Displaying publications 1 - 20 of 79 in total

Abstract:
Sort:
  1. DNA Barcoding of Simulium asakoae (Diptera: Simuliidae) From Northern Thailand
    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: Electron Transport Complex IV/genetics
  2. Fulltext Population genetic structure of Aedes albopictus in Penang, Malaysia
    Zawani MK, Abu HA, Sazaly AB, Zary SY, Darlina MN
    Genet. Mol. Res., 2014;13(4):8184-96.
    PMID: 25299203 DOI: 10.4238/2014.October.7.13
    The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  3. Fulltext Is there a cryptic species of the golden snapper (Lutjanus johnii)?
    Adibah AB, Darlina MN
    Genet. Mol. Res., 2014;13(4):8094-104.
    PMID: 25299194 DOI: 10.4238/2014.October.7.4
    For centuries, morphology-based fish identification has been applied without molecular evaluation. Many studies showed that specimens with a similar morphology are frequently found to be quite genetically distinct. One of the fish species that still remains taxonomically problematic is a commercial snapper species, Lutjanus johnii. Because of morphological ambiguities among local fish taxonomists in Malaysia, we examined the ability of the cytochrome oxidase I (COI) gene to genetically examine the taxonomic status of L. johnii. A 626-base pair COI region was successfully amplified and aligned with conspecific sequences that were retrieved from GenBank. The phylogenetic tree obtained showed two major clusters; the first cluster consists of L. johnii from Straits of Malacca, Thailand, Australia, and China while the second cluster comprises L. johnii from China and India. The latter group showed sequence divergence greater than 3.5%. After observing this, we suspected that there might be a cryptic species between the South China Sea and Indian Ocean. This is the first molecular report concerning the commercial species of snapper, L. johnii, in Malaysia, which had only gained provisional recognition from morphological examination.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  4. Fulltext Characterisation of Asian snakehead murrel Channa striata (Channidae) in Malaysia: an insight into molecular data and morphological approach
    Song LM, Munian K, Abd Rashid Z, Bhassu S
    ScientificWorldJournal, 2013;2013:917506.
    PMID: 24396312 DOI: 10.1155/2013/917506
    Conservation is imperative for the Asian snakeheads Channa striata, as the species has been overfished due to its high market demand. Using maternal markers (mitochondrial cytochrome c oxidase subunit 1 gene (COI)), we discovered that evolutionary forces that drove population divergence did not show any match between the genetic and morphological divergence pattern. However, there is evidence of incomplete divergence patterns between the Borneo population and the populations from Peninsular Malaysia. This supports the claim of historical coalescence of C. striata during Pleistocene glaciations. Ecological heterogeneity caused high phenotypic variance and was not correlated with genetic variance among the populations. Spatial conservation assessments are required to manage different stock units. Results on DNA barcoding show no evidence of cryptic species in C. striata in Malaysia. The newly obtained sequences add to the database of freshwater fish DNA barcodes and in future will provide information relevant to identification of species.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  5. Fulltext Distinct genetic lineages of Bactrocera caudata (Insecta: Tephritidae) revealed by COI and 16S DNA sequences
    Lim PE, Tan J, Suana IW, Eamsobhana P, Yong HS
    PLoS One, 2012;7(5):e37276.
