Displaying publications 1 - 20 of 38 in total

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  1. Fulltext Species identification of Malayan Gaur, Kedah-Kelantan and Bali cattle using polymerase chain reaction-restricted fragment length polymorphism
    Romaino SM, Fazly-Ann ZA, Loo SS, Hafiz MM, Hafiz MD, Iswadi MI, et al.
    Genet. Mol. Res., 2014;13(1):406-14.
    PMID: 24535867 DOI: 10.4238/2014.January.21.8
    Mitochondrial DNA (mtDNA) is a useful genetic marker that can be used for species identification. The cytochrome b (Cyt b) gene is a suitable mtDNA candidate gene for use in phylogenetic analyses due to its sequence variability, which makes it appropriate for comparisons at the subspecies, species, and genus levels. This study was conducted to develop a rapid molecular method for species identification of Malayan gaur (Bos gaurus hubbacki), Kedah-Kelantan (KK) (Bos indicus), and Bali (Bos javanicus) cattle in Malaysia. DNA was extracted from blood samples of 8 Malayan gaurs, 30 KK, and 28 Bali cattle. A set of both specific and universal primers for the Cyt b gene were used in PCR amplification. DNA sequences obtained were then analyzed using BioEdit and Restriction Mapper softwares. The PCR products obtained from Cyt b gene amplification were then subjected to restriction enzyme digestion. The amplification, using both specific and universal primers, produced a 154- and a 603-bp fragment, respectively, in all three species. Two restriction enzymes, NlaIV and SspI, were used to obtain specific restriction profiles that allowed direct identification of Malayan gaur, KK, and Bali cattle. Our findings indicate that all three species can be identified separately using a combination of universal primers and the restriction enzyme SspI.
    Matched MeSH terms: Cytochromes b/genetics
  2. Fulltext Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences
    Rosli MK, Zakaria SS, Syed-Shabthar SM, Zainal ZZ, Shukor MN, Mahani MC, et al.
    Genet. Mol. Res., 2011;10(1):482-93.
    PMID: 21476194 DOI: 10.4238/vol10-1gmr1002
    The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.
    Matched MeSH terms: Cytochromes b/genetics*
  3. Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland
    Ng CK, Tan J
    J Fish Biol, 2021 Oct;99(4):1256-1273.
    PMID: 34159593 DOI: 10.1111/jfb.14829
    Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.
    Matched MeSH terms: Cytochromes b/genetics
  4. Leucocytozoon caulleryi in Broiler Chicken Flocks: Clinical, Hematologic, Histopathologic, and Molecular Detection
    Elbestawy AR, Ellakany HF, Abd El-Hamid HS, Gado AR, Geneedy AM, Noreldin AE, et al.
    Avian Dis, 2021 09;65(3):407-413.
    PMID: 34427415 DOI: 10.1637/0005-2086-65.3.407
    Despite the vast Egyptian poultry production, scanty information is available concerning the infection of haemprotozoan parasites as pathogens in commercial broilers. In the present study, we provided the first detection of leucocytozoonosis in five broiler chicken flocks in El-Beheira Egyptian governorate. Despite the low mortality rates in the affected flocks (0.3%-1% as a 5-day mortality), severe postmortem (hemorrhagic spots and scars) and histopathologic lesions appeared in different organs including skeletal muscles, liver, kidney, pancreas, abdominal cavity, and bursa of Fabricius. Evaluation of blood smears revealed gametocytes in erythrocytes and leukocytes. Conventional reverse transcriptase-PCR and partial sequence analysis of mitochondrial cytochrome oxidase b gene detected Leucocytozoon caulleryi. GenBank accession numbers of the five Egyptian L. caulleryi isolates were obtained. The five L. caulleryi were 99.9% identical to each other and 99.14% similar to the L. caulleryi mitochondrial DNA gene of Asian strains from India, Japan, Malaysia, South Korea, Taiwan, and Thailand.
