A genome-wide approach for uncovering evolutionary relationships of Australian Bactrocera species complexes (Diptera: Tephritidae)

2019 ◽  
Author(s):  
Renee A. Catullo ◽  
Heng L. Yeap ◽  
Siu F. Lee ◽  
Jason G. Bragg ◽  
Jodie Cheesman ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Phylogenetic Reconstruction ◽  
Fruit Fly ◽  
Evolutionary Relationships ◽  
Pest Species ◽  
Nucleotide Polymorphisms ◽  
Male Response ◽  
Biogeographic History ◽  
A Genome ◽  
Important Pest

Australia and Southeast Asia are hotspots of global diversity in the fruit-fly genus Bactrocera. Although a great diversity of species has been long recognised, evolutionary relationships are poorly understood, largely because previous sequencing techniques have provided insufficient historical signal for phylogenetic reconstruction. Poorly understood biogeographic history in Bactrocera has prevented a deeper understanding of migratory patterns in this economically important pest group. Using representatives from Australia and Malaysia, we tested the utility of a genome-reduction approach that generates thousands of single-nucleotide polymorphisms for phylogenetic reconstructions. This approach has high utility for species identification because of the ease of sample addition over time, and the species-level specificity able to be achieved with the markers. These data have provided a strongly supported phylogenetic tree congruent with topologies generated using more intensive sequencing approaches. In addition, our results do not support taxonomic assignments to species complex for a number of species, such as B. endiandrae in the dorsalis complex, yet find a close relationship between B. pallida and the dorsalis species. Our data have further validated non-monophyletic evolution of male response to primary attractants. We also showed at least two diversification events between Australia and Southeast Asia, indicating trans-regional dispersal in important pest species.

Population genetics of the solanum fruit fly, Bactrocera latifrons (Hendel) (Diptera: Tephritidae)

Genome ◽  
2019 ◽  
Vol 62 (11) ◽  
pp. 739-747
Author(s):  
Chonticha Kunprom ◽  
Pairot Pramual
Keyword(s):  
Genetic Structure ◽  
Genetic Drift ◽  
Fruit Fly ◽  
Haplotype Network ◽  
Population History ◽  
Pest Species ◽  
Genetic Structuring ◽  
Low Genetic Diversity ◽  
Important Pest ◽  
Bactrocera Latifrons

The solanum fruit fly, Bactrocera latifrons (Hendel), is an important pest species of commercial plants in the family Solanaceae. In this study, the population genetic structure of B. latifrons was investigated using mitochondrial cytochrome c oxidase I sequences. A mitochondrial DNA haplotype network revealed no major genetic break, but haplotypes from recently invaded areas in Japan, Tanzania, and Kenya were genetically divergent. The overall haplotype network is approximately star-shaped, characteristic of recent demographic expansion of populations. This is also supported by large negative values of neutrality tests. Despite the overall pattern of recent population history, genetic structure analysis revealed considerable genetic structuring with 33% of pairwise comparisons being significantly different. Populations that were genetically different from the others usually possess low genetic diversity, suggesting that genetic drift is potentially a factor driving genetic differentiation. Local extinction and recolonization processes related to the availability of host plants are most likely responsible for a founder effect and subsequent genetic drift in a population.

Anastrepha ludens (Mexican fruit fly).

2021 ◽  
Author(s):  
Allen Norrbom
Keyword(s):  
Mangifera Indica ◽  
Fruit Fly ◽  
Anastrepha Ludens ◽  
Broad Host Range ◽  
Pest Species ◽  
Mexican Fruit Fly ◽  
Anastrepha Obliqua ◽  
The World ◽  
Important Pest ◽  
Major Pest

Abstract A. ludens has a broad host range and is a major pest, especially of citrus and mango (Mangifera indica) in most parts of its range. This species and Anastrepha obliqua are the most important pest species of Anastrepha in Central America and Mexico. It occurs in subtropical areas as far north as southern Texas, thus it may be more of a threat of introduction to other subtropical areas of the world than other species of Anastrepha. It is invasive at least in Panama and has been trapped in California, USA. It is considered an A1 quarantine pest by EPPO.

Anastrepha fraterculus (South American fruit fly).

2021 ◽  
Author(s):  
Allen Norrbom
Keyword(s):  
Cryptic Species ◽  
Fruit Fly ◽  
Anastrepha Ludens ◽  
Broad Host Range ◽  
South American ◽  
Pest Species ◽  
Anastrepha Fraterculus ◽  
The Family ◽  
Important Pest ◽  
South American Fruit Fly

Abstract A. fraterculus has a broad host range, particularly in the family Myrtaceae, but it is also a pest of citrus and apples [Malus domestica] in some areas. It is the most important pest species of Anastrepha in subtropical areas of South America, thus it and Anastrepha ludens may be more of a threat of introduction to other subtropical areas of the world than other species of Anastrepha. It is invasive in the Galapagos Islands. As it is probably a complex of cryptic species whose ranges and delimitation remain unresolved, there is also the threat of introduction of particular cryptic species to other areas within the range of the complex. It is considered an A1 quarantine pest by EPPO.