    PMID: 22615962 DOI: 10.1371/journal.pone.0037276
    The fruit fly Bactrocera caudata is a pest species of economic importance in Asia. Its larvae feed on the flowers of Cucurbitaceae such as Cucurbita moschata. To-date it is distinguished from related species based on morphological characters. Specimens of B. caudata from Peninsular Malaysia and Indonesia (Bali and Lombok) were analysed using the partial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA genes. Both gene sequences revealed that B. caudata from Peninsular Malaysia was distinctly different from B. caudata of Bali and Lombok, without common haplotype between them. Phylogenetic analysis revealed two distinct clades, indicating distinct genetic lineage. The uncorrected 'p' distance for COI sequences between B. caudata of Malaysia-Thailand-China and B. caudata of Bali-Lombok was 5.65%, for 16S sequences from 2.76 to 2.99%, and for combined COI and 16S sequences 4.45 to 4.46%. The 'p' values are distinctly different from intraspecific 'p' distance (0-0.23%). Both the B. caudata lineages are distinctly separated from related species in the subgenus Zeugodacus - B. ascita, B. scutellata, B. ishigakiensis, B. diaphora, B. tau, B. cucurbitae, and B. depressa. Molecular phylogenetic analysis indicates that the B. caudata lineages are closely related to B. ascita sp. B, and form a clade with B. scutellata, B. ishigakiensis, B. diaphora and B. ascita sp. A. This study provides additional baseline for the phylogenetic relationships of Bactrocera fruit flies of the subgenus Zeugodacus. Both the COI and 16S genes could be useful markers for the molecular differentiation and phylogenetic analysis of tephritid fruit flies.
    Matched MeSH terms: Electron Transport Complex IV/genetics*
  6. DNA-based characterisation and classification of forensically important flesh flies (Diptera: Sarcophagidae) in Malaysia
    Tan SH, Rizman-Idid M, Mohd-Aris E, Kurahashi H, Mohamed Z
    Forensic Sci Int, 2010 Jun 15;199(1-3):43-9.
    PMID: 20392577 DOI: 10.1016/j.forsciint.2010.02.034
    Insect larvae and adult insects found on human corpses provide important clues for the estimation of the postmortem interval (PMI). Among all necrophagous insects, flesh flies (Diptera: Sarcophagidae) are considered as carrion flies of forensic importance. DNA variations of 17 Malaysian, two Indonesian and one Japanese flesh fly species are analysed using the mitochondrial COI and COII. These two DNA regions were useful for identifying most species experimented. However, characterisation of the species was not sufficiently made in the case of Sarcophaga javanica. Seventeen Malaysian species of forensic importance were successfully clustered into distinct clades and grouped into the six species groups: peregrina, albiceps, dux, pattoni, princeps and ruficornis. These groups correspond with generic or subgeneric taxa of the subfamily Sarcophaginae: Boettcherisca, Parasarcophaga, Liosarcophaga, Sarcorohdendorfia-Lioproctia, Harpagophalla-Seniorwhitea and Liopygia. The genetic variations found in COI and COII can be applied not only to identify the species of forensic importance, but also to understand the taxonomic positions, generic or subgeneric status, of the sarcophagine species.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  7. Fulltext DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes)
    Mat Jaafar TN, Taylor MI, Mohd Nor SA, de Bruyn M, Carvalho GR
    PLoS One, 2012;7(11):e49623.
    PMID: 23209586 DOI: 10.1371/journal.pone.0049623
    DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI) in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA), to produce an initial reference DNA barcode library.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  8. Fulltext Limitations of cytochrome oxidase I for the barcoding of Neritidae (Mollusca: Gastropoda) as revealed by Bayesian analysis
    Chee SY
    Genet. Mol. Res., 2015;14(2):5677-84.
    PMID: 26125766 DOI: 10.4238/2015.May.25.20
    The mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) gene has been universally and successfully utilized as a barcoding gene, mainly because it can be amplified easily, applied across a wide range of taxa, and results can be obtained cheaply and quickly. However, in rare cases, the gene can fail to distinguish between species, particularly when exposed to highly sensitive methods of data analysis, such as the Bayesian method, or when taxa have undergone introgressive hybridization, over-splitting, or incomplete lineage sorting. Such cases require the use of alternative markers, and nuclear DNA markers are commonly used. In this study, a dendrogram produced by Bayesian analysis of an mtDNA COI dataset was compared with that of a nuclear DNA ATPS-α dataset, in order to evaluate the efficiency of COI in barcoding Malaysian nerites (Neritidae). In the COI dendrogram, most of the species were in individual clusters, except for two species: Nerita chamaeleon and N. histrio. These two species were placed in the same subcluster, whereas in the ATPS-α dendrogram they were in their own subclusters. Analysis of the ATPS-α gene also placed the two genera of nerites (Nerita and Neritina) in separate clusters, whereas COI gene analysis placed both genera in the same cluster. Therefore, in the case of the Neritidae, the ATPS-α gene is a better barcoding gene than the COI gene.