    Matched MeSH terms: Cytochromes b/genetics
  5. Fulltext Molecular phylogeny of the bamboo sharks (Chiloscyllium spp.)
    Masstor NH, Samat A, Nor SM, Md-Zain BM
    Biomed Res Int, 2014;2014:213896.
    PMID: 25013766 DOI: 10.1155/2014/213896
    Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences' lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species.
    Matched MeSH terms: Cytochromes b/genetics*
  6. Application of 16s rDNA and cytochrome b ribosomal markers in studies of lineage and fish populations structure of aquatic species
    Baharum SN, Nurdalila AA
    Mol Biol Rep, 2012 May;39(5):5225-32.
    PMID: 22167328 DOI: 10.1007/s11033-011-1320-2
    The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics.
    Matched MeSH terms: Cytochromes b/genetics*
  7. Fulltext Phylogenetic relationships of leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes
    Vun VF, Mahani MC, Lakim M, Ampeng A, Md-Zain BM
    Genet. Mol. Res., 2011;10(1):368-81.
    PMID: 21365553 DOI: 10.4238/vol10-1gmr1048
    Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.
    Matched MeSH terms: Cytochromes b/genetics*
  8. Phylogenetic analysis of hampala fishes (subfamily Cyprininae) in Malaysia inferred from partial mitochondrial cytochrome B DNA sequences
    Ryan JR, Esa YB
    Zoolog Sci, 2006 Oct;23(10):893-901.
    PMID: 17116992
    This study examined 396 base pairs of the mitochondrial cytochrome b gene from 110 individuals belonging to the genus Hampala, a group of freshwater cyprinids that inhabit Southeast Asia. The samples were taken from various locations throughout Sarawak, Sabah, and peninsular Malaysia. The nucleotide sequences were subjected to phylogenetic analyses by using the neighbor-joining, maximum parsimony, and maximum likelihood methods. All three methods revealed the reciprocally monophyletic relationship of Hampala macrolepidota to the other Hampala forms, thus strongly supporting its status as a distinct species. Phylogenetic analysis also discovered the existence of two H. bimaculata lineages endemic to Borneo: (1) a newly identified species from the southern and central part of Sarawak assigned as H. bimaculata Type A and (2) the previously described H. bimaculata from northern Sarawak and the west coast of Sabah assigned as H. bimaculata Type B. However, the status of H. sabana and an intermediate form were not elucidated. The results suggest that the intermediate form from the Tawau population is actually a subpopulation of H. sabana, while the highly divergent intermediate form from Kalabakan could represent a cryptic species. The sharing of H. macrolepidota haplotypes in the southern peninsular Malaysia and southern and central Sarawak samples (Hm1 and Hm2) reflected the recent disconnection of the two regions, during the late Pleistocene. Overall, the partial sequence of the mitochondrial cytochrome b gene was useful for resolving the phylogenetic relationships among Hampala fishes in Malaysia.
    Matched MeSH terms: Cytochromes b/genetics*
  9. Fulltext High connectivity in Rastrelliger kanagurta: influence of historical signatures and migratory behaviour inferred from mtDNA cytochrome b
    Akib NA, Tam BM, Phumee P, Abidin MZ, Tamadoni S, Mather PB, et al.
    PLoS One, 2015;10(3):e0119749.
    PMID: 25786216 DOI: 10.1371/journal.pone.0119749
    Phylogeographic patterns and population structure of the pelagic Indian mackerel, Rastrelliger kanagurta were examined in 23 populations collected from the Indonesian-Malaysian Archipelago (IMA) and the West Indian Ocean (WIO). Despite the vast expanse of the IMA and neighbouring seas, no evidence for geographical structure was evident. An indication that R. kanagurta populations across this region are essentially panmictic. This study also revealed that historical isolation was insufficient for R. kanagurta to attain migration drift equilibrium. Two distinct subpopulations were detected between the WIO and the IMA (and adjacent populations); interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the IMA and WIO regions suggest historical isolation as a result of fluctuations in sea levels during the late Pleistocene. This occurrence resulted in the evolution of a phylogeographic break for this species to the north of the Andaman Sea.
