Displaying publications 21 - 40 of 83 in total

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  1. Jisming-See SW, Sing KW, Wilson JJ
    Genome, 2016 Oct;59(10):879-888.
    PMID: 27333330 DOI: 10.1139/gen-2015-0156
    The "rings" belonging to the genus Ypthima are amongst the most common butterflies in Peninsular Malaysia. However, the species can be difficult to tell apart, with keys relying on minor and often non-discrete ring characters found on the hindwing. Seven species have been reported from Peninsular Malaysia, but this is thought to be an underestimate of diversity. DNA barcodes of 165 individuals, and wing and genital morphology, were examined to reappraise species diversity of this genus in Peninsular Malaysia. DNA barcodes collected during citizen science projects-School Butterfly Project and Peninsular Malaysia Butterfly Count-recently conducted in Peninsular Malaysia were included. The new DNA barcodes formed six groups with different Barcode Index Numbers (BINs) representing four species reported in Peninsular Malaysia. When combined with public DNA barcodes from the Barcode Of Life Datasystems, several taxonomic issues arose. We consider the taxon Y. newboldi, formerly treated as a subspecies of Y. baldus, as a distinct species. DNA barcodes also supported an earlier suggestion that Y. nebulosa is a synonym under Y. horsfieldii humei. Two BINs of the genus Ypthima comprising DNA barcodes collected during citizen science projects did not correspond to any species previously reported in Peninsular Malaysia.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  2. Skowron Volponi MA, Volponi P
    Zookeys, 2017.
    PMID: 29133989 DOI: 10.3897/zookeys.692.13587
    A new species of clearwing moth,Pyrophleps ellawiSkowron Volponi,sp. n., is described from Peninsular Malaysia. Information on the habitat, time and conditions of occurrence, flight and mud-puddling behaviour, functional morphology, and DNA barcode are also provided. Photographs and a supplementary video from the wild demonstrate the postures and behaviour of this species ofPyrophleps, whose remaining members were described only on the basis of pinned specimens. This is the first record of this genus in Peninsular Malaysia.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  3. Wilson JJ, Brandon-Mong GJ, Gan HM, Sing KW
    PMID: 29591722 DOI: 10.1080/24701394.2018.1455189
    Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.
    Matched MeSH terms: DNA Barcoding, Taxonomic/methods*; DNA Barcoding, Taxonomic/standards
  4. Skowron MA, Munisamy B, Hamid SB, Węgrzyn G
    Zootaxa, 2015;4032(4):426-34.
    PMID: 26624378 DOI: 10.11646/zootaxa.4032.4.7
    A new species of Sesiidae, tribe Osminiini from Peninsular Malaysia, Heterosphecia pahangensis Skowron, displaying numerous bee-mimicking features, is described. DNA barcodes showed significant differences with related taxa. However, the paucity of Sesiidae barcodes from Southeast Asia prevents meaningful taxonomic comparisons. The closest match out of published data on Sesiidae barcodes is Heterosphecia bantanakai, Arita & Gorbunov (2000a) from the tribe Osminiini, which has 9.98% sequence divergence from Heterosphecia pahangensis. Photographs of the moth in its natural habitat are shown. Behavioural aspects, such as mud-puddling and mode of flight, are described and presented in a video.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  5. Mokhtar AS, Braima KA, Peng Chin H, Jeffery J, Mohd Zain SN, Rohela M, et al.
    J Med Entomol, 2016 Apr 25.
    PMID: 27113101 DOI: 10.1093/jme/tjw014
    We report a case of human intestinal myiasis in a 41-yr-old female patient presented at a clinic in Seri Kembangan, Selangor, Malaysia. Larvae passed out in the patient's feces were sent to the Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. DNA barcoding confirmed the second case of intestinal myiasis in Malaysia involving the larvae of Clogmia albipunctatus (Duckhouse) (Diptera: Psychodidae). We review reported cases of myiasis and discuss the present case of intestinal myiasis in an urban patient.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  6. Mokhtar AS, Sridhar GS, Mahmud R, Jeffery J, Lau YL, Wilson JJ, et al.
    J Med Entomol, 2016 Sep 01;53(5):1234-1237.
