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Fulltext Antioxidative Potential of a Streptomyces sp. MUM292 Isolated from Mangrove Soil

Tan LT, Chan KG, Chan CK, Khan TM, Lee LH, Goh BH

Biomed Res Int, 2018;2018:4823126.
PMID: 29805975 DOI: 10.1155/2018/4823126

Mangrove derived microorganisms constitute a rich bioresource for bioprospecting of bioactive natural products. This study explored the antioxidant potentials of Streptomyces bacteria derived from mangrove soil. Based on 16S rRNA phylogenetic analysis, strain MUM292 was identified as the genus Streptomyces. Strain MUM292 showed the highest 16S rRNA gene sequence similarity of 99.54% with S. griseoruber NBRC12873T. Furthermore, strain MUM292 was also characterized and showed phenotypic characteristics consistent with Streptomyces bacteria. Fermentation and extraction were performed to obtain the MUM292 extract containing the secondary metabolites of strain MUM292. The extract displayed promising antioxidant activities, including DPPH, ABTS, and superoxide radical scavenging and also metal-chelating activities. The process of lipid peroxidation in lipid-rich product was also retarded by MUM292 extract and resulted in reduced MDA production. The potential bioactive constituents of MUM292 extract were investigated using GC-MS and preliminary detection showed the presence of pyrazine, pyrrole, cyclic dipeptides, and phenolic compound in MUM292 extract. This work demonstrates that Streptomyces MUM292 can be a potential antioxidant resource for food and pharmaceutical industries.

Matched MeSH terms: Phylogeny
Fulltext Malaria parasites of long-tailed macaques in Sarawak, Malaysian Borneo: a novel species and demographic and evolutionary histories

Nada Raja T, Hu TH, Zainudin R, Lee KS, Perkins SL, Singh B

BMC Evol. Biol., 2018 04 10;18(1):49.
PMID: 29636003 DOI: 10.1186/s12862-018-1170-9

BACKGROUND: Non-human primates have long been identified to harbour different species of Plasmodium. Long-tailed macaques (Macaca fascicularis), in particular, are reservoirs for P. knowlesi, P. inui, P. cynomolgi, P. coatneyi and P. fieldi. A previous study conducted in Sarawak, Malaysian Borneo, however revealed that long-tailed macaques could potentially harbour novel species of Plasmodium based on sequences of small subunit ribosomal RNA and circumsporozoite genes. To further validate this finding, the mitochondrial genome and the apicoplast caseinolytic protease M genes of Plasmodium spp. were sequenced from 43 long-tailed macaque blood samples.
RESULTS: Apart from several named species of malaria parasites, long-tailed macaques were found to be potentially infected with novel species of Plasmodium, namely one we refer to as "P. inui-like." This group of parasites bifurcated into two monophyletic clades indicating the presence of two distinct sub-populations. Further analyses, which relied on the assumption of strict co-phylogeny between hosts and parasites, estimated a population expansion event of between 150,000 to 250,000 years before present of one of these sub-populations that preceded that of the expansion of P. knowlesi. Furthermore, both sub-populations were found to have diverged from a common ancestor of P. inui approximately 1.5 million years ago. In addition, the phylogenetic analyses also demonstrated that long-tailed macaques are new hosts for P. simiovale.
CONCLUSIONS: Malaria infections of long-tailed macaques of Sarawak, Malaysian Borneo are complex and include a novel species of Plasmodium that is phylogenetically distinct from P. inui. These macaques are new natural hosts of P. simiovale, a species previously described only in toque monkeys (Macaca sinica) in Sri Lanka. The results suggest that ecological factors could affect the evolution of malaria parasites.

Matched MeSH terms: Phylogeny
Fulltext Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

Rosli R, Amiruddin N, Ab Halim MA, Chan PL, Chan KL, Azizi N, et al.

PLoS One, 2018;13(4):e0194792.
PMID: 29672525 DOI: 10.1371/journal.pone.0194792

Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.

