Displaying publications 21 - 40 of 127 in total

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  1. Fulltext DNA fingerprinting of human isolates of Burkholderia pseudomallei from different geographical regions of Malaysia
    Chua KH, See KH, Thong KL, Puthucheary SD
    Trop Biomed, 2010 Dec;27(3):517-24.
    PMID: 21399594 MyJurnal
    Melioidosis is an infectious disease caused by Burkholderia pseudomallei and endemic in Southeast Asia. One hundred and forty six clinical isolates of B. pseudomallei from different states in Malaysia were obtained and molecular typing was carried out using pulsed-field gel electrophoresis (PFGE). Overall, nine clusters were successfully identified. Burkholderia pseudomallei isolates used in this study were found to be genetically diverse and there were differences in the clusters of isolates from peninsular and east Malaysia. BS9 cluster was the most common cluster and found in all the states while BS2 cluster only existed in a particular state. Based on the PFGE analysis, the distribution of different B. pseudomallei clinical isolates in Malaysia was mapped.
    Matched MeSH terms: Phylogeography
  2. Fulltext Delineating taxonomic boundaries in the largest species complex of black flies (Simuliidae) in the Oriental Region
    Low VL, Takaoka H, Pramual P, Adler PH, Ya'cob Z, Huang YT, et al.
    Sci Rep, 2016 Feb 03;6:20346.
    PMID: 26839292 DOI: 10.1038/srep20346
    Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are of paramount importance in interpreting ecological and evolutionary phenomena among black flies (Simuliidae) and combating associated vector-borne diseases. Simulium tani Takaoka & Davies is the largest and perhaps the most taxonomically challenging species complex of black flies in the Oriental Region. We use a DNA sequence-based method to delineate currently recognized chromosomal and morphological taxa in the S. tani complex on the Southeast Asian mainland and Taiwan, while elucidating their phylogenetic relationships. A molecular approach using multiple genes, coupled with morphological and chromosomal data, supported recognition of cytoform K and morphoform 'b' as valid species; indicated that S. xuandei, cytoform L, and morphoform 'a' contain possible cryptic species; and suggested that cytoform B is in the early stages of reproductive isolation whereas lineage sorting is incomplete in cytoforms A, C, and G.
    Matched MeSH terms: Phylogeography
  3. Fulltext Demographic History and Genetic Adaptation in the Himalayan Region Inferred from Genome-Wide SNP Genotypes of 49 Populations
    Arciero E, Kraaijenbrink T, Asan, Haber M, Mezzavilla M, Ayub Q, et al.
    Mol Biol Evol, 2018 Aug 01;35(8):1916-1933.
    PMID: 29796643 DOI: 10.1093/molbev/msy094
    We genotyped 738 individuals belonging to 49 populations from Nepal, Bhutan, North India, or Tibet at over 500,000 SNPs, and analyzed the genotypes in the context of available worldwide population data in order to investigate the demographic history of the region and the genetic adaptations to the harsh environment. The Himalayan populations resembled other South and East Asians, but in addition displayed their own specific ancestral component and showed strong population structure and genetic drift. We also found evidence for multiple admixture events involving Himalayan populations and South/East Asians between 200 and 2,000 years ago. In comparisons with available ancient genomes, the Himalayans, like other East and South Asian populations, showed similar genetic affinity to Eurasian hunter-gatherers (a 24,000-year-old Upper Palaeolithic Siberian), and the related Bronze Age Yamnaya. The high-altitude Himalayan populations all shared a specific ancestral component, suggesting that genetic adaptation to life at high altitude originated only once in this region and subsequently spread. Combining four approaches to identifying specific positively selected loci, we confirmed that the strongest signals of high-altitude adaptation were located near the Endothelial PAS domain-containing protein 1 and Egl-9 Family Hypoxia Inducible Factor 1 loci, and discovered eight additional robust signals of high-altitude adaptation, five of which have strong biological functional links to such adaptation. In conclusion, the demographic history of Himalayan populations is complex, with strong local differentiation, reflecting both genetic and cultural factors; these populations also display evidence of multiple genetic adaptations to high-altitude environments.
    Matched MeSH terms: Phylogeography
  4. Fulltext Dispersal direction of Malaysian Fasciola gigantica from neighboring southeast Asian countries inferred using mitochondrial DNA analysis
    Ichikawa-Seki M, Hayashi K, Tashiro M, Khadijah S
    Infect Genet Evol, 2022 Nov;105:105373.