    PMID: 27208008 DOI: 10.1093/jme/tjw071
    We report an unusual cause of gastrointestinal infection occurring in a 1-year-old infant patient who was brought to a public hospital in Kuala Lumpur, Malaysia. Larvae passed out in the patient's feces were confirmed by DNA barcoding as belonging to the species, Lasioderma serricorne (F.), known as the cigarette beetle. We postulate that the larvae were acquired from contaminated food and were responsible for gastrointestinal symptoms in the patient. To our knowledge, this the first report of human canthariasis caused by larvae of L. serricorne.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  7. Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, et al.
    Zookeys, 2020;1003:31-55.
    PMID: 33384561 DOI: 10.3897/zookeys.1003.55541
    Ancyronyx lianlabangorumsp. nov. (Coleoptera, Elmidae), a new spider riffle beetle from the Kelabit Highlands (Sarawak, northern Borneo), is described. Illustrations of the habitus and diagnostic characters of the new species and the similar, polymorphic A. pulcherrimus Kodada et al. are presented. Differences to closely related species, based on COI nucleotide sequences and morphological characters, are discussed. Ancyronyx pulcherrimus is here recorded from Sarawak for the first time, based on DNA barcoding.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  8. Fadli N, Mohd Nor SA, Othman AS, Sofyan H, Muchlisin ZA
    PeerJ, 2020;8:e9641.
    PMID: 32844060 DOI: 10.7717/peerj.9641
    Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  9. Low VL, Srisuka W, Saeung A, Tan TK, Ya'cob Z, Yeong YS, et al.
    J Med Entomol, 2020 09 07;57(5):1675-1678.
    PMID: 32333022 DOI: 10.1093/jme/tjaa081
    Previous studies suggested the presence of species complex in the so-called Simulium asakoae Takaoka & Davies (Diptera: Simuliidae) in Thailand due to its high morphological variability and genetic divergence. To investigate whether the true S. asakoae is present in Thailand, we performed a detailed morphological identification of S. asakoae and compared its DNA barcodes with the morphospecies S. asakoae from Myanmar and the typical S. asakoae from Malaysia. Phylogenetic analysis revealed the Thai materials analyzed in this study were indeed genetically similar with those from Myanmar and Malaysia, though genetic distances 0-2.27% were observed. We tentatively regard this divergence as intraspecific variation, and the automatic barcode gap discovery analysis further supports them as a single species.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  10. Othman MNA, Hassan R, Harith MN, Sah ASRM
    Trop Life Sci Res, 2018 Mar;29(1):87-101.
    PMID: 29644017 MyJurnal DOI: 10.21315/tlsr2018.29.1.6
    Red seaweed Gracilaria, one of the largest genus in Division Rhodophyta inhabits Sarawak coastal water. This study was designed to identify the species of Gracilaria using morphological approach and to assess selected water quality parameters in Gracilaria habitats. Three field samplings were carried out in Santubong and Asajaya, Sarawak from November 2013 to December 2014. Overall, three species were identified namely Gracilaria changii, G. blodgettii and G. coronopifolia, attached to net of cage culture in Santubong and root of mangrove trees in Asajaya. In addition, three different taxa of aquatic macroinvertebrates (polychaete, small crab, bivalve) and single species of red seaweed (Acanthophora sp.) were observed in Gracilaria assemblages. An estimate of 37% to 40% of the upper part of the cage net in Santubong was covered by seaweeds and only 16% to 20% in Asajaya's mangrove. The study had provided better information on identification of Gracilaria and their habitat in Sarawak. Future work involving DNA barcoding of each species is in progress.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  11. Lee PS, Gan HM, Clements GR, Wilson JJ
    Genome, 2016 May 11.
    PMID: 27696907
    Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  12. Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, et al.
    Zookeys, 2020;912:25-64.
    PMID: 32123499 DOI: 10.3897/zookeys.912.47796
    Ancyronyx clisterisp. nov. (Coleoptera, Elmidae) a new spider riffle beetle discovered from northern Borneo (Brunei; Sabah and Sarawak, Malaysia) and the larva of Ancyronyx sarawacensis Jäch are described. Illustrations of the habitus and diagnostic characters of the new species and the similar and highly variable A. sarawacensis are presented. Differences to closely related species, based on DNA barcodes and morphological characters, are discussed. Association of the larva and the imago of A. sarawacensis, and the occurrence of Ancyronyx procerus Jäch in Peninsular Malaysia and Sabah are confirmed by using COI mtDNA sequences.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  13. Schilthuizen M, Berenyi AEA, Limin A, Brahim A, Cicuzza D, Eales AJ, et al.
