scholarly journals Haplotype Analysis and Phylogeny of Oryzaephilus surinamensis Populations from Four Regions in Peninsular Malaysia

2021 ◽  
Vol 44 (3) ◽  
Author(s):  
Syed Ahmad Syarifah-Zulaikha ◽  
Madihah Halim ◽  
Ameyra Zuki Aman ◽  
Salmah Yaakop
Keyword(s):  
Haplotype Diversity ◽  
Haplotype Network ◽  
Peninsular Malaysia ◽  
Small Scale ◽  
Pest Species ◽  
Oryzaephilus Surinamensis ◽  
Storage Losses ◽  
Similar Haplotype ◽  
Coi Sequences ◽  
Haplotype 1

The sawtoothed grain beetle, Oryzaephilus surinamensis, is a secondary pest that damages rice products and other stored grains. Analysis based on the cytochrome oxidase subunit I (COI) sequences data, the number of haplotypes (Hap) (n), haplotype diversity (Hd), haplotype network, genetic distance, and phylogeny between O. surinamensis populations from four regions (small-scale), viz. the northern area (Seberang Perai), middle area (Klang), southern area (Pasir Gudang), and east coast (Kuantan) of Peninsular Malaysia, as model sampling locations, were obtained. A total of five haplotypes were detected in all the test populations, two shared (Haplotype 1 and Haplotype 3) and three unique haplotypes (Haplotype 2, Haplotype 4, and Haplotype 5) with haplotype diversity value, Hd = 0.6789 were recorded. Furthermore, the neighbour-joining (NJ), maximum parsimony (MP), and Bayesian inference (BI) trees showed a mixture of individuals from all regions in Peninsular Malaysia (Haplotype 1 to Haplotype 4), except Haplotype 5, which was grouped with foreign populations that inherited similar haplotype with those of the European samples. This study assumed a mixture of populations presumably due to human activities and related explicitly to the exportation and importation of rice products across regions. This information is vital for strategising the control management of this pest species to reduce rice storage losses.

scholarly journals Spatial and temporal aggregation of Oryzaephilus surinamensis from Peninsular Malaysia

2021 ◽  
Vol 58 (04) ◽  
pp. 1123-1130
Author(s):  
Syed Ahmad Syarifah Zulaikha
Keyword(s):  
Central Zone ◽  
Temporal Distribution ◽  
Peninsular Malaysia ◽  
Management Control ◽  
P Value ◽  
Distribution Analysis ◽  
Pest Species ◽  
Stored Products ◽  
Population Abundance ◽  
Oryzaephilus Surinamensis

The saw-toothed grain beetle, Oryzaephilus surinamensis (Linnaeus) is a secondary pest of rice grains and other stored products. Lack of information on the population abundance, spatial, and temporal distribution of O. surinamensis rendered the management control strategy of this pest species less effective. The objective of this study was to investigate the abundance, spatial and temporal pattern of O. surinamensis populations from nine rice warehouses in three zones of Peninsular Malaysia (i.e., the northern, central and southern zones) for three continuous months. The results showed that the abundance of O. surinamensis populations varied significantly (p<0.05, p= 0.00) between zones, with the highest abundance for this species (69%) recorded from the Klang District, in the central zone, followed by Pasir Gudang (27%) in the southern zone, and Seberang Prai (4%) in the northern zone. The patterns of population abundance also showed significant differences between months, p<0.05 (p-value= 0.00-0.011) between all the warehouses. The factors that could be associated with the highest abundance of the pest were attributed to poor sanitation at the warehouses and inconsistency in the fumigation regime. For the spatial distribution analysis, SADIEShell_122 and Surfer8 software were applied. The distribution patterns of O. surinamensis populations varied significantly in all the warehouses, being significantly aggregated at p<0.05 (p=0.0385-0.0513) and Ia>1.0 (1.212-1.579), whilst being non-significantly and randomly distributed at p>0.05 (p=0.1154-0.91032) and Ia>1.0 (0.852- 0.929). The significance of the aggregation might be due to the rapidly changing volume of the rice stock caused by the active and rapid turnover of the storage inventory. The results obtained were very valuable and informative in managing O. surinamensis infestation of stored rice by incorporating the spatial and temporal information of the pest populations in the management strategy for improving the rice and other stored products.

Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Heliothis Virescens ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Haplotype Network ◽  
Demographic Expansion ◽  
Significant Genetic Structure ◽  
History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

scholarly journals Phylogeography and Molecular Species Delimitation of Pratylenchus capsici n. sp., a New Root-Lesion Nematode in Israel on Pepper (Capsicum annuum)

2019 ◽  
Vol 109 (5) ◽  
pp. 847-858 ◽  
Author(s):  
Xue Qing ◽  
Wim Bert ◽  
Abraham Gamliel ◽  
Patricia Bucki ◽  
Svetlana Duvrinin ◽  
...  
Keyword(s):  
New Species ◽  
Capsicum Annuum ◽  
Molecular Species ◽  
Species Delimitation ◽  
Chenopodium Album ◽  
Haplotype Diversity ◽  
Small Scale ◽  
Growing Seasons ◽  
Contemporary Gene Flow ◽  
A New Species

Root-lesion nematodes of the genus Pratylenchus parasitize the roots of numerous plants and can cause severe damage and yield loss. Here, we report on a new species, Pratylenchus capsici n. sp., from the Arava rift, Israel, which was characterized by integrative methods, including detailed morphology, molecular phylogeny, population genetics, and phylogeography. This species is widely spread across the Arava rift, causing significant infection in pepper (Capsicum annuum) roots and inhibiting plant growth. Both morphological and molecular species delimitation support the recovered species as a new species. We found high cytochrome oxidase subunit I haplotype diversity, and phylogeography analysis suggests that contemporary gene flow is prevented among different agricultural farms, while population dispersal from weeds (Chenopodium album and Sonchus oleraceus) to pepper occurs on a relatively small scale. Our results suggest that weeds are an important reservoir for the dispersal of P. capsici n. sp., either as the original nematode source or at least in maintaining the population between growing seasons.

scholarly journals Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories

2019 ◽  
Author(s):  
Camiel Doorenweerd ◽  
Michael San Jose ◽  
Norman Barr ◽  
Luc Leblanc ◽  
Daniel Rubinoff
Keyword(s):  
Haplotype Diversity ◽  
Fruit Fly ◽  
Coi Gene ◽  
Invasive Pest ◽  
Pest Species ◽  
Invasion Pathways ◽  
Geographic Ranges ◽  
Bactrocera Correcta ◽  
Invasive Pest Species ◽  
Source Populations

AbstractDistance decay principles predict that species with larger geographic ranges would have greater intraspecific genetic diversity than more restricted species. However, invasive pest species may not follow this prediction, with confounding implications for tracking phenomena including original ranges, invasion pathways and source populations. We sequenced an 815 base-pair section of the COI gene for 441 specimens of Bactrocera correcta, 214 B. zonata and 372 Zeugodacus cucurbitae; three invasive pest fruit fly species with overlapping hostplants. For each species, we explored how many individuals would need to be included in a study to sample the majority of their haplotype diversity. We also tested for phylogeographic signal and used demographic estimators as a proxy for invasion potency. We find contrasting patterns of haplotype diversity amongst the species, where B. zonata has the highest diversity but most haplotypes were represented by singletons; B. correcta has ∼7 dominant haplotypes more evenly distributed; Z. cucurbitae has a single dominant haplotype with closely related singletons in a ‘star-shape’ surrounding it. We discuss how these differing patterns relate to their invasion histories. None of the species showed meaningful phylogeographic patterns, possibly due to gene-flow between areas across their distributions, obscuring or eliminating substructuring.

scholarly journals Spatiotemporal Changes in Plasmodium vivax msp142 Haplotypes in Southern Mexico: From the Control to the Pre-Elimination Phase

2022 ◽  
Vol 10 (1) ◽  
pp. 186
Author(s):  
Alejandro Flores-Alanis ◽  
Lilia González-Cerón ◽  
Frida Santillán-Valenzuela ◽  
Cecilia Ximenez ◽  
Marco A. Sandoval-Bautista ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Southern Mexico ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Elimination Phase ◽  
Infected Blood ◽  
Malaria Species ◽  
Over Time

For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp142 fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R2 index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.

A new matrix for toxic baits for control of the leaf-cutting ant Acromyrmex octospinosus (Reich) (Hymenoptera: Formicidae)

1981 ◽  
Vol 71 (4) ◽  
pp. 607-616 ◽  
Author(s):  
A. R. Jutsum ◽  
J. M. Cherrett
Keyword(s):  
Slow Release ◽  
Weight Ratio ◽  
Small Scale ◽  
Pest Species ◽  
Light Weight ◽  
Acromyrmex Octospinosus ◽  
Aerial Application ◽  
Citrus Pulp ◽  
Leaf Cutting ◽  
Excellent Control

AbstractA new easily-produced cheap compound for use as a bait matrix is described. The light-weight matrix of polyurethane is prepared from dense precursors into which suitable attractants and toxicants can be incorporated for the pest species in question. It has a high bait effectiveness/weight ratio, and so is very suitable for aerial application as large economically viable payloads can be achieved. When tested both in the laboratory and in the field on a small scale against the leaf-cutting ant Acromyrmex octospinosus (Reich), the bait was highly acceptable to the ants. Some formulations, especially those coated with mirex gave excellent control of ants in the field in Trinidad, killing all occupants of nests within four days of baiting. The bait exhibited good weathering properties, was resistant to fungus attack, and allowed the slow release of pheromones. It was much cheaper than the citrus pulp baits normally used in Trinidad.