    Matched MeSH terms: Electron Transport Complex IV/genetics*
  9. Development of allele-specific single-nucleotide polymorphism-based polymerase chain reaction markers in cytochrome oxidase I for the differentiation of Bactrocera papayae and Bactrocera carambolae (Diptera: Tephritidae)
    Chua TH, Song BK, Chong YV
    J Econ Entomol, 2010 Dec;103(6):1994-9.
    PMID: 21309218
    Differentiation of Bactrocera papayae Drew & Hancock and Bactrocera carambolae Drew & Hancock (Diptera: Tephritidae) based on morphological characters has often been problematical. We describe here a single-nucleotide polymorphism (SNP)-based polymerase chain reaction (PCR) assay to differentiate between these two species. For detection of SNPs, fragments derived from each species were amplified using two primer pairs, COIF/COIR and UEA7/UEA10, sequenced, and aligned to obtain a contiguous 1,517-bp segment. Two new sets of primers were designed based on the 11 SNPs identified in the region. Results of the SNP-PCR test using any one of these species-specific primer sets indicate that these two species could be differentiated on basis of presence or absence of a band in the gel profile. We also tested the SNP-PCR primers on Bactrocera umbrosa F., Bactrocera cucurbitae Coquillett, Bactrocera latifrons Hendel, and Bactrocera tau (Walker) but did not detect any band in the gel, indicating the likelihood of a false positive for B. papayae is nil. This SNP-PCR method is efficient and useful, especially for immature life stages or when only adult body parts of the two species are available for identification, as encountered often in quarantine work.
    Matched MeSH terms: Electron Transport Complex IV/genetics*
  10. DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene
    Aziz NMA, Esa Y, Arshad A
    J Environ Biol, 2016 07;37(4 Spec No):725-33.
    PMID: 28779732
    The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?
    Matched MeSH terms: Electron Transport Complex IV/genetics*
  11. Fulltext Ancient River Inference Explains Exceptional Oriental Freshwater Mussel Radiations
    Bolotov IN, Kondakov AV, Vikhrev IV, Aksenova OV, Bespalaya YV, Gofarov MY, et al.
    Sci Rep, 2017 05 18;7(1):2135.
    PMID: 28522869 DOI: 10.1038/s41598-017-02312-z
    The concept of long-lived (ancient) lakes has had a great influence on the development of evolutionary biogeography. According to this insight, a number of lakes on Earth have existed for several million years (e.g., Baikal and Tanganyika) and represent unique evolutionary hotspots with multiple intra-basin radiations. In contrast, rivers are usually considered to be variable systems, and the possibility of their long-term existence during geological epochs has never been tested. In this study, we reconstruct the history of freshwater basin interactions across continents based on the multi-locus fossil-calibrated phylogeny of freshwater mussels (Unionidae). These mussels most likely originated in Southeast and East Asia in the Jurassic, with the earliest expansions into North America and Africa (since the mid-Cretaceous) following the colonization of Europe and India (since the Paleocene). We discovered two ancient monophyletic mussel radiations (mean age ~51-55 Ma) within the paleo-Mekong catchment (i.e., the Mekong, Siam, and Malacca Straits paleo-river drainage basins). Our findings reveal that the Mekong may be considered a long-lived river that has existed throughout the entire Cenozoic epoch.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  12. Extensive sharing of mitochondrial COI and CYB haplotypes among reef-building staghorn corals (Acropora spp.) in Sabah, North Borneo
    Robert R, Rodrigues KF, Waheed Z, Kumar SV
    Mitochondrial DNA A DNA Mapp Seq Anal, 2019 01;30(1):16-23.