Matched MeSH terms: Phylogeny
Fulltext Cryptic diversity: Two morphologically similar species of invasive apple snail in Peninsular Malaysia

Rama Rao S, Liew TS, Yow YY, Ratnayeke S

PLoS One, 2018;13(5):e0196582.
PMID: 29734361 DOI: 10.1371/journal.pone.0196582

Invasive snails in the genus Pomacea have spread across Southeast Asia including Peninsular Malaysia. Their effects on natural and agricultural wetlands are appreciable, but species-specific effects are less clear because of morphological similarity among the species. Our objective was to establish diagnostic characteristics of Pomacea species in Malaysia using genetic and morphological criteria. The mitochondrial COI gene of 52 adult snails from eight localities in Peninsular Malaysia was amplified, sequenced, and analysed to verify species and phylogenetic relationships. Shells were compared using geometric morphometric and covariance analyses. Two monophyletic taxa, P. canaliculata and P. maculata, occurred in our samples. The mean ratio of shell height: aperture height (P = 0.042) and shell height: shell width (P = 0.007) was smaller in P. maculata. P. maculata co-occurred with P. canaliculata in five localities, but samples from three localities contained only P. canaliculata. This study is the first to confirm the presence of two of the most invasive species of Pomacea in Peninsular Malaysia using a molecular technique. P. canaliculata appears to be the more widespread species. Despite statistical differences, both quantitative and qualitative morphological characteristics demonstrated much interspecific overlap and intraspecific variability; thus, shell morphology alone cannot reliably verify species identity. Molecular techniques for distinguishing between these two highly invasive Pomacea species are needed to understand their specific ecological niches and to develop effective protocols for their management.

Matched MeSH terms: Phylogeny
Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide

Balakrishnan KN, Abdullah AA, Bala J, Abba Y, Sarah SA, Jesse FFA, et al.

Infect Genet Evol, 2017 10;54:81-90.
PMID: 28642159 DOI: 10.1016/j.meegid.2017.06.020

BACKGROUND: Rat cytomegalovirus ALL-03 (Malaysian strain) which was isolated from a placenta and uterus of a house rat, Rattus rattus diardii has the ability to cross the placenta and infecting the fetus. To further elucidate the pathogenesis of the Malaysian strain of Rat Cytomegalovirus ALL-03 (RCMV ALL-03), detailed analysis on the viral genome sequence is crucial.
METHODS: Genome sequencing of RCMV ALL-03 was carried out in order to identify the open reading frame (ORF), homology comparison of ORF with other strains of CMV, phylogenetic analysis, classifying ORF with its corresponding conserved genes, and determination of functional proteins and grouping of gene families in order to obtain fundamental knowledge of the genome.
RESULTS: The present study revealed a total of 123 Coding DNA sequences (CDS) from RCMV ALL-03 with 37 conserved ORF domains as with all herpesvirus genomes. All the CDS possess similar function with RCMV-England followed by RCMV-Berlin, RCMV-Maastricht, and Human CMV. The phylogenetic analysis of RCMV ALL-03 based on conserving genes of herpes virus showed that the Malaysian RCMV isolate is closest to RCMV-English and RCMV-Berlin strains, with 99% and 97% homology, respectively. Similarly, it also demonstrated an evolutionary relationship between RCMV ALL-03 and other strains of herpesviruses from all the three subfamilies. Interestingly, betaherpesvirus subfamily, which has been shown to be more closely related with gammaherpesviruses as compared to alphaherpesviruses, shares some of the functional ORFs. In addition, the arrangement of gene blocks for RCMV ALL-03, which was conserved among herpesvirus family members was also observed in the RCMV ALL-03 genome.
CONCLUSION: Genomic analysis of RCMV ALL-03 provided an overall picture of the whole genome organization and it served as a good platform for further understanding on the divergence in the family of Herpesviridae.

Matched MeSH terms: Phylogeny
Disruption of predicted dengue virus type 3 major outbreak cycle coincided with switching of the dominant circulating virus genotype

Tan KK, Zulkifle NI, Abd-Jamil J, Sulaiman S, Yaacob CN, Azizan NS, et al.