    PMID: 36202207 DOI: 10.1016/j.meegid.2022.105373
    Fasciola gigantica and hybrid Fasciola flukes, responsible for the disease fasciolosis, are found in Southeast Asian countries. In the present study, we performed molecular species identification of Fasciola flukes distributed in Terengganu, Malaysia using multiplex PCR for phosphoenolpyruvate carboxykinase (pepck) and PCR-restriction fragment length polymorphism (RFLP) for DNA polymerase delta (pold). Simultaneously, phylogenetic analysis based on mitochondrial NADH dehydrogenase subunit 1 (nad1) was performed for the first time on Malaysian Fasciola flukes to infer the dispersal direction among neighboring countries. A total of 40 flukes used in this study were identified as F. gigantica. Eight nad1 haplotypes were identified in the F. gigantica population of Terengganu. Median-joining network analysis revealed that the Malaysian population was related to those obtained from bordering countries such as Thailand and Indonesia. However, genetic differentiation was detected using population genetics analyses. Nevertheless, the nucleotide diversity (π) value suggested that F. gigantica with the predominant haplotypes was introduced into Malaysia from Thailand and Indonesia. The dispersal direction suggested by population genetics in the present study may not be fully reliable since Fasciola flukes were collected from a single location in one state of Malaysia. Further studies analyzing more samples from many locations are required to validate the dispersal direction proposed herein.
    Matched MeSH terms: Phylogeography/methods
  5. Fulltext Distribution and prevalence of malaria parasites among long-tailed macaques (Macaca fascicularis) in regional populations across Southeast Asia
    Zhang X, Kadir KA, Quintanilla-Zariñan LF, Villano J, Houghton P, Du H, et al.
    Malar J, 2016 09 02;15(1):450.
    PMID: 27590474 DOI: 10.1186/s12936-016-1494-0
    BACKGROUND: Plasmodium knowlesi and Plasmodium cynomolgi are two malaria parasites naturally transmissible between humans and wild macaque through mosquito vectors, while Plasmodium inui can be experimentally transmitted from macaques to humans. One of their major natural hosts, the long-tailed macaque (Macaca fascicularis), is host to two other species of Plasmodium (Plasmodium fieldi and Plasmodium coatneyi) and is widely distributed in Southeast Asia. This study aims to determine the distribution of wild macaques infected with malarial parasites by examining samples derived from seven populations in five countries across Southeast Asia.

    METHODS: Plasmodium knowlesi, P. cynomolgi, P. coatneyi, P. inui and P. fieldi, were detected using nested PCR assays in DNA samples from 276 wild-caught long-tailed macaques. These samples had been derived from macaques captured at seven locations, two each in the Philippines (n = 68) and Indonesia (n = 70), and one each in Cambodia (n = 54), Singapore (n = 40) and Laos (n = 44). The results were compared with previous studies of malaria parasites in long-tailed macaques from other locations in Southeast Asia. Fisher exact test and Chi square test were used to examine the geographic bias of the distribution of Plasmodium species in the macaque populations.

    RESULTS: Out of 276 samples tested, 177 were Plasmodium-positive, with P. cynomolgi being the most common and widely distributed among all long-tailed macaque populations (53.3 %) and occurring in all populations examined, followed by P. coatneyi (20.4 %), P. inui (12.3 %), P. fieldi (3.4 %) and P. knowlesi (0.4 %). One P. knowlesi infection was detected in a macaque from Laos, representing the first documented case of P. knowlesi in wildlife in Laos. Chi square test showed three of the five parasites (P. knowlesi, P. coatneyi, P. cynomolgi) with significant bias in prevalence towards macaques from Malaysian Borneo, Cambodia, and Southern Sumatra, respectively.

    CONCLUSIONS: The prevalence of malaria parasites, including those that are transmissible to humans, varied among all sampled regional populations of long-tailed macaques in Southeast Asia. The new discovery of P. knowlesi infection in Laos, and the high prevalence of P. cynomolgi infections in wild macaques in general, indicate the strong need of public advocacy in related countries.