    Matched MeSH terms: Cytochromes b/genetics*
  10. Tracking the southern river terrapin (Batagur affinis) through environmental DNA: prospects and challenges
    Wilson JJ, Sing KW, Chen PN, Zieritz A
    Mitochondrial DNA A DNA Mapp Seq Anal, 2018 08;29(6):862-866.
    PMID: 28885060 DOI: 10.1080/24701394.2017.1373109
    Environmental DNA detection has emerged as a powerful tool to monitor aquatic species without the need for capture or visual identification and is particularly useful for rare or elusive species. Our objective was to develop an eDNA approach for detecting the southern river terrapin (Batagur affinis) in Malaysia. We designed species-specific primers for a fragment of B. affinis mtDNA and evaluated their effectiveness in silico, in vitro and in situ. The primers amplified 110 bp of the cytochrome b mtDNA sequence of B. affinis from aquarium water samples housing nine juvenile B. affinis. We also successfully detected B. affinis eDNA from river samples taken from a site where turtles were known to be in the vicinity. Prospects and challenges of using an eDNA approach to help determine the distribution of B. affinis, essential information for an effective conservation plan, are discussed.
    Matched MeSH terms: Cytochromes b/genetics
  11. 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: Cytochromes b/genetics*
  12. Fulltext Detection and molecular identification of blood parasites in rodents captured from urban areas of southern Sarawak, Malaysian Borneo
    Perison PWD, Amran NS, Adrus M, Anwarali Khan FA
    Vet Med Sci, 2022 Sep;8(5):2059-2066.
    PMID: 35636429 DOI: 10.1002/vms3.849
    BACKGROUND: Rodent species are well known for their potential as hosts and reservoirs for various zoonotic diseases. Studies on blood parasite infection in small mammals focused on urban cities in Peninsular Malaysia and have been conducted over the years. In contrast, there are information gaps related to molecular detection of blood parasites in urban areas of Sarawak that are associated with veterinary importance and zoonotic spillover potential. Increasing prevalence and transmission of blood parasite diseases is the most crucial public health issue, particularly in developing urban areas of Sarawak. Therefore, molecular identification studies were performed to determine and identify the blood parasites infecting rodents.

    METHODS: A total of 40 rodent blood samples were analysed for blood parasite infection and a combined approach using polymerase chain reaction-based technique, and traditional microscopic examination (blood smear test) was conducted. 18s rRNA (Plasmodium spp.) and cytochrome b (Hepatocystis spp.) gene marker were used to identify the blood parasites.

    RESULTS: Note that 67.5% (n = 27) blood samples were tested negative for blood parasites, while 32.5% (n = 13) blood samples collected were infected with at least one protozoan parasite. Out of 13 samples, 69.2% (n = 9) were detected with Hepatocystis sp., while 15.4% (n = 2) were positive with Hepatozoon ophisauri. Two individuals had multiple infections from both species. No Plasmodium spp. have been detected throughout this study using universal primer (targeted Plasmodium spp.); however, different parasite species which were H. ophisauri were detected.

    CONCLUSION: Although there is no evidence of human infection from H. ophisauri and Hepatocystis sp. detected from the study, the data show the host species are heavily infected, and the information is essential for future prevention of zoonotic outbreaks and surveillance programmes. Therefore, it is suggested that the surveillance programmes should be incorporated in targeted areas with a high risk of disease emergence.

    Matched MeSH terms: Cytochromes b/genetics
  13. Genetic diversity of avian haemosporidians in Malaysia: cytochrome b lineages of the genera Plasmodium and Haemoproteus (Haemosporida) from Selangor
    Ivanova K, Zehtindjiev P, Mariaux J, Georgiev BB
    Infect Genet Evol, 2015 Apr;31:33-9.