Infect Genet Evol, 2017 Oct;54:271-275.
PMID: 28698156 DOI: 10.1016/j.meegid.2017.07.008

Dengue is hyperendemic in most of Southeast Asia. In this region, all four dengue virus serotypes are persistently present. Major dengue outbreak cycle occurs in a cyclical pattern involving the different dengue virus serotypes. In Malaysia, since the 1980s, the major outbreak cycles have involved dengue virus type 3 (DENV3), dengue virus type 1 (DENV1) and dengue virus type 2 (DENV2), occurring in that order (DENV3/DENV1/DENV2). Only limited information on the DENV3 cycles, however, have been described. In the current study, we examined the major outbreak cycle involving DENV3 using data from 1985 to 2016. We examined the genetic diversity of DENV3 isolates obtained during the period when DENV3 was the dominant serotype and during the inter-dominant transmission period. Results obtained suggest that the typical DENV3/DENV1/DENV2 cyclical outbreak cycle in Malaysia has recently been disrupted. The last recorded major outbreak cycle involving DENV3 occurred in 2002, and the expected major outbreak cycle involving DENV3 in 2006-2012 did not materialize. DENV genome analyses revealed that DENV3 genotype II (DENV3/II) was the predominant DENV3 genotype (67%-100%) recovered between 1987 and 2002. DENV3 genotype I (DENV3/I) emerged in 2002 followed by the introduction of DENV3 genotype III (DENV3/III) in 2008. These newly emerged DENV3 genotypes replaced DENV3/II, but there was no major upsurge of DENV3 cases that accompanied the emergence of these viruses. DENV3 remained in the background of DENV1 and DENV2 until now. Virus genome sequence analysis suggested that intrinsic differences within the different dengue virus genotypes could have influenced the transmission efficiency of DENV3. Further studies and continuous monitoring of the virus are needed for better understanding of the DENV transmission dynamics in hyperendemic regions.

Matched MeSH terms: Phylogeny
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: Phylogeny
Hookworm infections among migrant workers in Malaysia: Molecular identification of Necator americanus and Ancylostoma duodenale

Sahimin N, Lim YAL, Douadi B, Mohd Khalid MKN, Wilson JJ, Behnke JM, et al.

Acta Trop, 2017 Sep;173:109-115.
PMID: 28610937 DOI: 10.1016/j.actatropica.2017.06.011

Ongoing urbanisation of the working population as well as cross-border migration of workers particularly into large cities has contributed to the development and growth of urban slums. These deprived areas are conducive for the transmission of intestinal pathogens including hookworm. The aim of this study was to determine both the prevalence and species identity of hookworm infections among the migrant worker community in Malaysia. A total of 388 faecal samples were collected from migrant workers between September 2014 and August 2015, representing workers from five employment sectors: construction, manufacturing, agriculture and plantations, food services and domestic services. Faecal samples were examined by microscopy and positive samples were subjected to molecular analysis. A total of 51 samples (13.1%) were positive by microscopy for hookworm infections. A two-step PCR based method amplifying a fragment of the 28S rRNA-ITS2 region was used to identify infections by Necator americanus and Ancylostoma spp. PCR products positive for Ancylostoma spp. were sequenced bidirectionally, and sequences analysed through BLAST and phylogenetic analysis. Samples containing Ancylostoma duodenale were further characterized by amplification and sequencing a fragment of cytochrome c oxidase subunit 1 (cox1) gene. PCR amplicons were successfully obtained from 42 (82.4%) of 51 samples, with 81.0% (34 of 42) identified as Necator americanus, 16.7% (7 of 42) as Ancylostoma spp. and 2.4% (1 of 42) as mixed infections of both species. All eight Ancylostoma spp. were confirmed to be Ancylostoma duodenale and this is the first time A. duodenale was reported in Malaysia. Samples containing A. duodenale from Nepalese and Indonesian workers shared high-similarity and were distinct compared to sequences from other countries. This study highlights the prevalence of hookworm infections among migrant workers living in Malaysia. Our findings underscore the necessity of screening migrant workers for hookworm infections, particularly those working in food-related services and industries.

