Displaying publications 361 - 380 of 1878 in total

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  1. Fulltext Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)
    Flury JM, Haas A, Brown RM, Das I, Pui YM, Boon-Hee K, et al.
    Mol Phylogenet Evol, 2021 10;163:107210.
    PMID: 34029720 DOI: 10.1016/j.ympev.2021.107210
    One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.
    Matched MeSH terms: Phylogeny
  2. Fulltext First Report of Trypanosoma theileri in Equine Host and Tabanus sp. in Malaysia
    Tan LP, Mohd Rajdi NZI, Mohamad MA, Mohamed M, Hamdan RH, Goriman Khan MAK, et al.
    J Equine Vet Sci, 2022 01;108:103807.
    PMID: 34875427 DOI: 10.1016/j.jevs.2021.103807
    Trypanosoma (Megatrypanum) theileri is a non-pathogenic or weakly pathogenic parasite of domestic cattle that is cyclically transmitted by blood-sucking insects, mainly tabanid flies. It has been reported in several countries like Brazil, Venezuela, Japan, Taiwan, Thailand, Vietnam, and the Philippines. Although the ruminant industry is actively expanded in Malaysia, T. theileri and T. theileri-like trypanosomes have never been reported from Malaysia. The low pathogenicity of this species might be the main reason for overlooking T. theileri in this country. This paper describes an unforeseen finding of T. theileri from the outbreak of T. evansi in the state of Kelantan, Malaysia. This is the first time T. theileri reported in Malaysia, and also the first time T. theileri is reported in equid. Clinical signs compatible with infection by blood protozoa were observed; however, it was uncertain whether they were due to T. theileri infection. The detection of T. theileri from the blood sample and Tabanus sp. were confirmed through molecular analysis with PCR and DNA sequencing. In the present study, T. theileri from one horse and one Tabanus sp. were clustered with sequences of the previously described phylogenetic lineages from Japan, Chad and Brazil cattle. Even though this species is claimed to be host-specific with ruminant host restriction, the finding from this study suggested that T. theileri can infect equine whilst other isolates are known to infect ruminant species only. It is suspected there were two genotypes of T. theileri circulating in at least two districts of Kelantan. Thus, further study on multiple DNA regions should be conducted to determine the strains of detected T. theileri in Malaysia. Its impact on the horse and cattle industry should also be revised.
    Matched MeSH terms: Phylogeny
  3. Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)
    Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, et al.
    Curr Biol, 2021 03 08;31(5):1002-1011.e9.
    PMID: 33485466 DOI: 10.1016/j.cub.2020.12.045
    Despite more than 2,000-fold variation in genome size, key features of genome architecture are largely conserved across angiosperms. Parasitic plants have elucidated the many ways in which genomes can be modified, yet we still lack comprehensive genome data for species that represent the most extreme form of parasitism. Here, we present the highly modified genome of the iconic endophytic parasite Sapria himalayana Griff. (Rafflesiaceae), which lacks a typical plant body. First, 44% of the genes conserved in eurosids are lost in Sapria, dwarfing previously reported levels of gene loss in vascular plants. These losses demonstrate remarkable functional convergence with other parasitic plants, suggesting a common genetic roadmap underlying the evolution of plant parasitism. Second, we identified extreme disparity in intron size among retained genes. This includes a category of genes with introns longer than any so far observed in angiosperms, nearing 100 kb in some cases, and a second category of genes with exceptionally short or absent introns. Finally, at least 1.2% of the Sapria genome, including both genic and intergenic content, is inferred to be derived from host-to-parasite horizontal gene transfers (HGTs) and includes genes potentially adaptive for parasitism. Focused phylogenomic reconstruction of HGTs reveals a hidden history of former host-parasite associations involving close relatives of Sapria's modern hosts in the grapevine family. Our findings offer a unique perspective into how deeply angiosperm genomes can be altered to fit an extreme form of plant parasitism and demonstrate the value of HGTs as DNA fossils to investigate extinct symbioses.
    Matched MeSH terms: Phylogeny
  4. Fulltext Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines
    Mohd Yussup SS, Marzukhi M, Md-Zain BM, Mamat K, Mohd Yusof FZ
    Evol Bioinform Online, 2017;13:1176934317735318.
    PMID: 29085238 DOI: 10.1177/1176934317735318
    The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.