    Matched MeSH terms: Phylogeography
  6. Divergence of the dengue virus type 2 Cosmopolitan genotype associated with two predominant serotype shifts between 1 and 2 in Surabaya, Indonesia, 2008-2014
    Kotaki T, Yamanaka A, Mulyatno KC, Churrotin S, Sucipto TH, Labiqah A, et al.
    Infect Genet Evol, 2016 Jan;37:88-93.
    PMID: 26553170 DOI: 10.1016/j.meegid.2015.11.002
    Indonesia is one of the biggest dengue endemic countries, and, thus, is an important place to investigate the evolution of dengue virus (DENV). We have continuously isolated DENV in Surabaya, the second biggest city in Indonesia, since 2008. We previously reported sequential changes in the predominant serotype from DENV type 2 (DENV-2) to DENV type 1 (DENV-1) in November 2008 and from DENV-1 to DENV-2 in July 2013. The predominance of DENV-2 continued in 2014, but not in 2015. We herein phylogenetically investigated DENV-2 transitions in Surabaya between 2008 and 2014 to analyze the divergence and evolution of DENV-2 concomitant with serotype shifts. All DENV-2 isolated in Surabaya were classified into the Cosmopolitan genotype, and further divided into 6 clusters. Clusters 1-3, dominated by Surabaya strains, were defined as the "Surabaya lineage". Clusters 4-6, dominated by strains from Singapore, Malaysia, and many parts of Indonesia, were the "South East Asian lineage". The most recent common ancestor of these strains existed in 1988, coinciding with the time that an Indonesian dengue outbreak took place. Cluster 1 appeared to be unique because no other DENV-2 isolate was included in this cluster. The predominance of DENV-2 in 2008 and 2013-14 were caused by cluster 1, whereas clusters 2 and 3 sporadically emerged in 2011 and 2012. The characteristic amino acids of cluster 1, E-170V and E-282Y, may be responsible for its prevalence in Surabaya. No amino acid difference was observed in the envelope region between strains in 2008 and 2013-14, suggesting that the re-emergence of DENV-2 in Surabaya was due to the loss or decrease of herd immunity in the 5-year period when DENV-2 subsided. The South East Asian lineage primarily emerged in Surabaya in 2014, probably imported from other parts of Indonesia or foreign countries.
    Matched MeSH terms: Phylogeography
  7. Fulltext Diversity of the Monstrilloida (Crustacea: Copepoda)
    Suárez-Morales E
    PLoS One, 2011;6(8):e22915.
    PMID: 21853055 DOI: 10.1371/journal.pone.0022915
    Monstrilloid copepods are protelean parasites of different groups of marine benthic invertebrates. Only their first naupliar, preadult, and adult phases are planktonic. Monstrilloids are currently represented by more than 115 nominal species contained in four genera. Its taxonomic knowledge has been hampered by nomenclatural and descriptive problems derived from their peculiar ontogeny and poor definitions of taxa. One of the most important difficulties is that of matching males to females. The only reliable methods to link the sexes of a species are the confirmation of particular apomorphies shared by both sexes, finding both sexes in the same host or as a pre-copulatory male-female pair in the plankton, or by the use of molecular markers. A general overview of the morphology of the group and its life cycle is provided herein. Recently, upgraded descriptive standards have been established and the relevance of redescribing taxa based on type and museum specimens has been demonstrated. The rate of species description per decade has had several peaks between 1840 and 2010: (1971-1980, 1991-2000, 2001-2010), each related to the activity of a few researchers. An analysis of the world distribution of published records of the Monstrilloida revealed that the Northeast Atlantic is the best studied region (45% of all records), followed by the Northwestern Atlantic (17%); the least surveyed areas include regions of the southern hemisphere (less than 3%). The Northeast Atlantic region harbors the highest number of known species (32 nominal species), followed by the Caribbean Sea/Gulf of Mexico (24), the Mediterranean/Black Sea (19), Indonesia-Malaysia-Philippines region (17), Japanese waters (17), and the Brazil-Argentina area (16). Other than these generalized patterns, little can be concluded concerning the biogeography of the group. Many species records are doubtful or improbable, and purportedly cosmopolitan nominal species are being revealed as species complexes yet to be studied.
    Matched MeSH terms: Phylogeography
  8. Fulltext Dormant phages of Helicobacter pylori reveal distinct populations in Europe
    Vale FF, Vadivelu J, Oleastro M, Breurec S, Engstrand L, Perets TT, et al.
    Sci Rep, 2015;5:14333.