Matched MeSH terms: Phylogeny
Fulltext Contrasting evolutionary patterns between two haplogroups of Haematobia exigua (Diptera: Muscidae) from the mainland and islands of Southeast Asia

Low VL, Tan TK, Prakash BK, Vinnie-Siow WY, Tay ST, Masmeatathip R, et al.

Sci Rep, 2017 07 19;7(1):5871.
PMID: 28724923 DOI: 10.1038/s41598-017-05921-w

Uncovering the hidden diversity and evolutionary history of arthropods of medico-veterinary importance could have significant implications for vector-borne disease control and epidemiological intervention. The buffalo fly Haematobia exigua is an obligate bloodsucking ectoparasite of livestock. As an initial step towards understanding its population structures and biogeographic patterns, we characterized partial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) sequences of H. exigua from three distinct geographic regions in Southeast Asia. We detected two distinct mitochondrial haplogroups of H. exigua in our surveyed geographic regions. Haplogroup I is widespread in the Southeast Asian mainland whereas haplogroup II is generally restricted to the type population Java Island. Both haplogroups were detected co-occurring on Borneo Island. Additionally, both haplogroups have undergone contrasting evolutionary histories, with haplogroup I exhibited a high level of mitochondrial diversity indicating a population expansion during the Pleistocene era dating back to 98,000 years ago. However, haplogroup II presented a low level of mitochondrial diversity which argues against the hypothesis of recent demographic expansion.

Matched MeSH terms: Phylogeny
Morphological and Molecular Evidence for Multiple Taxa in Simulium parahiyangum (Diptera: Simuliidae), a Geographic Generalist Black Fly in Southeast Asia

Takaoka H, Low VL, Srisuka W, Ya'cob Z, Saeung A

J Med Entomol, 2018 Oct 25;55(6):1453-1463.
PMID: 30060220 DOI: 10.1093/jme/tjy109

Seven populations of Simulium parahiyangum Takaoka & Sigit (Diptera: Simuliidae), a geographically widespread nominal species of black fly in Southeast Asia, were morphologically and molecularly studied. Three morphoforms based on male and pupal morphological features, and two primary lineages based on the COI gene sequence analysis were recognized. Morphoform 1 (lineage 1) from Sarawak, Malaysia, is identified as S. parahiyangum sensu stricto and morphoform 2 (lineage 2) from Thailand and Vietnam, and morphoform 3 (lineage 1) from Peninsular Malaysia are each regarded as distinct species, although morphoform 3 is partially homosequential for the COI gene with morphoform 1. Morphoforms 2 and 3 are described as Simulium ngaoense sp. nov. and Simulium sazalyi sp. nov., respectively. Overall, S. parahiyangum is not a single geographic generalist but a composite of multiple species.

Matched MeSH terms: Phylogeny
Fulltext Exploratory Analysis of the Microbiological Potential for Efficient Utilization of Fiber Between Lantang and Duroc Pigs

Cheng P, Wang Y, Liang J, Wu Y, Wright A, Liao X

Front Microbiol, 2018;9:1342.
PMID: 29988353 DOI: 10.3389/fmicb.2018.01342

There is growing interest in the use of unconventional feed ingredients containing higher dietary fiber for pig production due to increasing prices of cereal grains and the potential health benefits of dietary fiber on host animals. This study aimed to gain insight into the community-wide microbiome population between the Chinese native Lantang pigs and the commercial Duroc pigs to uncover the microbiological mechanisms for the degradation capacity of fiber in pigs. Utilizing the metagenomics approach, we compared the phylogeny and functional capacity of the fecal microbiome from approximately 150-day-old female Lantang and Duroc pigs fed a similar diet. The structure of the fecal microbial community from the two pig breeds was different at the genus level; the number of genes associated with fiber degradation was higher in Lantang pigs. Further analysis and prediction of their functions from the fecal microbiomes of the two pig breeds revealed that the degradation capacities of fiber, branched chain fatty acids, and oligosaccharides were higher in Lantang pigs. The ability of lignocellulose bonding modules and the transport capacities of xylose, L-arabinose, ribose and methyl galactose were also higher in Lantang pigs. Similarly, the metabolic capacities of xylose, ribose, and fucose and the potential effectiveness of the tricarboxylic acid cycle (TCA) and gene abundance in the hydrogen sink pathway were higher in the fecal microbiome from Lantang pigs. Lantang pigs have a higher capacity to utilize dietary fiber than Duroc pigs, and the differences in the capability to utilize dietary fiber between the indigenous and commercial pigs could be differences in the composition and biological function of the gut microbiota.