    Matched MeSH terms: Phylogeny
  5. Fulltext Detection and genetic characterization of canine astroviruses in pet dogs in Guangxi, China
    Zhou H, Liu L, Li R, Qin Y, Fang Q, Balasubramaniam VR, et al.
    Virol J, 2017 08 17;14(1):156.
    PMID: 28814340 DOI: 10.1186/s12985-017-0823-4
    BACKGROUND: Astroviruses (AstVs) have been reported to infect and cause gastroenteritis in most animal species. Human AstVs were regarded the causative agent of viral diarrhea in children. In dogs, little is known about the epidemiology and clinical significance of AstV infection.

    FINDINGS: In this study, we collected and tested 253 rectal swabs from pet dogs; of which 64 samples (25.3%) tested positive for AstVs with diarrhea and 15 more samples (5.9%) also was identified as AstVs, however without any clinical signs. Phylogenetic analysis of 39 partial ORF1b sequences from these samples revealed that they are similar to AstVs, which can be subdivided into three lineages. Interestingly, out of the 39 isolates sequenced, 16 isolates are shown to be in the Mamastrovirus 5/canine astrovirus (CAstV) lineage and the remaining 23 isolates displayed higher similarities with known porcine astrovirus (PoAstV) 5 and 2. Further, analysis of 13 capsid sequences from these isolates showed that they are closely clustered with Chinese or Italy CAstV isolates.

    CONCLUSIONS: The findings indicate that CAstVs commonly circulate in pet dogs, and our sequencing results have shown the genomic diversity of CAstVs leading to increasing number of clusters.

    Matched MeSH terms: Phylogeny
  6. What are the evolutionary mechanisms explaining the similar species richness patterns in tropical mosses? Insights from the phylogeny of the pantropical genus Pelekium
    Norhazrina N, Vanderpoorten A, Hedenäs L, Patiño J
    Mol Phylogenet Evol, 2016 12;105:139-145.
    PMID: 27530707 DOI: 10.1016/j.ympev.2016.08.008
    As opposed to angiosperms, moss species richness is similar among tropical regions of the world, in line with the hypothesis that tropical bryophytes are extremely good dispersers. Here, we reconstructed the phylogeny of the pantropical moss genus Pelekium to test the hypothesis that high migration rates erase any difference in species richness among tropical regions. In contrast with this hypothesis, several species considered to have a pantropical range were resolved as a complex of species with a strong geographic structure. Consequently, a significant phylogeographical signal was found in the data, evidencing that cladogenetic diversification within regions takes place at a faster rate than intercontinental migration. The shape of the Pelekium phylogeny, along with the selection of a constant-rate model of diversification among species in the genus, suggests, however, that the cladogenetic speciation patterns observed in Pelekium are not comparable to some of the spectacular examples of tropical radiations reported in angiosperms. Rather, the results presented here point to the constant accumulation of diversity through time in Pelekium. This, combined with evidence for long-distance dispersal limitations in the genus, suggests that the similar patterns of species richness among tropical areas are better explained in terms of comparable rates of diversification across tropical regions than by the homogenization of species richness by recurrent migrations.
    Matched MeSH terms: Phylogeny
  7. Fulltext Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora
    Chung KF, Leong WC, Rubite RR, Repin R, Kiew R, Liu Y, et al.
    Bot Stud, 2014 Dec;55(1):1.
    PMID: 28510906 DOI: 10.1186/1999-3110-55-1
    BACKGROUND: The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia, a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species.

    RESULTS: Except for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia (SVLB), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium, Leprosae, and Petermannia, are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB, coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area.

    CONCLUSIONS: Based on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium: B. cavaleriei, B. pulvinifera, and B. wangii; sect. Leprosae: B. cylindrica and B. leprosa; sect. Petermannia: B. sinofloribunda). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB. Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.

    Matched MeSH terms: Phylogeny
  8. Effects of fermented soybean meal on carbon and nitrogen metabolisms in large intestine of piglets
    Zhang YT, Lu DD, Chen JY, Yu B, Liang JB, Mi JD, et al.
    Animal, 2018 Oct;12(10):2056-2064.