    PMID: 29521145 DOI: 10.1080/24701394.2018.1448080
    This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts/Tv), synonymous-to-nonsynonymous rate ratio (dN/dS), and substitution patterns at the three codon positions. Despite the relatively high haplotype diversity (Hd), nucleotide diversity (π) of the haplotype datasets was low due to stringent purifying selection operating on the genes. Subsequently, we identified individual COI and CYB haplotypes that were each extensively shared across sympatrically and allopatrically distributed Indo-Pacific Acropora. These reciprocally common mtDNA types were suspected to be ancestral forms of the genes whereas other haplotypes have mostly evolved from autoapomorphic mutations which have not been fixed within the species even though they are selectively neutral. To our knowledge, this is the first report on DNA barcodes of Acropora species in North Borneo and this understanding will play an important role in the management and conservation of these important reef-building corals.
    Matched MeSH terms: Electron Transport Complex IV/genetics*
  13. Fulltext Utility of COX1 phylogenetics to differentiate between locally acquired and imported Plasmodium knowlesi infections in Singapore
    Loh JP, Gao QH, Lee VJ, Tetteh K, Drakeley C
    Singapore Med J, 2016 Dec;57(12):686-689.
    PMID: 26805667 DOI: 10.11622/smedj.2016016
    INTRODUCTION: Although there have been several phylogenetic studies on Plasmodium knowlesi (P. knowlesi), only cytochrome c oxidase subunit 1 (COX1) gene analysis has shown some geographical differentiation between the isolates of different countries.

    METHODS: Phylogenetic analysis of locally acquired P. knowlesi infections, based on circumsporozoite, small subunit ribosomal ribonucleic acid (SSU rRNA), merozoite surface protein 1 and COX1 gene targets, was performed. The results were compared with the published sequences of regional isolates from Malaysia and Thailand.

    RESULTS: Phylogenetic analysis of the circumsporozoite, SSU rRNA and merozoite surface protein 1 gene sequences for regional P. knowlesi isolates showed no obvious differentiation that could be attributed to their geographical origin. However, COX1 gene analysis showed that it was possible to differentiate between Singapore-acquired P. knowlesi infections and P. knowlesi infections from Peninsular Malaysia and Sarawak, Borneo, Malaysia.

    CONCLUSION: The ability to differentiate between locally acquired P. knowlesi infections and imported P. knowlesi infections has important utility for the monitoring of P. knowlesi malaria control programmes in Singapore.

    Matched MeSH terms: Electron Transport Complex IV/genetics*
  14. Fulltext Complete mitochondrial genome of Zeugodacus tau (Insecta: Tephritidae) and differentiation of Z. tau species complex by mitochondrial cytochrome c oxidase subunit I gene
    Yong HS, Song SL, Lim PE, Eamsobhana P
    PLoS One, 2017;12(12):e0189325.
    PMID: 29216281 DOI: 10.1371/journal.pone.0189325
    The tephritid fruit fly Zeugodacus tau (Walker) is a polyphagous fruit pest of economic importance in Asia. Studies based on genetic markers indicate that it forms a species complex. We report here (1) the complete mitogenome of Z. tau from Malaysia and comparison with that of China as well as the mitogenome of other congeners, and (2) the relationship of Z. tau taxa from different geographical regions based on sequences of cytochrome c oxidase subunit I gene. The complete mitogenome of Z. tau had a total length of 15631 bp for the Malaysian specimen (ZT3) and 15835 bp for the China specimen (ZT1), with similar gene order comprising 37 genes (13 protein-coding genes-PCGs, 2 rRNA genes, and 22 tRNA genes) and a non-coding A + T-rich control region (D-loop). Based on 13 PCGs and 15 mt-genes, Z. tau NC_027290 (China) and Z. tau ZT1 (China) formed a sister group in the lineage containing also Z. tau ZT3 (Malaysia). Phylogenetic analysis based on partial sequences of cox1 gene indicates that the taxa from China, Japan, Laos, Malaysia, Bangladesh, India, Sri Lanka, and Z. tau sp. A from Thailand belong to Z. tau sensu stricto. A complete cox1 gene (or 13 PCGs or 15 mt-genes) instead of partial sequence is more appropriate for determining phylogenetic relationship.