    PMID: 26387443 DOI: 10.1038/srep14333
    Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.
    Matched MeSH terms: Phylogeography
  9. Fulltext Emergence of the Asian lineage dengue virus type 3 genotype III in Malaysia
    Tan KK, Zulkifle NI, Sulaiman S, Pang SP, NorAmdan N, MatRahim N, et al.
    BMC Evol. Biol., 2018 04 24;18(1):58.
    PMID: 29699483 DOI: 10.1186/s12862-018-1175-4
    BACKGROUND: Dengue virus type 3 genotype III (DENV3/III) is associated with increased number of severe infections when it emerged in the Americas and Asia. We had previously demonstrated that the DENV3/III was introduced into Malaysia in the late 2000s. We investigated the genetic diversity of DENV3/III strains recovered from Malaysia and examined their phylogenetic relationships against other DENV3/III strains isolated globally.

    RESULTS: Phylogenetic analysis revealed at least four distinct DENV3/III lineages. Two of the lineages (DENV3/III-B and DENV3/III-C) are current actively circulating whereas the DENV3/III-A and DENV3/III-D were no longer recovered since the 1980s. Selection pressure analysis revealed strong evidence of positive selection on a number of amino acid sites in PrM, E, NS1, NS2a, NS2b, NS3, NS4a, and NS5. The Malaysian DENV3/III isolates recovered in the 1980s (MY.59538/1987) clustered into DENV3/III-B, which was the lineage with cosmopolitan distribution consisting of strains actively circulating in the Americas, Africa, and Asia. The Malaysian isolates recovered after the 2000s clustered within DENV3/III-C. This DENV3/III-C lineage displayed a more restricted geographical distribution and consisted of isolates recovered from Asia, denoted as the Asian lineage. Amino acid variation sites in NS5 (NS5-553I/M, NS5-629 T, and NS5-820E) differentiated the DENV3/III-C from other DENV3 viruses. The codon 629 of NS5 was identified as a positively selected site. While the NS5-698R was identified as unique to the genome of DENV3/III-C3. Phylogeographic results suggested that the recent Malaysian DENV3/III-C was likely to have been introduced from Singapore in 2008 and became endemic. From Malaysia, the virus subsequently spread into Taiwan and Thailand in the early part of the 2010s and later reintroduced into Singapore in 2013.

    CONCLUSIONS: Distinct clustering of the Malaysian old and new DENV3/III isolates suggests that the currently circulating DENV3/III in Malaysia did not descend directly from the strains recovered during the 1980s. Phylogenetic analyses and common genetic traits in the genome of the strains and those from the neighboring countries suggest that the Malaysian DENV3/III is likely to have been introduced from the neighboring regions. Malaysia, however, serves as one of the sources of the recent regional spread of DENV3/III-C3 within the Asia region.

    Matched MeSH terms: Phylogeography
  10. Epidemiology of henipavirus disease in humans
    Luby SP, Gurley ES
    Curr. Top. Microbiol. Immunol., 2012;359:25-40.
    PMID: 22752412 DOI: 10.1007/82_2012_207
    All seven recognized human cases of Hendra virus (HeV) infection have occurred in Queensland, Australia. Recognized human infections have all resulted from a HeV infected horse that was unusually efficient in transmitting the virus and a person with a high exposure to infectious secretions. In the large outbreak in Malaysia where Nipah virus (NiV) was first identified, most human infections resulted from close contact with NiV infected pigs. Outbreak investigations in Bangladesh have identified drinking raw date palm sap as the most common pathway of NiV transmission from Pteropus bats to people, but person-to-person transmission of NiV has been repeatedly identified in Bangladesh and India. Although henipaviruses are not easily transmitted to people, these newly recognized, high mortality agents warrant continued scientific attention.
    Matched MeSH terms: Phylogeography
  11. Evolution of endemism on a young tropical mountain
    Merckx VS, Hendriks KP, Beentjes KK, Mennes CB, Becking LE, Peijnenburg KT, et al.
    Nature, 2015 Aug 20;524(7565):347-50.
    PMID: 26266979 DOI: 10.1038/nature14949
    Tropical mountains are hot spots of biodiversity and endemism, but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue' in montane biodiversity hot spots under climate change scenarios.