Haplotype Network Analysis and Phylogenetic Tree Construction of Hepatitis C Virus (HCV) Isolated from Tuban, Indonesia

2021 ◽  
pp. 4231-4235
Author(s):  
Supiana Dian Nurtjahyani ◽  
Rasyadan Taufiq Probojati ◽  
Arif Nur Muhammad Ansori ◽  
Mochammad Amin ◽  
Retno Handajani
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Phylogenetic Tree ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Likelihood Method ◽  
Tree Construction ◽  
Transfusion Center ◽  
Genealogical Relationship ◽  
Blood Transfusion Center

This study aimed to analyzed the haplotype network and constructed the phylogenetic tree topology of hepatitis C virus (HCV) in Tuban, Indonesia and those from other countries, to determine the visualize genealogical relationship and inference about gene connected. The HCV isolates were collected from blood transfusion center of Tuban, East Java, Indonesia in 2015 and as a comparison, also the sequences of HCV isolates were retrieved from the GenBank®, National Center of Biotechnology Information (NCBI), USA database. To constructed of distribution map was performed through median joining analysis using Haplotype Network v4.6, whereas to constructed and phylogenetic model analyses were constructed based on the NS5B and 5’UTR regions using MEGA X, maximum-likelihood method based on the Tamura-Nei model. In the HCV NS5B region haplotype network showed high haplotype diversity (Hd=1.00) in 22 haplotypes. Based on phylogenetic analysis 3 sample isolates Tuban (BDT-55-p23, BDT-79-p23 and BDT-112-p23) were identified one group and closely related to isolates from Indonesia. However, isolates Tuban also have the same sequence characters as the isolates from Thailand. It was also confirmed in haplotype network that the three isolates are connected to each other. The identification of HCV genotypes circulating in blood donors in the Tuban of East Java confirmed were closely related to HCV isolates from Indonesia and Thailand. Therefore, this result might contribute in a better medical management towards HCV.

Mitochondrial DNA revealed the extent of genetic diversity and invasion origin of populations from two separate invaded areas of a newly invasive pest,Cydia pomonella(L.) (Lepidoptera: Tortricidae) in China

2015 ◽  
Vol 105 (4) ◽  
pp. 485-496 ◽  
Author(s):  
Y. Li ◽  
X. Duan ◽  
X. Qiao ◽  
X. Li ◽  
K. Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Continuous Monitoring ◽  
Insect Pest ◽  
Cydia Pomonella ◽  
Haplotype Diversity ◽  
Northwestern China ◽  
Invasive Pest ◽  
Mitochondrial Coi ◽  
Similar Haplotype ◽  
Northeast Of China

AbstractCydia pomonellais a serious invasive insect pest in China, and has caused severe damage to the production of apple and pear in its invaded areas. This species is distributing in the northwest and northeast of China, but no occurrence of it has been recorded in the large areas (about 3000–5000 km away) between the invaded northwestern and northeastern regions despite continuous monitoring. As yet the genetic diversity and invasion origin of theC. pomonellapopulations in Northwestern and Northeastern China is obscure. In this study, we investigate the genetic diversity of 14 populations ofC. pomonellasampled throughout the main distribution regions in Northwestern (Xinjiang and Gansu Provinces) and Northeastern (Heilongjiang Province) China and compared them with nine populations from Europe and other continents using the mitochondrial COI, COII and Cytb genes. Both the populations from Northeastern and Northwestern China shared some haplotypes with populations from other countries. Haplotypes of the three mitochondrial genes had a different distribution in Northeastern and Northwestern China. The northeastern populations had more private haplotypes than the northwestern populations. A large number of the individuals from northwestern populations shared a few haplotypes of each of the three genes. The haplotype numbers and haplotype diversities of the northeastern populations were similar to those of field populations in other countries, but were higher than those of the northwestern populations. Populations from the Northwestern China showed similar haplotype number and haplotype diversity. We conclude that the population genetic background ofC. pomonellapopulations in Northeastern and Northwestern China varies due to different invasion sources and that this should be considered before the application of new pest control tactics.

scholarly journals Phylogenetics and population genetics of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters

2016 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
Natrah Fatin Mohd Ikhsan ◽  
S.M Nurul Amin
Keyword(s):  
Genetic Structure ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Marine Species ◽  
Peninsular Malaysia ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of more COI genes and nuclear hypervariable markers.

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