Matched MeSH terms: Phylogeny
Genomic evaluations of Wolbachia and mtDNA in the population of coconut hispine beetle, Brontispa longissima (Coleoptera: Chrysomelidae)

Ali H, Muhammad A, Bala NS, Wang G, Chen Z, Peng Z, et al.

Mol Phylogenet Evol, 2018 10;127:1000-1009.
PMID: 29981933 DOI: 10.1016/j.ympev.2018.07.003

Wolbachia pipientis is a diverse, ubiquitous and most prevalent intracellular bacterial group of alpha-Proteobacteria that is concerned with many biological processes in arthropods. The coconut hispine beetle (CHB), Brontispa longissima (Gestro) is an economically important pest of palm cultivation worldwide. In the present study, we comprehensively surveyed the Wolbachia-infection prevalence and mitochondrial DNA (mtDNA) polymorphism in CHB from five different geographical locations, including China's Mainland and Taiwan, Vietnam, Thailand, Malaysia and Indonesia. A total of 540 sequences were screened in this study through three different genes, i.e., cytochrome oxidase subunit I (COI), Wolbachia outer surface protein (wsp) and multilocus sequencing type (MLST) genes. The COI genetic divergence ranges from 0.08% to 0.67%, and likewise, a significant genetic diversity (π = 0.00082; P = 0.049) was noted within and between all analyzed samples. In the meantime, ten different haplotypes (H) were characterized (haplotype diversity = 0.4379) from 21 different locations, and among them, H6 (46 individuals) have shown a maximum number of population clusters than others. Subsequently, Wolbachia-prevalence results indicated that all tested specimens of CHB were found positive (100%), which suggested that CHB was naturally infected with Wolbachia. Wolbachia sequence results (wsp gene) revealed a high level of nucleotide diversity (π = 0.00047) under Tajima's D test (P = 0.049). Meanwhile, the same trend of nucleotide diversity (π = 0.00041) was observed in Wolbachia concatenated MLST locus. Furthermore, phylogenetic analysis (wsp and concatenated MLST genes) revealed that all collected samples of CHB attributed to same Wolbachia B-supergroup. Our results strongly suggest that Wolbachia bacteria and mtDNA were highly concordant with each other and Wolbachia can affect the genetic structure and diversity within the CHB populations.

Matched MeSH terms: Phylogeny
Fulltext Three members of Opisthomonorcheides Parukhin, 1966 (Digenea: Monorchiidae) from carangid fishes (Perciformes) from Indonesia, with a review of the genus

Bray RA, Palm HW, Cutmore SC, Cribb TH

Syst Parasitol, 2017 05;94(4):443-462.
PMID: 28337682 DOI: 10.1007/s11230-017-9717-5