    PMID: 25577987 DOI: 10.1016/j.meegid.2015.01.004
    The knowledge of the diversity of haemosporidian parasites is of primary importance as their representatives include agents of bird malaria. We investigated the occurrence of Haemoproteus spp. and Plasmodium spp. in bird populations from a single locality in the State of Selangor, Peninsular Malaysia, and report on the parasite prevalence of the two genera. A combination of methods (molecular and morphological) was used for detecting these parasites. Seventy-nine bird individuals were caught using mist-nets in July and August 2010 at Gombak Field Station of the University of Malaya, Kuala Lumpur. In total, 23 birds were identified as positive for Haemoproteus or Plasmodium infection and one individual was recognized as carrying mixed infection. The total prevalence of haemosporidians in the collected samples was 30.3%. Infections with parasites of the genus Haemoproteus were predominant compared to those of the genus Plasmodium. In total, 10 new cyt b lineages of Haemoproteus spp. and 3 new cyt b lineages of Plasmodium spp. were recorded in this study. From all recorded haemosporidian lineages (16 in total), 3 were known from previous studies - hCOLL2, hYWT2 and pNILSUN1. Two of them are linked with their corresponding morphospecies - Haemoproteus pallidus (COLL2) and Haemoproteus motacillae (YWT2). The morphological analysis in the present study confirmed the results obtained by the PCR method relative to prevalence, with 25.3% total prevalence of Haemoproteus and Plasmodium parasites. The intensities of infection varied between 0.01% and 19%. Most infections were light, with intensities below 0.1%. The present study is the first molecular survey of the protozoan blood parasites of the order Haemosporida recorded in Malaysia.
    Matched MeSH terms: Cytochromes b/genetics
  14. 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: Cytochromes b/genetics
  15. 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: Cytochromes b/genetics
  16. PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia
    Rahim MH, Ismail P, Alias R, Muhammad N, Mat Jais AM
    Gene, 2012 Feb 15;494(1):1-10.
    PMID: 22197656 DOI: 10.1016/j.gene.2011.12.015
    Haruan (Channa striatus) is in great demand in the Malaysian domestic fish market. In the present study, mtDNA cyt b was used to investigate genetic variation of C. striatus among populations in Peninsular Malaysia. The overall population of C. striatus demonstrated a high level of haplotype diversity (h) and a low-to-moderate level of nucleotide diversity (π). Analysis of molecular variance (AMOVA) results showed a significantly different genetic differentiation among 6 populations (F(ST)=0.37566, P=0.01). Gene flow (Nm) was high and ranged from 0.32469 to infinity (∞). No significant relationship between genetic distance and geographic distance was detected. A UPGMA tree based on the distance matrix of net interpopulation nucleotide divergence (d(A)) and haplotype network of mtDNA cyt b revealed that C. striatus is divided into 2 major clades. The neutrality and mismatch distribution tests for all populations suggested that C. striatus in the study areas had undergone population expansion. The estimated time of population expansion in the mtDNA cyt b of C. striatus populations occurred 0.72-6.19 million years ago. Genetic diversity of mtDNA cyt b and population structure among Haruan populations in Peninsular Malaysia will be useful in fisheries management for standardization for Good Agriculture Practices (GAP) in fish-farming technology, as well as providing the basis for Good Manufacturing Practices (GMP).
    Matched MeSH terms: Cytochromes b/genetics*
  17. Fulltext Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers
    Ang KC, Leow JW, Yeap WK, Hood S, Mahani MC, Md-Zain BM
    Genet. Mol. Res., 2011;10(2):640-9.
    PMID: 21491374 DOI: 10.4238/vol10-2gmr1011
    Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory.
    Matched MeSH terms: Cytochromes b/genetics
  18. Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia
    Lim HC, Sheldon FH
    Mol Ecol, 2011 Aug;20(16):3414-38.
