

This study is focused on Bachok Marine Research Station (BMRS) which is exposed to different scales of meteorological condition during the northeast (NE) and southwest (SW) monsoons. BMRS experiences both synoptic and land–sea breeze events during the NE monsoon, but only the land–sea breezes are dominant during the SW monsoon. Two case studies were investigated in which the first case study (CS1) was conducted from 25 to 27 January 2016 while the second one (CS2) from 3 to 5 June 2016. BMRS experienced strong synoptic effect during CS1 with strong northeasterly winds (wind speed > 10 ms−1) up to an altitude of 2500 m and vertical thermal gradient only up to 600 m. Using Concentrated Weighted Trajectory (CWT) analysis, BMRS was shown to be influenced by the regional sources of pollutants originated from the central region of China and areas along coastal Vietnam during CS1. Meanwhile, CS2 was associated with daily land–sea breeze event, strong diurnal effect and closely linked to the local source of pollutants from areas along the east coast of Peninsular Malaysia. The concentrations of PM10 and PM2.5 were two times higher when offshore winds dominated BMRS, suggesting its great relation to the local emissions. Overall, BMRS presents a valuable opportunity to study the influence of regional and local atmospheric flows to the variabilities of air pollutants, thus enabling better understanding and providing a key reference to formulate effective pollution abatement strategies. [ABSTRACT FROM AUTHOR]

Severe rainfall events are common in western Peninsular Malaysia. They are usually short and intense, and occasionally cause flash floods and landslides. Forecasting these local events is difficult and understanding the mechanisms of the rainfall events is vital for the advancement of tropical weather forecasting. This study investigates the mechanisms responsible for a local heavy rainfall event on 2 May 2012 that caused flash floods and landslides using both observations and simulations with the limited-area high-resolution Met Office Unified Model (MetUM). Results suggest that previous day rainfalls over Peninsular Malaysia and Sumatra Island influenced the development of overnight rainfall over the Strait of Malacca by low-level flow convergence. Afternoon convection over the Titiwangsa Mountains over Peninsular Malaysia then induced rainfall development and the combination of these two events influenced the development of severe convective storm over western Peninsular Malaysia. Additionally, anomalously strong low-level northwesterlies also contributed to this event. Sensitivity studies were carried out to investigate the influence of the local orography on this event. Flattened Peninsular Malaysia orography causes a lack of rainfall over the central part of Peninsular Malaysia and Sumatra Island and produces a weaker overnight rainfall over the Strait of Malacca. By removing Sumatra Island in the final experiment, the western and inland parts of Peninsular Malaysia would receive more rainfall, as this region is more influenced by the westerly wind from the Indian Ocean. These results suggest the importance of the interaction between landmasses, orography, low-level flow, and the diurnal cycle on the development of heavy rainfall events. [ABSTRACT FROM AUTHOR]

We evaluated genetic differentiation among ten presumed Japanese threadfin bream,Nemipterus japonicuspopulations along the coast of Peninsular Malaysia based on the partial sequence of the mitochondrial cytochromebgene (982 bp). Genetic divergences (Kimura-2 parameter) ranged from 0.5% to 0.8% among nine of the ten populations while these nine populations were 4.4% to 4.6% diverged from the Kuala Besar population located at the Northeast coast. The constructed Neighbour Joining (NJ) phylogenetic trees based on haplotypes showed the Kuala Besar population forming an isolated cluster. The Analysis of Molecular Variance (AMOVA) of the ten populationsa prioriassigned into four regions, revealed that most of the variation occurred within population with a fairly low but significant level of regional differentiation (FST = 0.07,p < 0.05, FSC = 0.00,p > 0.05 and FCT = 0.07,p < 0.05) attributed to the Kuala Besar population.pValue after Bonferroni correction revealed that only pairwise FSTvalues involving the Kuala Besar population with the other nine populations were significant. Thus, this study revealed that theN. japonicuspopulations off Peninsular Malaysia were panmictic. However, the Kuala Besar population, although morphologically identical was composed of a genetically discrete taxon from the rest. These findings are important contributions in formulating sustainable fishery management policies for this important fishery in Peninsular Malaysia. [ABSTRACT FROM AUTHOR]