Three species of Opisthomonorcheides Parukhin, 1966 are reported for the first time from Indonesian waters: O. pampi (Wang, 1982) Liu, Peng, Gao, Fu, Wu, Lu, Gao & Xiao, 2010 and O. ovacutus (Mamaev, 1970) Machida, 2011 from Parastromateus niger (Bloch), and O. decapteri Parukhin, 1966 from Atule mate (Cuvier). Both O. pampi and O. ovacutus can now be considered widespread in the Indo-Pacific region, with earlier records of these species being from Fujian Province, China and Penang, Malaysia, respectively. We redescribe O. decapteri from one of its original hosts, Atule mate, off New Caledonia, and report this species from Jakarta Bay, Indonesia, extending its range throughout the Indian Ocean into the south-western Pacific. All three species possess a genital atrium that is long, sometimes very long, and a genital pore that is located in the forebody. This validates the interpretation that the original description was erroneous in reporting the genital pore in the hindbody, well posterior to the ventral sucker. These observations verify the synonymy of Retractomonorchis Madhavi, 1977 with Opisthomonorcheides. A major discrepancy between the species of Opisthomonorcheides is that some are described with the uterus entering the terminal organ laterally and some with it entering terminally; this feature needs further analysis. Based on the length of the genital atrium and the posterior extent of the vitellarium, the 27 species of Opisthomonorcheides considered valid can be divided into four groups. Among the 53 host records analysed, the families Carangidae (53% of records), Stromateidae (17%) and Serranidae (5.7%) are the most common; the reports are overwhelmingly from members of the Perciformes (91%), with further records in the Clupeiformes (5.7%), Gadiformes (1.9%) and Pleuronectiformes (1.9%). Two fish genera (Parastromateus Bleeker and Pampus Bonaparte) dominate the recorded hosts, with the black pomfret Parastromateus niger harbouring six species, the silver pomfret Pampus argenteus (Euphrasen) harbouring six, and the Chinese silver pomfret P. chinensis (Euphrasen) two. A host-parasite checklist is presented. We discuss the host-specificity of members of the genus, questioning some records such as that of O. decapteri in a deep-sea macrourid. We also comment on the morphological similarity, but phylogenetic distance, between the various Pomfret species, advancing the possibility that a series of host misidentifications has occurred. Sequences of the ITS2 rDNA gene generated for O. pampi and O. ovacutus are briefly discussed and molecular data are lodged in the GenBank database.

Matched MeSH terms: Phylogeny
Fulltext Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba

Yang Y, Li J, Yang S, Li X, Fang L, Zhong C, et al.

BMC Evol. Biol., 2017 01 18;17(1):22.
PMID: 28100168 DOI: 10.1186/s12862-016-0849-z

BACKGROUND: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation.
RESULTS: In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes.
CONCLUSION: Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level.

Matched MeSH terms: Phylogeny
Habitat segregation and cryptic adaptation of species of Periophthalmus (Gobioidei: Gobiidae)

Polgar G, Zaccara S, Babbucci M, Fonzi F, Antognazza CM, Ishak N, et al.

J Fish Biol, 2017 May;90(5):1926-1943.
PMID: 28239874 DOI: 10.1111/jfb.13276

A study was conducted on the habitat distribution of four sympatric species of Periophthalmus (the silver-lined mudskipper Periophthalmus argentilineatus, the slender mudskipper Periophthalmus gracilis, the kalolo mudskipper Periophthalmus kalolo and the Malacca mudskipper Periophthalmus malaccensis) from northern Sulawesi. Molecular phylogenetic reconstructions based on one mtDNA marker (16S) were used to validate the morphological taxa, identifying five molecular clades. Periophthalmus argentilineatus includes two molecular species, which are named Periophthalmus argentilineatus clades F and K. Multivariate direct gradient analysis show that these species form three distinct ecological guilds, with the two molecular species occurring in different guilds. Periophthalmus clade F is ecologically eurytypic; Periophthalmus clade K and P. kalolo are prevalent in ecosystems isolated by strong oceanic currents and at shorter distances from the sea; P. gracilis plus P. malaccensis are prevalent in ecosystems connected by shallow coastal waters, in vegetated habitats at larger distances from the sea. This indicates for the first time that mudskipper species exhibit a range of adaptations to semiterrestrialism not only within genera, but even within morphospecies, delineating a much more complex adaptive scenario than previously assumed.

Matched MeSH terms: Phylogeny
Fulltext Myrteae phylogeny, calibration, biogeography and diversification patterns: Increased understanding in the most species rich tribe of Myrtaceae

Vasconcelos TNC, Proença CEB, Ahmad B, Aguilar DS, Aguilar R, Amorim BS, et al.