    Matched MeSH terms: Phylogeography*
  12. Evolutionary and biogeographic history of the black fly Simulium wayani (Diptera: Simuliidae) on the island of Timor
    Adler PH, Takaoka H, Sofian-Azirun M, Chen CD, Suana IW
    Acta Trop, 2019 May;193:1-6.
    PMID: 30772330 DOI: 10.1016/j.actatropica.2019.02.017
    A recently described species of black fly, Simulium wayani Takaoka and Chen, from the island of Timor was chromosomally mapped to provide insights into its evolutionary and biogeographic history. The morphologically based species status of S. wayani is supported by a suite of fixed chromosomal rearrangements and unique sex chromosomes derived primarily from a large pool of polymorphisms in the S. ornatipes complex in Australia. The banding patterns of its polytene chromosomes indicate that S. wayani is closely related to a pair of homosequential cryptic species (S. norfolkense Dumbleton and S. ornatipes cytoform A2) in the S. ornatipes Skuse complex on mainland Australia; all three species uniquely share the same amplified band in their chromosomal complement. The low level of polymorphism and heterozygosity in S. wayani, relative to Australian populations of the S. ornatipes complex, suggests few colonization events from the larger land mass.
    Matched MeSH terms: Phylogeography
  13. Evolutionary and ecological forces influencing population diversification in Bornean montane passerines
    Chua VL, Smith BT, Burner RC, Rahman MA, Lakim M, Prawiradilaga DM, et al.
    Mol Phylogenet Evol, 2017 Aug;113:139-149.
    PMID: 28545973 DOI: 10.1016/j.ympev.2017.05.016
    The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal. Morphological and ecological characteristics of each species are also examined using phylogenetic generalized least-squares (PGLS) for correlation with population structure. Populations in only four of the 12 species are subdivided into distinct clades or haplotype groups. Although this subdivision occurred at about the same time in each species (ca. 0.6-0.7Ma), the spatial positioning of the genetic break differs among the species. In two species, northeastern populations are genetically divergent from populations elsewhere on the island. In the other two species, populations in the main Bornean mountain chain, including the northeast, are distinct from those on two isolated peaks in northwestern Borneo. We suggest different historical forces played a role in shaping these two distributions, despite commonality in timing. PGLS analysis showed that only a single characteristic-hand-wing index-is correlated with population structure. Birds with longer wings, and hence potentially more dispersal power, have less population structure. To understand historical forces influencing montane population structure on Borneo, future studies must compare populations across the entirety of Sundaland.
    Matched MeSH terms: Phylogeography
  14. Fulltext First molecular data and the phylogenetic position of the millipede-like centipede Edentistoma octosulcatum Tömösváry, 1882 (Chilopoda: Scolopendromorpha: Scolopendridae)
    Vahtera V, Edgecombe GD
    PLoS One, 2014;9(11):e112461.
    PMID: 25389773 DOI: 10.1371/journal.pone.0112461
    Edentistoma octosulcatum Tömösváry, 1882, is a rare, superficially millipede-like centipede known only from Borneo and the Philippines. It is unique within the order Scolopendromorpha for its slow gait, robust tergites, and highly modified gizzard and mandible morphology. Not much is known about the biology of the species but it has been speculated to be arboreal with a possibly vegetarian diet. Until now its phylogenetic position within the subfamily Otostigminae has been based only on morphological characters, being variably ranked as a monotypic tribe (Arrhabdotini) or classified with the Southeast Asian genus Sterropristes Attems, 1934. The first molecular data for E. octosulcatum sourced from a newly collected specimen from Sarawak were analysed with and without morphology. Parsimony analysis of 122 morphological characters together with two nuclear and two mitochondrial loci resolves Edentistoma as sister group to three Indo-Australian species of Rhysida, this clade in turn grouping with Ethmostigmus, whereas maximum likelihood and parsimony analyses of the molecular data on their own ally Edentistoma with species of Otostigmus. A position of Edentistoma within Otostigmini (rather than being its sister group as predicted by the Arrhabdotini hypothesis) is consistently retrieved under different analytical conditions, but support values within the subfamily remain low for most nodes. The species exhibits strong pushing behaviour, suggestive of burrowing habits. Evidence against a suggested vegetarian diet is provided by observation of E. octosulcatum feeding on millipedes in the genus Trachelomegalus.