    PMID: 21777318 DOI: 10.1111/j.1365-294X.2011.05190.x
    Sundaland has a dynamic geographic history because its landmasses were periodically interconnected when sea levels fell during glacial periods. Superimposed on this geographic dynamism were environmental changes related to climatic oscillations. To investigate how tropical taxa responded to such changes, we studied the divergence and demographic history of two co-distributed rainforest passerine species, Arachnothera longirostra and Malacocincla malaccensis. We sampled birds primarily from Borneo and the Malay Peninsula, which straddle the now-submerged Sunda shelf, and analysed multilocus DNA data with a variety of coalescent and gene genealogy methods. Cross-shelf divergence in both species occurred well before the last glacial maximum, i.e., before the most recent land connection. However, post-divergence gene flow occurred, and it was more pronounced in A. longirostra (a highly vagile nectarivore/insectivore) than in M. malaccensis (an understory insectivore). Despite current habitat continuity on Borneo, the population of M. malaccensis in northeastern Borneo is substantially divergent from that on the rest of the island. The NE population experienced dramatic demographic fluctuations, probably because of competition with the other population, which expanded from western Borneo after the mid-Pleistocene. In contrast, the Borneo population of A. longirostra has little structure and appears to have experienced demographic expansion 16 kya, long after it had diverged from the Malay Peninsula population (630-690 kya). Malay Peninsula populations of both species have remained relatively stable. Overall, the most recent glacial period was not the chief determinant of the evolutionary dynamics of our study species, and in this respect, they are different from temperate species.
    Matched MeSH terms: Cytochromes b/genetics
  19. Fulltext Optimization of PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA
    Rosli MK, Zamzuriada AS, Syed-Shabthar SM, Mahani MC, Abas-Mazni O, Md-Zain BM
    Genet. Mol. Res., 2011;10(4):2554-68.
    PMID: 22033937 DOI: 10.4238/2011.October.19.2
    PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
    Matched MeSH terms: Cytochromes b/genetics*
  20. Morphological divergence, reproductive isolating mechanism, and molecular phylogenetic relationships among Indonesia, Malaysia, and Japan populations of the Fejervarya limnocharis complex (Anura, Ranidae)
    Djong TH, Matsui M, Kuramoto M, Belabut DM, Sen YH, Nishioka M, et al.
    Zoolog Sci, 2007 Dec;24(12):1197-212.
    PMID: 18271636 DOI: 10.2108/zsj.24.1197
    In order to elucidate the taxonomic status of the Fejervarya limnocharis complex relative to Malaysia and Japan populations, morphological observations and molecular phylogenetic analysis were carried out using three populations from Indonesia (type locality), Malaysia, and Japan. In addition, we conducted histological and spermatogenic observations using hybrids among these populations. Principal component and cluster analyses demonstrated that these populations could be clearly separated from one another. Abnormal testes were found in the hybrids between the Japan and Indonesia populations and between the Japan and Malaysia populations, but testes of the controls and hybrids between the Malaysia and Indonesia populations were quite normal. The mean number of univalents per cell was 5.42, 4.58, and 0.20 in hybrids between the Indonesia and Japan populations, Malaysia and Japan populations, and Indonesia and Malaysia populations, respectively. Sequence divergences in 16S rRNA and Cyt b genes were 0-0.4% (xbar=0.2%) and 0.3-1.5% (xbar=1.0%), respectively, between the Malaysia and Indonesia populations, and 2.4-2.6% (xbar=2.5%) and 11.0-12.0% (xbar=11.5%) between the Japan population and F. limnocharis complex, including the Malaysia and Indonesia populations and F. multistriata from China. This study indicated that the Malaysia population and F. multistriata from China should be designated as a subspecies of topotypic F. limnocharis, and that the Japan population should be regarded as a distinct species.
    Matched MeSH terms: Cytochromes b/genetics*
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