Mol Phylogenet Evol, 2017 04;109:113-137.
PMID: 28069533 DOI: 10.1016/j.ympev.2017.01.002

Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a comprehensive understanding of the relationships within the tribe. The resultant topology was used as a base for key evolutionary analyses such as age estimation, historical biogeography and diversification rate patterns. One nuclear (ITS) and seven chloroplast (psbA-trnH, matK, ndhF, trnl-trnF, trnQ-rps16, rpl16 and rpl32-trnL) DNA regions for 115 taxa representing 46 out of the 51 genera in the tribe were accessed and analysed using maximum likelihood and Bayesian inference tools for phylogenetic reconstruction. Dates of diversification events were estimated and contrasted using two distinct fossil sets (macro and pollen) in BEAST. The subsequent dated phylogenies were compared and analysed for biogeographical patterns using BioGeoBEARS and diversification rates using BAMM. Myrteae phylogeny presents strong statistical support for three major clades within the tribe: Australasian group, Myrtus group and Main Neotropical Lineage. Dating results from calibration using macrofossil are an average of 20 million years older and show an early Paleocene origin of Myrteae, against a mid-Eocene one from the pollen fossil calibration. Biogeographic analysis shows the origin of Myrteae in Zealandia in both calibration approaches, followed by a widespread distribution throughout the still-linked Gondwana continents and diversification of Neotropical endemic lineages by later vicariance. Best configuration shift indicates three points of acceleration in diversification rates, all of them occurring in the Main Neotropical Lineage. Based on the reconstructed topology, several new taxonomic placements were recovered, including: the relative position of Myrtus communis, the placement of the Blepharocalyx group, the absence of generic endemism in the Caribbean, and the paraphyletism of the former Pimenta group. Distinct calibration approaches affect biogeography interpretation, increasing the number of necessary long distance dispersal events in the topology with older nodes. It is hypothesised that biological intrinsic factors such as modifications of embryo type and polyploidy might have played a role in accelerating shifts of diversification rates in Neotropical lineages. Future perspectives include formal subtribal classification, standardization of fossil calibration approaches and better links between diversification shifts and trait evolution.

Matched MeSH terms: Phylogeny
Fulltext Convergence between the microcosms of Southeast Asian and North American pitcher plants

Bittleston LS, Wolock CJ, Yahya BE, Chan XY, Chan KG, Pierce NE, et al.

Elife, 2018 08 28;7.
PMID: 30152327 DOI: 10.7554/eLife.36741

The 'pitchers' of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities.

Matched MeSH terms: Phylogeny
In silico characterization and expression profiling of the diacylglycerol acyltransferase gene family (DGAT1, DGAT2, DGAT3 and WS/DGAT) from oil palm, Elaeis guineensis

Rosli R, Chan PL, Chan KL, Amiruddin N, Low EL, Singh R, et al.

Plant Sci, 2018 Oct;275:84-96.
PMID: 30107884 DOI: 10.1016/j.plantsci.2018.07.011

The diacylglycerol acyltransferases (DGAT) (diacylglycerol:acyl-CoA acyltransferase, EC 2.3.1.20) are a key group of enzymes that catalyse the final and usually the most important rate-limiting step of triacylglycerol biosynthesis in plants and other organisms. Genes encoding four distinct functional families of DGAT enzymes have been characterised in the genome of the African oil palm, Elaeis guineensis. The contrasting features of the various isoforms within the four families of DGAT genes, namely DGAT1, DGAT2, DGAT3 and WS/DGAT are presented both in the oil palm itself and, for comparative purposes, in 12 other oil crop or model/related plants, namely Arabidopsis thaliana, Brachypodium distachyon, Brassica napus, Elaeis oleifera, Glycine max, Gossypium hirsutum, Helianthus annuus, Musa acuminata, Oryza sativa, Phoenix dactylifera, Sorghum bicolor, and Zea mays. The oil palm genome contains respectively three, two, two and two distinctly expressed functional copies of the DGAT1, DGAT2, DGAT3 and WS/DGAT genes. Phylogenetic analyses of the four DGAT families showed that the E. guineensis genes tend to cluster with sequences from P. dactylifera and M. acuminata rather than with other members of the Commelinid monocots group, such as the Poales which include the major cereal crops such as rice and maize. Comparison of the predicted DGAT protein sequences with other animal and plant DGATs was consistent with the E. guineensis DGAT1 being ER located with its active site facing the lumen while DGAT2, although also ER located, had a predicted cytosol-facing active site. In contrast, DGAT3 and some (but not all) WS/DGAT in E. guineensis are predicted to be soluble, cytosolic enzymes. Evaluation of E. guineensis DGAT gene expression in different tissues and developmental stages suggests that the four DGAT groups have distinctive physiological roles and are particularly prominent in developmental processes relating to reproduction, such as flowering, and in fruit/seed formation especially in the mesocarp and endosperm tissues.