    Matched MeSH terms: Phylogeography
  15. From discovery to spread: The evolution and phylogeny of Getah virus
    Li YY, Liu H, Fu SH, Li XL, Guo XF, Li MH, et al.
    Infect Genet Evol, 2017 11;55:48-55.
    PMID: 28827175 DOI: 10.1016/j.meegid.2017.08.016
    Getah virus (GETV) was first isolated in Malaysia in 1955. Since then, epidemics in horses and pigs caused by GETV have resulted in huge economic losses. At present, GETV has spread across Eurasia and Southeast Asia, including mainland China, Korea, Japan, Mongolia, and Russia. Data show that the Most Recent Common Ancestor (MRCA) of GETV existed about 145years ago (95% HPD: 75-244) and gradually evolved into four distinct evolutionary populations: Groups I-IV. The MRCA of GETVs in Group III, which includes all GETVs isolated from mosquitoes, pigs, horses, and other animals since the 1960s (from latitude 19°N to 60°N), existed about 51years ago (95% HPD: 51-72). Group III is responsible for most viral epidemics among domestic animals. An analysis of the GETV E2 protein sequence and structure revealed seven common amino acid mutation sites. These sites are responsible for the structural and electrostatic differences detected between widespread Group III isolates and the prototype strain MM2021. These differences may account for the recent geographical radiation of the virus. Considering the economic significance of GETV infection in pigs and horses, we recommend the implementation of strict viral screening and monitoring programs.
    Matched MeSH terms: Phylogeography
  16. Fulltext Genetic Diversity and Demographic History of Ganoderma boninense in Oil Palm Plantations of Sarawak, Malaysia Inferred from ITS Regions
    Midot F, Lau SYL, Wong WC, Tung HJ, Yap ML, Lo ML, et al.
    Microorganisms, 2019 Oct 16;7(10).
    PMID: 31623251 DOI: 10.3390/microorganisms7100464
    Ganoderma boninense causes basal stem rot (BSR) and is responsible for substantial economic losses to Southeast Asia's palm oil industry. Sarawak, a major producer in Malaysia, is also affected by this disease. Emergence of BSR in oil palm planted on peat throughout Sarawak is alarming as the soil type was previously regarded as non-conducive. Phylogenetic analysis indicated a single species, G. boninense as the cause of BSR in Sarawak. Information on evolutionary and demographic history for G. boninense in Sarawak inferred through informative genes is lacking. Hence, a haplotype study on single nucleotide polymorphisms in internal transcribed spacers (SNPs-ITS) of G. boninense was carried out. Sequence variations were analysed for population structure, phylogenetic and phylogeographic relationships. The internal transcribed spacers (ITS) region of 117 isolates from four populations in eight locations across Sarawak coastal areas revealed seven haplotypes. A major haplotype, designated GbHap1 (81.2%), was found throughout all sampling locations. Single nucleotide polymorphisms were observed mainly in the ITS1 region. The genetic structure was not detected, and genetic distance did not correlate with geographical distance. Haplotype network analysis suggested evidence of recent demographic expansion. Low genetic differences among populations also suggested that these isolates belong to a single G. boninense founder population adapting to oil palm as the host.
    Matched MeSH terms: Phylogeography
  17. Genetic Diversity and Phylogenetic Relationships of Cytochrome C Oxidase Subunit I in Cimex hemipterus (Hemiptera: Cimicidae) Populations in Malaysia
    Seri Masran SNA, Ab Majid AH
    J Med Entomol, 2017 Jul 01;54(4):974-979.
    PMID: 28399302 DOI: 10.1093/jme/tjw227
    The tropical bed bug is scientifically recognized as a significant public health problem. While there is an increased awareness about their resurgence by medical and life science committees, efficient bed bug management still remains unresolved. The solution may soon arise, as information about bed bugs' infestation dynamics and systematics are becoming more distinguishable. Recent developments in studies about bed bugs are based on molecular intervention by determining their genetic variation and phylogeography. The aim of this study is to assess the phylogenetic relationships and genetic diversity among the populations of tropical bed bugs inhabiting Malaysia. A molecular genotyping study was conducted with 22 tropical bed bug populations composed of three individuals per population. The mitochondrial (COI) gene was used as a marker. The data obtained were analyzed using the T-Coffee, ClustalX, MEGA 6.0, and PAUP software. The results showed one main monophyletic clade that consisted of two groups: Ch01 and Ch02. Ch02 consists of samples from the Bandar Hilir population, differing from the other populations studied by one singleton base. However, as there were no changes in the amino acid, this singleton genetic variation was considered to have no effect on genetic differentiation. Ch01 shows similarity with some sequence of Cimex hemipterus (F.) from Thailand, suggesting an international diversity connection. The disparity index apparently suggests that all isolates are homogeneous populations and are supported by the low value of the mean pairwise distance between isolates. This study will increase the knowledge about phylogeographic diversity of tropical bed bug in Malaysia.