    Matched MeSH terms: Electron Transport Complex IV/genetics*
  15. First blood-meal record of Simulium asakoae (Diptera: Simuliidae) in Malaysia, with notes on its distribution in Asia and status as a potential vector
    Izwan-Anas N, Ya'cob Z, Low VL, Lourdes EY, Teoh BT, Mansor MS, et al.
    Trop Biomed, 2024 Sep 01;41(3):251-256.
    PMID: 39548777 DOI: 10.47665/tb.41.3.003
    Simulium asakoae Takaoka and Davies has been confirmed to bite humans and has been incriminated as a vector of blood protozoan parasites of the genera Leucocytozoon and Trypanosoma, as well as an unknown filarial parasite in Thailand. However, its attraction to humans has remained uninvestigated in Malaysia. Recently, 27 black flies were collected in Pahang, Malaysia, of which 25 were captured in CO2-baited Malaise traps and two were collected from humans during trapping activity. All specimens were morphologically identified as S. asakoae. Cytochrome c oxidase I sequences of the two specimens caught on humans showed 100% similarity with those of S. asakoae in the NCBI GenBank, confirming their morphological identity. Blood-meal analysis using a HAL·HARTM kit did not show the presence of domestic or wild animal DNA. However, human DNA was amplified from one engorged fly in the cytochrome b gene amplification assay, providing the first evidence of blood-feeding by S. asakoae in Malaysia.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  16. DNA barcoding reveals neritid diversity (Mollusca: Gastropoda) diversity in Malaysian waters
    Chee SY, Mohd Nor SA
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2282-4.
    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: Electron Transport Complex IV/genetics
  17. Use of COI, CytB and ND5 genes for intra- and inter-specific differentiation of Haematobia irritans and Haematobia exigua
    Low VL, Tan TK, Lim PE, Domingues LN, Tay ST, Lim YA, et al.
    Vet Parasitol, 2014 Aug 29;204(3-4):439-42.
    PMID: 24912955 DOI: 10.1016/j.vetpar.2014.05.036
    A multilocus sequence analysis using mitochondria-encoded cytochrome c oxidase subunit I (COI), cytochrome B (CytB), NADH dehydrogenase subunit 5 (ND5); nuclear encoded 18S ribosomal RNA (18S) and 28S ribosomal RNA (28S) genes was performed to determine the levels of genetic variation between the closely related species Haematobia irritans Linnaeus and Haematobia exigua de Meijere. Among these five genes, ND5 and CytB genes were found to be more variable and informative in resolving the interspecific relationships of both species. In contrast, the COI gene was more valuable in inferring the intraspecific relationships. The ribosomal 18S and 28S sequences of H. irritans and H. exigua were highly conserved with limited intra- and inter-specific variation. Molecular evidence presented in this study demonstrated that both flies are genetically distinct and could be differentiated based on sequence analysis of mitochondrial genes.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  18. Mitochondrial DNA diversity of mud crab Scylla olivacea (Portunidae) in Peninsular Malaysia: a preliminary assessment
    Rosly HA, Nor SA, Yahya K, Naim DM
    Mol Biol Rep, 2013 Nov;40(11):6407-18.