    PMID: 30740026 DOI: 10.3897/BDJ.7.e32555
    Background: Clavicornaltica is a genus of very small flea beetles living in the leaf litter layer of Asian forests, easily sampled with Winkler extraction. The genus is presumably very rich in species, but their taxonomy is hampered by their small size and morphological uniformity.

    New information: On a 'taxon expedition'-style field course at Kuala Belalong Field Studies Centre in Brunei Darussalam (Borneo), a new species, Clavicornaltica belalongensis n. sp., was discovered and taxonomically treated by the course participants. We also present the first DNA barcodes for the genus.

    Matched MeSH terms: DNA Barcoding, Taxonomic
  14. Naim DM, Nor SAM, Mahboob S
    Saudi J Biol Sci, 2020 Feb;27(2):643-652.
    PMID: 32210683 DOI: 10.1016/j.sjbs.2019.11.030
    This study utilized genetic and morphometric approaches to assess the molecular and morphometric differentiation among commercially important species of mud crab. Molecular investigations were derived from 542 bp mitochondrial DNA COI on 249 individuals within genus Scylla from nine states in Malaysia represents four marine regions; South China Sea, Sulu Sea, Straits of Singapore and Straits of Malacca. Four specimens were obtained from Indonesia to give a robust analysis in this study. For species delimitation, Automatic Barcode Gap Discovery (ABGD) method on a web interface was employed. Analysis on phylogenetics was implemented utilizing Neighbour joining (NJ) and Maximum Parsimony (MP) methods. The inter- and intraspecies genetic distances (Ds ) was computed using Kimura 2-parameter distance and executed in MEGA version 5.05. All samples were genetically and morphologically identified and clustered into four distinct species. Among the species, S. olivacea was the most abundant (n = 111), on the other hand the occurrence of S. paramamosain in Malaysia was very low (n = 29). No single individual of S. serrata from Malaysia was recorded in this study. Both genetic distance and phylogenetic approaches exhibited a correlative monophyletic association among all specimens analysed. This present study is crucial as it reports the reassessment of all species within genus Scylla in Malaysia, eventually could be employed as a reference source for subsequent research mainly on mariculture and other conservation efforts for the species.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  15. Wahyuni DK, Yoku BF, Mukarromah SR, Purnama PR, Ilham M, Rakashiwi GA, et al.
    Braz J Biol, 2023;83:e274315.
    PMID: 38126630 DOI: 10.1590/1519-6984.274315
    Safety regarding herbal products is very necessary; therefore, routine identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. In order for the identification-related data obtained to be accurate, the identification of various kinds of markers is also very necessary. The purpose of this study was to describe the characteristics of Eclipta alba (L.) Hassk. based on qualitative morpho-anatomical markers and quantitative DNA coding. The morphology of this plant has herbaceous habit with a taproot and a stem with branches that appear from the middle. Leaves are single type imperfectly arranged oppositely, lanceolatus, finely serrated on the edges, tapered at the base, pointed at the end, and have a pinnate and hairy leaf surface. The flowers consist of ray flowers and tube flowers with a cup shape. Meanwhile, in terms of anatomy, E. alba has aerenchyma, which are scattered in the cortex of the root and stem. In addition, there are anisocytic stomata, glandular trichomes, and non-glandural trichomes with an elongated shape accompanied by ornamentation found on the leaf epidermis. The results of sequence alignment and phylogenetic tree reconstruction show that the sample plants are closely related to species in the genus Eclipta.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  16. Chee SY, Mohd Nor SA
    PMID: 25471442 DOI: 10.3109/19401736.2014.987237
    This is the first study to identify and determine the phylogenetics of neritids found in Malaysia. In total, twelve species from the family Neritidae were recorded. Ten species were from the genus Nerita and two species were from the genus Neritina. DNA barcodes were successfully assigned to each species. Although some of these species were previously reported in the region, three are only presently reported in this study. The dendrogram showed Nerita and Neritina strongly supported in their respective monophyletic clades. Phylogenetic positions of some species appeared unstable in the trees. This could be due to the differences in a small number of nucleotides, thus minimizing genetic variation between each specimen and species.
    Matched MeSH terms: DNA Barcoding, Taxonomic*
  17. Sutou M, Kato T, Ito M
    Mol Ecol Resour, 2011 Nov;11(6):992-1001.