    PMID: 29362016 DOI: 10.1017/S1751731118000058
    Fermented soybean meal (FSM), which has lower anti-nutritional factors and higher active enzyme, probiotic and oligosaccharide contents than its unfermented form, has been reported to improve the feeding value of soybean meal, and hence, the growth performance of piglets. However, whether FSM can affect the bacterial and metabolites in the large intestine of piglets remains unknown. This study supplemented wet-FSM (WFSM) or dry-FSM (DFSM) (5% dry matter basis) in the diet of piglets and investigated its effects on carbon and nitrogen metabolism in the piglets' large intestines. A total of 75 41-day-old Duroc×Landrace×Yorkshire piglets with an initial BW of 13.14±0.22 kg were used in a 4-week feeding trial. Our results showed that the average daily gain of piglets in the WFSM and DFSM groups increased by 27.08% and 14.58% and that the feed conversion ratio improved by 18.18% and 7.27%, respectively, compared with the control group. Data from the prediction gene function of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on 16S ribosomal RNA (rRNA) sequencing showed that carbohydrate metabolism function families in the WFSM and DFSM groups increased by 3.46% and 2.68% and that the amino acid metabolism function families decreased by 1.74% and 0.82%, respectively, compared with the control group. These results were consistent with those of other metabolism studies, which showed that dietary supplementation with WFSM and DFSM increased the level of carbohydrate-related metabolites (e.g. 4-aminobutanoate, 5-aminopentanoate, lactic acid, mannitol, threitol and β-alanine) and decreased the levels of those related to protein catabolism (e.g. 1,3-diaminopropane, creatine, glycine and inosine). In conclusion, supplementation with the two forms of FSM improved growth performance, increased metabolites of carbohydrate and reduced metabolites of protein in the large intestine of piglets, and WFSM exhibited a stronger effect than DFSM.
    Matched MeSH terms: Phylogeny
  9. [A study on identification of edible bird's nests by DNA barcodes]
    Chen YJ, Liu WJ, Chen DN, Chieng SH, Jiang L
    Zhongguo Zhong Yao Za Zhi, 2017 Dec;42(23):4593-4597.
    PMID: 29376257 DOI: 10.19540/j.cnki.cjcmm.20171030.018
    To provide theoretical basis for the traceability and quality evaluation of edible bird's nests (EBNs), the Cytb sequence was applied to identify the origin of EBNs. A total of 39 experiment samples were collected from Malaysia, Indonesia, Vietnam and Thailand. Genomic DNA was extracted for the PCR reaction. The amplified products were sequenced. 36 sequences were downloaded from Gen Bank including edible nest swiftlet, black nest swiftlet, mascarene swiftlet, pacific swiftlet and germain's swiftlet. MEGA 7.0 was used to analyze the distinction of sequences by the method of calculating the distances in intraspecific and interspecific divergences and constructing NJ and UPMGA phylogenetic tree based on Kimera-2-parameter model. The results showed that 39 samples were from three kinds of EBNs. Interspecific divergences were significantly greater than the intraspecific one. Samples could be successfully distinguished by NJ and UPMGA phylogenetic tree. In conclusion, Cytb sequence could be used to distinguish the origin of EBNs and it is efficient for tracing the origin species of EBNs.
    Matched MeSH terms: Phylogeny
  10. Revision of Chimarrogale (Lipotyphla: Soricidae) from Vietnam with comments on taxonomy and biogeography of Asiatic water shrews
    Abramov AV, Bannikova AA, Lebedev VS, Rozhnov VV
    Zootaxa, 2017 Feb 15;4232(2):zootaxa.4232.2.5.
    PMID: 28264392 DOI: 10.11646/zootaxa.4232.2.5
    We analyzed the complete mitochondrial cytochrome b (cytb) gene and fragments of four nuclear loci: ApoB, RAG2, IRBP1 and BRCA1. These data allowed us to provide new insights into the diversity of the Asiatic water shrews of Indochina. A new, highly divergent genetic lineage of Chimarrogale was found in southern Vietnam, and this lineage included specimens from the provinces of Kon Tum, Dak Lak, and Lam Dong. Such finding represents the newest and southernmost records of Chimarrogale in Indochina. Morphological analysis classified the specimens from southern Vietnam as C. varennei proper, which is restricted to that region, whereas the polymorphic C. himalayica, which contained at least four cytochrome b haplogroups, occurred in central and northern Vietnam and southern China. This distinct C. varennei lineage closely related to the C. platycephalus + C. leander clade suggests the existence of an unknown glacial refuge in Tay Nguyen Plateau, southern Vietnam. Because the Bornean C. phaeura (i) was sister-group of the rest of Chimarrogale sensu lato and (ii) had a high genetic divergence (~15% for cytochrome b) and geographical isolation, we suggest that C. phaeura be placed into a separate genus, Crossogale Thomas, 1921. This genus should also include C. sumatrana (Sumatra) and C. hantu (Peninsular Malaysia). On those grounds, we propose a new classification system for Asiatic water shrews.