    PMID: 24062076 DOI: 10.1007/s11033-013-2755-4
    A primary factor in population management and wildlife conservation is the delineation of population units derived from descriptions of population genetic structure. Yet, predicting factors that influence the patterns of gene flow in a population particularly at landscape scales remains a major challenge in evolutionary biology. Here we report a population genetic study of the mud crab Scylla olivacea examined based on a 542 bp segment of the mitochondrial DNA cytochrome c oxidase I gene among 91 individuals from six localities in the west and east coast of Peninsular Malaysia. In total 55 unique haplotypes were distinguished with 45 private haplotypes and a single common haplotype shared among all populations studied. The other ten haplotypes were shared among various populations. The sharing of this haplotype reflects the connection of the mangrove areas between east and west coast of Peninsular Malaysia. High haplotype diversity (h = 0.968 ± 0.021; mean ± SD) and low nucleotide diversity (π = 0.120 ± 0.015; mean ± SD) were displayed, which may be indicative of genetic bottleneck events. No significant phylogenetic lineages were recognized using neighbour-joining and maximum parsimony methods. Hierarchical AMOVA analysis indicated that 99.33 % of the genetic variation was contained within populations and 0.67 % occurred among populations, suggesting no geographical patterning among populations studied, supported by F st test. Mismatch distribution analysis showed that the observed distribution of the pairwise mutation differences among haplotypes was multimodal, which is not concordant with a sudden range expansion scenario. However, neutrality tests showed non-significant negative values suggesting that the populations studied may have experienced past population growth, but the expansion may have been restricted to separate local areas that resulted in the non-significant negative Fu's Fs and Tajima's D value. Overall, this present preliminary study was able to be a reference on the phylogenetic relationships and assessment of genetic structure of Scylla sp. in Malaysia.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  19. Molecular characterization of relatedness among colour variants of Asian Arowana (Scleropages formosus)
    Mohd-Shamsudin MI, Fard MZ, Mather PB, Suleiman Z, Hassan R, Othman RY, et al.
    Gene, 2011 Dec 15;490(1-2):47-53.
    PMID: 21945689 DOI: 10.1016/j.gene.2011.08.025
    Morphological identification of fish taxa can sometimes prove difficult because phenotypic variation is either being affected by environmental factors, phenotypic characters are highly conserved or marker selection has been inappropriate. DNA based markers especially neutral mitochondrial DNA (mtDNA) have been used widely in recent times to provide better resolution of systematic relationships among vertebrate taxa. The Asian Arowana (Scleropages formosus) is a high value ornamental fish belonging to the family Osteoglossidae with a number of different colour variants distributed geographically across different locations around Southeast Asia. Systematic relationships among colour variants still remain unresolved. Partial sequences of the Cytochrome B (Cyt B) and DNA barcoding gene, Cytochrome C Oxidase I (COI) were used here to assess genetic relationships among colour variants and as a tool for molecular identification for differentiating among colour variants in this species. Results of the study show that in general, colour pattern shows no relationship with extent of COI or Cyt B mtDNA differentiation and so cannot be used to identify taxa. Partial sequences of the mtDNA genes were sufficient however, to identify S. formosus from a closely related species within the order Osteoglossidae.
    Matched MeSH terms: Electron Transport Complex IV/genetics
  20. Fulltext Evidence for a higher number of species of Odontotermes (Isoptera) than currently known from Peninsular Malaysia from mitochondrial DNA phylogenies
    Cheng S, Kirton LG, Panandam JM, Siraj SS, Ng KK, Tan SG
    PLoS One, 2011;6(6):e20992.
    PMID: 21687629 DOI: 10.1371/journal.pone.0020992
    Termites of the genus Odontotermes are important decomposers in the Old World tropics and are sometimes important pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to differentiate based on morphology. As a result, the taxonomy of Odontotermes in Peninsular Malaysia has not been adequately worked out. In this study, we examined the phylogeny of 40 samples of Odontotermes from Peninsular Malaysia using two mitochondrial DNA regions, that is, the 16S ribosomal RNA and cytochrome oxidase subunit I genes, to aid in elucidating the number of species in the peninsula. Phylogenies were reconstructed from the individual gene and combined gene data sets using parsimony and likelihood criteria. The phylogenies supported the presence of up to eleven species in Peninsular Malaysia, which were identified as O. escherichi, O. hainanensis, O. javanicus, O. longignathus, O. malaccensis, O. oblongatus, O. paraoblongatus, O. sarawakensis, and three possibly new species. Additionally, some of our taxa are thought to comprise a complex of two or more species. The number of species found in this study using DNA methods was more than the initial nine species thought to occur in Peninsular Malaysia. The support values for the clades and morphology of the soldiers provided further evidence for the existence of eleven or more species. Higher resolution genetic markers such as microsatellites would be required to confirm the presence of cryptic species in some taxa.
    Matched MeSH terms: Electron Transport Complex IV/genetics
Related Terms
Filters
Contact Us

Please provide feedback to Administrator ([email protected])

External Links