Matched MeSH terms: Phylogeny
Isolation and Quantification of Mimivirus-Like and Marseillevirus-Like Viruses from Soil Samples in An Aboriginal (Orang asli) Village in Peninsular Malaysia

Tan YF, Lim CY, Chong CW, Lim PKC, Yap IKS, Leong PP, et al.

Intervirology, 2018;61(2):92-95.
PMID: 30121676 DOI: 10.1159/000491602

BACKGROUND: The giant amoebal viruses of Mimivirus and Marseillevirus are large DNA viruses and have been documented in water, soil, and sewage samples. The trend of discovering these giant amoebal viruses has been increasing throughout Asia with Japan, India, and Saudi Arabia being the latest countries to document the presence of these viruses. To date, there have been no reports of large amoebal viruses being isolated in South East Asia.
OBJECTIVE: In this study, we aim to discover these viruses from soil samples in an aboriginal village (Serendah village) in Peninsular -Malaysia.
METHOD AND RESULTS: We successfully detected and isolated both Mimivirus-like and Marseillevirus-like viruses using Acanthamoeba castellanii. Phylogeny analysis identified them as Mimivirus and Marseillevirus, respectively.
CONCLUSION: The ubiquitous nature of both Mimivirus and Marseillevirus is further confirmed in our study as they are detected in higher quantity in soil that is near to water vicinities in an aboriginal village in Peninsular Malaysia. However, this study is limited by our inability to investigate the impact of Mimivirus and Marseillevirus on the aboriginal villagers. More studies on the potential impact of these viruses on human health, especially on the aborigines, are warranted.

Matched MeSH terms: Phylogeny
Fulltext Diagnostic and Vaccination Approaches for Newcastle Disease Virus in Poultry: The Current and Emerging Perspectives

Bello MB, Yusoff K, Ideris A, Hair-Bejo M, Peeters BPH, Omar AR

Biomed Res Int, 2018;2018:7278459.
PMID: 30175140 DOI: 10.1155/2018/7278459

Newcastle disease (ND) is one of the most devastating diseases that considerably cripple the global poultry industry. Because of its enormous socioeconomic importance and potential to rapidly spread to naïve birds in the vicinity, ND is included among the list of avian diseases that must be notified to the OIE immediately upon recognition. Currently, virus isolation followed by its serological or molecular identification is regarded as the gold standard method of ND diagnosis. However, this method is generally slow and requires specialised laboratory with biosafety containment facilities, making it of little relevance under epidemic situations where rapid diagnosis is seriously needed. Thus, molecular based diagnostics have evolved to overcome some of these difficulties, but the extensive genetic diversity of the virus ensures that isolates with mutations at the primer/probe binding sites escape detection using these assays. This diagnostic dilemma leads to the emergence of cutting-edge technologies such as next-generation sequencing (NGS) which have so far proven to be promising in terms of rapid, sensitive, and accurate recognition of virulent Newcastle disease virus (NDV) isolates even in mixed infections. As regards disease control strategies, conventional ND vaccines have stood the test of time by demonstrating track record of protective efficacy in the last 60 years. However, these vaccines are unable to block the replication and shedding of most of the currently circulating phylogenetically divergent virulent NDV isolates. Hence, rationally designed vaccines targeting the prevailing genotypes, the so-called genotype-matched vaccines, are highly needed to overcome these vaccination related challenges. Among the recently evolving technologies for the development of genotype-matched vaccines, reverse genetics-based live attenuated vaccines obviously appeared to be the most promising candidates. In this review, a comprehensive description of the current and emerging trends in the detection, identification, and control of ND in poultry are provided. The strengths and weaknesses of each of those techniques are also emphasised.

Matched MeSH terms: Phylogeny

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