    Matched MeSH terms: Phylogeography
  18. Fulltext Genetic Diversity and Phylogeography of Thottapalayam thottimvirus (Hantaviridae) in Asian House Shrew (Suncus murinus) in Eurasia
    Kikuchi F, Aoki K, Ohdachi SD, Tsuchiya K, Motokawa M, Jogahara T, et al.
    Front Cell Infect Microbiol, 2020;10:438.
    PMID: 32974220 DOI: 10.3389/fcimb.2020.00438
    Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3-96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.
    Matched MeSH terms: Phylogeography
  19. Genetic Diversity of Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex Across Malaysia
    Shadmany M, Boykin LM, Muhamad R, Omar D
    J Econ Entomol, 2019 02 12;112(1):75-84.
    PMID: 30272175 DOI: 10.1093/jee/toy273
    The tobacco whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex with members capable of inducing huge economic losses. Precise identification of members of this complex proves essential in managing existing populations and preventing new incursions. Despite records of serious outbreaks of this pest in Malaysia little is known about species status of B. tabaci in this region. To address this, a comprehensive sampling of B. tabaci from different host plants was conducted in 10 states of Malaysia from 2010 to 2012. Members of the complex were identified by sequencing partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene and constructing a Bayesian phylogenetic tree. Seven putative species were identified including Asia I, Mediterranean (MED), China 1, China 2, Asia II 6, Asia II 7, and Asia II 10. The most important finding of the study is the identification of the invasive MED species from locations without previous records of this species. All putative species except Asia I and MED are recorded from Malaysia for the first time. This study provided the first introductory map of B. tabaci species composition in Malaysia and emphasizes the urgent need for further studies to assess the status of MED invasion in this country.
    Matched MeSH terms: Phylogeography
  20. Fulltext Genetic and morphological analyses of Gracilaria firma and G. changii (Gracilariaceae, Rhodophyta), the commercially important agarophytes in western Pacific
    Ng PK, Lin SM, Lim PE, Hurtado AQ, Phang SM, Yow YY, et al.
    PLoS One, 2017;12(7):e0182176.
    PMID: 28759629 DOI: 10.1371/journal.pone.0182176
    Many studies classifying Gracilaria species for the exploitation of agarophytes and the development of the agar industry were conducted before the prevalence of molecular tools, resulting in the description of many species based solely on their morphology. Gracilaria firma and G. changii are among the commercially important agarophytes from the western Pacific; both feature branches with basal constrictions that taper toward acute apices. In this study, we contrasted the morpho-anatomical circumscriptions of the two traditionally described species with molecular data from samples that included representatives of G. changii collected from its type locality. Concerted molecular analyses using the rbcL and cox1 gene sequences, coupled with morphological observations of the collections from the western Pacific, revealed no inherent differences to support the treatment of the two entities as distinct taxa. We propose merging G. changii (a later synonym) into G. firma and recognize G. firma based on thallus branches with abrupt basal constrictions that gradually taper toward acute (or sometimes broken) apices, cystocarps consisting of small gonimoblast cells and inconspicuous multinucleate tubular nutritive cells issuing from gonimoblasts extending into the inner pericarp at the cystocarp floor, as well as deep spermatangial conceptacles of the verrucosa-type. The validation of specimens under different names as a single genetic species is useful to allow communication and knowledge transfer among groups from different fields. This study also revealed considerably low number of haplotypes and nucleotide diversity with apparent phylogeographic patterns for G. firma in the region. Populations from the Philippines and Taiwan were divergent from each other as well as from the populations from Malaysia, Thailand, Singapore and Vietnam. Establishment of baseline data on the genetic diversity of this commercially important agarophyte is relevant in the context of cultivation, as limited genetic diversity may jeopardize the potential for its genetic improvement over time.
    Matched MeSH terms: Phylogeography
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