Fossil fuels comprise 93% of Malaysia's electricity generation and account for 36% of the country's 2010 Greenhouse Gas (GHG) emissions. The government has targeted the installation of 330 MW of biomass electricity generation capacity by 2015 to avoid 1.3 Mt of CO2 emissions annually and offset some emissions due to increased coal use. One biomass option is to co-fire with coal, which can result in reduced GHG emissions, coal use, and costs of electricity. A linear optimization cost model was developed using seven types of biomass residues for Peninsular Malaysia. Results suggest that about 12 Mt/year of residues are available annually, of which oil-palm residues contribute 77%, and rice and logging residues comprise 17%. While minimizing the cost of biomass and biomass residue transport, co-firing at four existing coal plants in Peninsular Malaysia could meet the 330 MW biomass electricity target and reduce costs by about $24 million per year compared to coal use alone and reduces GHG emissions by 1.9 Mt of CO2. Maximizing emissions reduction for biomass co-firing results in 17 Mt of CO2 reductions at a cost of $23/t of CO2 reduced. [ABSTRACT FROM AUTHOR]

Fish parasites such as Caligus clemensi are a serious concern for cultured fish in many regions of the world, including Malaysia. This study was designed to elucidate the parasites' prevalence and intensity coupled with the morphology and molecular identification of C. clemensi on cultured Lutjanus erythropterus in Jerejak Island, Penang, Peninsular Malaysia. The study was carried out on 200 fish specimens of cultured L. erythropterus obtained from the GST group aquaculture farm. Parasites were collected from the infested part of L. erythropterus fish, and their prevalence and intensity were determined. The parasites were identified morphologically using a field emission scanning electron microscope. Molecular studies were performed through PCR amplification and sequencing. MEGA 5 was used to construct a phylogenetic tree using the pairwise distance method. The results showed that only the C. clemensi parasite was found prevalent on L. erythropterus fish with a prevalence and mean intensity (S.D) of 198 (99%) and 36.4 ± 12.2, respectively. The prevalence varied significantly with respect to fish length (p < 0.05). The nucleotide BLAST sequence for 18S ribosomal RNA partial sequences showed 97% with 100% query similarity, E-value 0 with C. clemensi with the accession number DQ123833.1. Conclusively, C. clemensi remains a major parasite of L. erythropterus in the study area. [ABSTRACT FROM AUTHOR]

• Genetic diversity of wild Clarias macrocephalus populations were higher in the Mekong Delta than in Peninsular Malaysia. • No evidence of recent bottleneck events among all populations suggesting the wild populations were at healthy conditions at present. • Translocation of the catfish could have occurred as evidenced by movement of immigrants from the Mekong Delta to Peninsular Malaysia. • Deviation from HWE and homozygous excess in Peninsular Malaysia populations could be consequence of inbreeding. The tropical freshwater bighead catfish Clarias macrocephalus is widely distributed in Southeast Asia and is economically important in both the aquaculture and fisheries industries. In the current study, eight polymorphic microsatellite markers were employed to evaluate the genetic variation of 15 C. macrocephalus populations from Peninsular Malaysia, and the Mekong Delta populations of Cambodia and Vietnam. Overall, the number of alleles in C. macrocephalus populations ranged from 1 to 25 alleles. In general, genetic diversity was higher in the mainland populations (Cambodia, H E = 0.761 to 0.813 and Vietnam, H E = 0.759 to 0.789 with mean number of alleles of 10.13–13.88) compared to Peninsular Malaysia (H E = 0.519 to 0.699 with mean number of alleles of 4.5–10.75). High linkage disequilibrium and deviation from HWE suggest inbreeding in most Peninsular Malaysia populations which was also reflected by significant F IS values (0.217 to 0.410, p < 0.05). All pairwise F ST (p < 0.05) values were significant. No evidence of bottlenecks was detected among all populations. The 15 populations formed two evolutionary units; Peninsular Malaysia versus the Mekong Delta-Cambodia and Vietnam. The findings from this study will serve as a reference for a systematic aquaculture programme and the conservation and management of wild populations of C. macrocephalus. [ABSTRACT FROM AUTHOR]

The earliest settlers in Peninsular Malaysia are the Orang Asli population, namely Semang, Senoi and Proto Malays. In the present study, we typed the HLA-A, -B and -DRB1 loci of the Kensiu and Semai Orang Asli sub-groups. Sequence-based HLA typing was performed on 59 individuals from two Orang Asli sub-groups. A total of 11, 18 and 14 HLA-A, -B and -DRB1 alleles were identified, respectively. These data are available in the Allele Frequencies Net Database under the population name “Malaysia Kedah Kensiu” and “Malaysia Pahang Semai”. [ABSTRACT FROM AUTHOR]