    Matched MeSH terms: Phylogeny
  11. Fulltext Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species
    Kaewdaungdee S, Sudmoon R, Tanee T, Lee SY, Chaveerach A
    Genes (Basel), 2022 Sep 22;13(10).
    PMID: 36292590 DOI: 10.3390/genes13101705
    In order to authenticate the genomic information of Barleriacristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997-152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae.
    Matched MeSH terms: Phylogeny
  12. A new species of Cyrtodactylus (Squamata: Gekkonidae) and the first record of C. otai from Son La Province, Vietnam
    Nguyen TQ, Pham AV, Ziegler T, Ngo HT, LE MD
    Zootaxa, 2017 Oct 30;4341(1):25-40.
    PMID: 29245698 DOI: 10.11646/zootaxa.4341.1.2
    We describe a new species of Cyrtodactylus on the basis of four specimens collected from the limestone karst forest of Phu Yen District, Son La Province, Vietnam. Cyrtodactylus sonlaensis sp. nov. is distinguished from the remaining Indochinese bent-toed geckos by a combination of the following characters: maximum SVL of 83.2 mm; dorsal tubercles in 13-15 irregular rows; ventral scales in 34-42 rows; ventrolateral folds prominent without interspersed tubercles; enlarged femoral scales 15-17 on each thigh; femoral pores 14-15 on each thigh in males, absent in females; precloacal pores 8, in a continuous row in males, absent in females; postcloacal tubercles 2 or 3; lamellae under toe IV 18-21; dorsal head with dark brown markings, in oval and arched shapes; nuchal loop discontinuous; dorsum with five brown bands between limb insertions, third and fourth bands discontinuous; subcaudal scales distinctly enlarged. In phylogenetic analyses, the new species is nested in a clade consisting of C. huongsonensis and C. soni from northern Vietnam and C. cf. pulchellus from Malaysia based on maximum likelihood and Bayesian analyses. In addition, we record Cyrtodactylus otai Nguyen, Le, Pham, Ngo, Hoang, Pham & Ziegler for the first time from Son La Province based on specimens collected from Van Ho District.
    Matched MeSH terms: Phylogeny
  13. Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
    Dow RA, Stokvis F, Ngiam RWJ
    Zootaxa, 2017 Nov 29;4358(2):201-257.
    PMID: 29245467 DOI: 10.11646/zootaxa.4358.2.1
    The Bornean members of the genus Leptogomphus Selys are revised. Two new species are described: Leptogomphus schieli sp. nov. (holotype ♂, Gunung Penrissen, Kuching Division, Sarawak, Malaysia, to be deposited in BMNH) and Leptogomphus sii sp. nov. (holotype ♂, Sungai Sii, upper Baram, Miri Division, Sarawak, Malaysia, in RMNH). Leptogomphus mariae Lieftinck, 1948 is considered to be a junior synonym of L. coomansi Laidlaw, 1936. The true male of L. pasia van Tol, 1990 is described for the first time; male specimens previously treated as L. pasia or L. cf pasia actually belong to a taxon closely allied to, and possibly merely a form of, L. coomansi. A description is given of the female of another new species, but the species is not named in the absence of the male. Female specimens from south-western Sarawak, similar to L. williamsoni Laidlaw, 1912, are considered likely to also represent a distinct species. The female of L. pendleburyi Laidlaw, 1934 is described for the first time and fresh descriptions of the males of L. coomansi, L. pendleburyi and L. williamsoni, and the female of L. coomansi are given. Keys to both sexes, and distribution maps are given. A molecular analysis of the Bornean species (except L. schieli) using the COI and ITS markers is presented.
    Matched MeSH terms: Phylogeny
  14. Blastocystis occurrence in water sources worldwide from 2005 to 2022: a review
    Attah AO, Sanggari A, Li LI, Nik Him NAII, Ismail AH, Meor Termizi FH
    Parasitol Res, 2023 Jan;122(1):1-10.