    PMID: 21693000 DOI: 10.1111/j.1755-0998.2011.03040.x
    Long columns of migrating larval sciarid armyworms were discovered in central and northern Japan, specifically Kanagawa, Gunma, Miyagi and Akita prefectures, as well as Hokkaido. This is the first examination of armyworms in East Asia. In Europe, armyworms have been identified as Sciara militaris, belonging to the family Sciaridae (sciarid flies or black fungus gnats), by rearing them to adulthood. In Japan, we were unable to obtain live samples for rearing; therefore, DNA barcodes were obtained from the samples of armyworms collected in the Gunma and Miyagi prefectures. The DNA barcodes were compared with those obtained from the following samples: pupae of S. militaris from UK, adults of Sciara kitakamiensis, Sciara humeralis, Sciara hemerobioides, Sciara thoracica, Sciara helvola and Sciara melanostyla from Japan, and adults of one undescribed Sciara species from Malaysia. Neighbour-joining, maximum parsimony, and maximum likelihood analyses revealed that the armyworms discovered in Japan are S. kitakamiensis. Although adults of this species have been recorded in several locations in Japan, this is the first report of migrating larval armyworms. DNA barcodes were effectively used to link different life stages of this species. The average intraspecific and interspecific pairwise genetic distances of the genus Sciara were 0.3% and 12.6%, respectively. The present study illustrates that DNA barcodes are an effective means of identifying sciarid flies in Japan.
    Matched MeSH terms: DNA Barcoding, Taxonomic/methods*
  18. Jamaluddin JAF, Mohammed Akib NA, Ahmad SZ, Abdul Halim SAA, Abdul Hamid NK, Mohd Nor SA
    PMID: 31012766 DOI: 10.1080/24701394.2019.1597073
    A total of 74 shrimp specimens were sequenced at a 584 bp segment of the cytochrome oxidase subunit I (COI) gene to examine patterns of DNA barcode variation in a mangrove biodiversity hotspot. The Maximum Likelihood tree, barcode gap analysis, Automatic Barcode Gap Discovery analysis and sequence comparisons with data available from Barcode of Life Data System and GenBank recovered 18 taxa of which 15 were identified to species level, 2 at genus level and a single taxon at order level. Two deep mitochondrial DNA lineage divergences were found in the giant tiger prawn, Penaeus monodon. It is suggested that one of the lineages is a consequence of an introduction from aquaculture activity. These results have provided a reliable barcode library for cataloguing shrimps in this area.
    Matched MeSH terms: DNA Barcoding, Taxonomic*
  19. Casas PAS, Sing KW, Lee PS, Nuñeza OM, Villanueva RJT, Wilson JJ
    PMID: 28155593 DOI: 10.1080/24701394.2016.1267157
    Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
    Matched MeSH terms: DNA Barcoding, Taxonomic/methods*
  20. Hossain MAM, Uddin SMK, Chowdhury ZZ, Sultana S, Johan MR, Rohman A, et al.
    PMID: 30865559 DOI: 10.1080/19440049.2019.1580389
    Mislabelling in fish products is a highly significant emerging issue in world fish trade in terms of health and economic concerns. DNA barcoding is an efficient sequencing-based tool for detecting fish species substitution but due to DNA degradation, it is in many cases difficult to amplify PCR products of the full-length barcode marker (~650 bp), especially in severely processed products. In the present study, a pair of universal primers targeting a 198 bp sequence of the mitochondrial 16s rRNA gene was designed for identification of fish species in the processed fish products commonly consumed in Malaysia. The specificity of the universal primers was tested by both in-silico studies using bioinformatics software and through cross-reaction assessment by practical PCR experiments against the DNA from 38 fish species and 22 other non-target species (animals and plants) and found to be specific for all the tested fish species. To eliminate the possibility of any false-negative detection, eukaryotic endogenous control was used during specificity evaluation. The developed primer set was validated with various heat-treated (boiled, autoclaved and microwaved) fish samples and was found to show high stability under all processing conditions. The newly developed marker successfully identified 92% of the tested commercial fish products with 96-100% sequence similarities. This study reveals a considerable degree of species mislabelling (20.8%); 5 out of 24 fish products were found to be mislabelled. The new marker developed in this work is a reliable tool to identify fish species even in highly processed products and might be useful in detecting fish species substitution thus protecting consumers' health and economic interests.
    Matched MeSH terms: DNA Barcoding, Taxonomic*
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