    PMID: 36434314 DOI: 10.1007/s00436-022-07731-0
    There has been increasing interest in the study of Blastocystis in the last two decades. Many studies have been carried out in human and animal hosts including environmental sources, but there is little or no information on the occurrence of Blastocystis in water sources worldwide. Therefore, this study aimed at assessing the occurrence of Blastocystis in water sources across the world from 2005 to 2022, noting the method of detection and the distribution of the subtypes from various water sources. A literature search was performed on internet-based databases including Google search, PubMed, Scopus, and Web of Science. Upon application of the criteria for inclusion, 25 articles revealing the occurrence of Blastocystis in water sources in 15 countries were included in the review. Blastocystis occurrence varies across water sources ranging from 0% in a drinking water source in Venezuela to 100% in rivers; well water, stored water, and fishpond in Nepal and Malaysia; and fountain water, irrigation water, and rainwater in Italy, Spain, and Thailand. The occurrence of the parasite was significantly associated with the coliform count, temperature, conductivity, dissolved oxygen, turbidity, total dissolved solids, and chemical oxygen demand. A total of 11 Blastocystis subtypes were identified in water sources worldwide, namely, ST1-ST8, ST10, ST23, and ST26 in which ST1 and ST3 were the most prevalent subtypes. Considering the importance of Blastocystis as a waterborne parasite, the subtype distribution and morphological distinction in water sources need to be carried out using molecular and electron microscopic techniques. Existing studies have covered only about 10% of the world's countries.
    Matched MeSH terms: Phylogeny
  15. Fulltext Genetic Diversity and Clustering of the Rhoptry Associated Protein-1 of Plasmodium knowlesi from Peninsular Malaysia and Malaysian Borneo
    Azlan UW, Lau YL, Fong MY
    Korean J Parasitol, 2022 Dec;60(6):393-400.
    PMID: 36588415 DOI: 10.3347/kjp.2022.60.6.393
    Human infection with simian malaria Plasmodium knowlesi is a cause for concern in Southeast Asian countries, especially in Malaysia. A previous study on Peninsular Malaysia P. knowlesi rhoptry associated protein-1 (PkRAP1) gene has discovered the existence of dimorphism. In this study, genetic analysis of PkRAP1 in a larger number of P. knowlesi samples from Malaysian Borneo was conducted. The PkRAP1 of these P. knowlesi isolates was PCR-amplified and sequenced. The newly obtained PkRAP1 gene sequences (n = 34) were combined with those from the previous study (n = 26) and analysed for polymorphism and natural selection. Sequence analysis revealed a higher genetic diversity of PkRAP1 compared to the previous study. Exon II of the gene had higher diversity (π = 0.0172) than exon I (π = 0.0128). The diversity of the total coding region (π = 0.0167) was much higher than those of RAP1 orthologues such as PfRAP-1 (π = 0.0041) and PvRAP1 (π = 0.00088). Z-test results indicated that the gene was under purifying selection. Phylogenetic tree and haplotype network showed distinct clustering of Peninsular Malaysia and Malaysian Borneo PkRAP1 haplotypes. This geographical-based clustering of PkRAP1 haplotypes provides further evidence of the dimorphism of the gene and possible existence of 2 distinct P. knowlesi lineages in Malaysia.
    Matched MeSH terms: Phylogeny
  16. Genetic variation of Trigonobalanus verticillata, a primitive species of Fagaceae, in Malaysia revealed by chloroplast sequences and AFLP markers
    Kamiya K, Harada K, Clyde MM, Mohamed AL
    Genes Genet Syst, 2002 Jun;77(3):177-86.
    PMID: 12207039
    The genetic variation of Trigonobalanus verticillata, the most recently described genus of Fagaceae, was studied using chloroplast DNA sequences and AFLP fingerprinting. This species has a restricted distribution that is known to include seven localities in tropical lower montane forests in Malaysia and Indonesia. A total of 75 individuals were collected from Bario, Kinabalu, and Fraser's Hill in Malaysia. The sequences of rbcL, matK, and three non-coding regions (atpB-rbcL spacer, trnL intron, and trnL-trnF spacer) were determined for 19 individuals from these populations. We found a total of 30 nucleotide substitutions and four length variations, which allowed identification of three haplotypes characterizing each population. No substitutions were detected within populations, while the tandem repeats in the trnL -trnF spacer had a variable repeat number of a 20-bp motif only in Kinabalu. The differentiation of the populations inferred from the cpDNA molecular clock calibrated with paleontological data was estimated to be 8.3 MYA between Bario and Kinabalu, and 16.7 MYA between Fraser's Hill and the other populations. In AFLP analysis, four selective primer pairs yielded a total of 431 loci, of which 340 (78.9%) were polymorphic. The results showed relatively high gene diversity (H(S) = 0.153 and H(T) = 0.198) and nucleotide diversity (pi(S) = 0.0132 and pi(T) = 0.0168) both within and among the populations. Although the cpDNA data suggest that little or no gene flow occurred between the populations via seeds, the fixation index estimated from AFLP data (F(ST) = 0.153 and N(ST) = 0.214) implies that some gene flow occurs between populations, possibly through pollen transfer.
    Matched MeSH terms: Phylogeny
  17. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge
    Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, et al.
    Mol Ecol, 2022 Dec;31(24):6407-6421.
    PMID: 34748674 DOI: 10.1111/mec.16267
    The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
    Matched MeSH terms: Phylogeny
  18. Integrative microbiomics in bronchiectasis exacerbations
    Mac Aogáin M, Narayana JK, Tiew PY, Ali NABM, Yong VFL, Jaggi TK, et al.
    Nat Med, 2021 Apr;27(4):688-699.
    PMID: 33820995 DOI: 10.1038/s41591-021-01289-7
    Bronchiectasis, a progressive chronic airway disease, is characterized by microbial colonization and infection. We present an approach to the multi-biome that integrates bacterial, viral and fungal communities in bronchiectasis through weighted similarity network fusion ( https://integrative-microbiomics.ntu.edu.sg ). Patients at greatest risk of exacerbation have less complex microbial co-occurrence networks, reduced diversity and a higher degree of antagonistic interactions in their airway microbiome. Furthermore, longitudinal interactome dynamics reveals microbial antagonism during exacerbation, which resolves following treatment in an otherwise stable multi-biome. Assessment of the Pseudomonas interactome shows that interaction networks, rather than abundance alone, are associated with exacerbation risk, and that incorporation of microbial interaction data improves clinical prediction models. Shotgun metagenomic sequencing of an independent cohort validated the multi-biome interactions detected in targeted analysis and confirmed the association with exacerbation. Integrative microbiomics captures microbial interactions to determine exacerbation risk, which cannot be appreciated by the study of a single microbial group. Antibiotic strategies probably target the interaction networks rather than individual microbes, providing a fresh approach to the understanding of respiratory infection.
    Matched MeSH terms: Phylogeny
  19. Fulltext Detection of a Babesia sp. genotype closely related to marsupial-associated Babesia spp. in male Haemaphysalis shimoga from Sarawak, Malaysian Borneo
    Lau AC, Qiu Y, Moustafa MAM, Nakao R, Shimozuru M, Onuma M, et al.
    J Vet Med Sci, 2022 Nov 01;84(11):1469-1473.
    PMID: 36123016 DOI: 10.1292/jvms.22-0304
    In this study, Babesia screening was conducted in 55 rodents and 160 tick samples collected from primary forests and an oil palm plantation in Sarawak, Malaysian Borneo. PCR targeting the 18S ribosomal DNA revealed the presence of Babesia spp. DNA detected in two questing male Haemaphysalis shimoga ticks collected from the oil palm plantation. Sequence analysis revealed that both sequences were identical and had 98.6% identity to a Babesia macropus sequence obtained from Eastern grey kangaroos (Macropus giganteus) in Australia. Phylogenetic tree revealed clustering with marsupial-associated Babesia spp. in the Babesia sensu stricto clade. Whether or not H. shimoga is the competent vector and the importance of the Babesia sp. detected in this study warrants more investigation.
    Matched MeSH terms: Phylogeny
  20. Fulltext Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea
    Jamaludin NA, Jamaluddin JAF, Rahim MA, Mohammed Akib NA, Ratmuangkhwang S, Mohd Arshaad W, et al.
    PeerJ, 2022;10:e13706.
    PMID: 35860045 DOI: 10.7717/peerj.13706
    The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91-1.00), and nucleotide diversity (π) was low (0.002-0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and F ST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant F STpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.
    Matched MeSH terms: Phylogeny
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