Revision of the subgenus Ceratitis (Ceratalaspis) Hancock (Diptera: Tephritidae)

1998 ◽  
Vol 88 (3) ◽  
pp. 257-290 ◽  
Author(s):  
M. De Meyer
Keyword(s):  
Middle East ◽  
Host Plant ◽  
Fruit Fly ◽  
Pest Species ◽  
Wide Range ◽  
Wing Patterns ◽  
Important Pest ◽  
Plant Data ◽  
Species Groups ◽  
Sub Saharan

AbstractThe fruit fly genus Ceratitis (Diptera: Tephritidae) comprises several important pest species attacking a wide range of unrelated fruits. This is the second paper in a series revising this genus, and deals with representatives of the subgenus Ceratalaspis. Thirty-six species are recognized, of which five are described as new: C. sucinisp. n., C. hancockisp. n., C. neosticticasp. n., C. paradumetisp. n. and C. mlimaensissp. n.Ceratitis pycnanthi (Ghesquière) is considered to be synonymous with C. striatella Munro, and the possible synonymies of C. giffardi Bezzi and C. sarcocephali (Bezzi) with C. cosyra (Walker), as well as C. lineata (Hering) with C. striatella Munro are discussed. Lectotypes are designated for the following species: C. connexa (Bezzi), C. discussa Munro, C. divaricata (Munro), C. dumeti Munro, C. lentigera Munro, C. lunata Munro, C. marriotti Munro, C. melanopus (Hering), C. parinarii (Hering), C. quinaria (Bezzi), C. scaevolae (Munro), and C. simi Munro. A key is provided, with illustrations of mesonotal and wing patterns and shape of aculeus tip. All species are Afrotropical and most are restricted to the sub-saharan region, except for C. quinaria which is also known from the Middle East (Yemen). Distribution and known host plant data are given. Tentative species groups within the subgenus are discussed.

scholarly journals Inferring Modes of Colonization for Pest Species Using Heterozygosity Comparisons and a Shared-Allele Test

Genetics ◽  
2003 ◽  
Vol 163 (2) ◽  
pp. 823-831
Author(s):  
J A Sved ◽  
H Yu ◽  
B Dominiak ◽  
A S Gilchrist
Keyword(s):  
Distance Measure ◽  
Fruit Fly ◽  
Small Samples ◽  
Pest Species ◽  
Long Distance ◽  
Resampling Methods ◽  
Shared Allele ◽  
The Core ◽  
Direct Sampling ◽  
Long Distance Movement

Abstract Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone.

EXPRESS: Effect of genetic liability to visceral adiposity on stroke and its subtypes: a Mendelian randomization study

2021 ◽  
pp. 174749302110062
Author(s):  
Bin Yan ◽  
Jian Yang ◽  
Li Qian ◽  
Fengjie Gao ◽  
Ling Bai ◽  
...  
Keyword(s):  
Sensitivity Analysis ◽  
Ischemic Stroke ◽  
Genome Wide Association Study ◽  
Mendelian Randomization ◽  
Visceral Adiposity ◽  
Large Artery ◽  
Nucleotide Polymorphisms ◽  
Genetic Liability ◽  
A Genome ◽  
Increased Risk

Background: Observational studies have found an association between visceral adiposity and stroke. Aims: The purpose of this study was to investigate the role and genetic effect of visceral adipose tissue (VAT) accumulation on stroke and its subtypes. Methods: In this two-sample Mendelian randomization (MR) study, genetic variants (221 single nucleotide polymorphisms; P<5×10-8) using as instrumental variables for MR analysis was obtained from a genome-wide association study (GWAS) of VAT. The outcome datasets for stroke and its subtypes were obtained from the MEGASTROKE consortium (up to 67,162 cases and 453,702 controls). MR standard analysis (inverse variance weighted method) was conducted to investigate the effect of genetic liability to visceral adiposity on stroke and its subtypes. Sensitivity analysis (MR-Egger, weighted median, MR-PRESSO) were also utilized to assess horizontal pleiotropy and remove outliers. Multi-variable MR analysis was employed to adjust potential confounders. Results: In the standard MR analysis, genetically determined visceral adiposity (per 1 SD) was significantly associated with a higher risk of stroke (odds ratio [OR] 1.30; 95% confidence interval [CI] 1.21-1.41, P=1.48×10-11), ischemic stroke (OR 1.30; 95% CI 1.20-1.41, P=4.01×10-10), and large artery stroke (OR 1.49; 95% CI 1.22-1.83, P=1.16×10-4). The significant association was also found in sensitivity analysis and multi-variable MR analysis. Conclusions: Genetic liability to visceral adiposity was significantly associated with an increased risk of stroke, ischemic stroke, and large artery stroke. The effect of genetic susceptibility to visceral adiposity on the stroke warrants further investigation.

scholarly journals An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Misbah Razzaq ◽  
Maria Jesus Iglesias ◽  
Manal Ibrahim-Kosta ◽  
Louisa Goumidi ◽  
Omar Soukarieh ◽  
...  
Keyword(s):  
Pulmonary Embolism ◽  
Genome Wide Association Study ◽  
Susceptibility Gene ◽  
Biological Traits ◽  
Nucleotide Polymorphisms ◽  
Ann Model ◽  
Neural Network Approach ◽  
A Genome ◽  
Increased Risk ◽  
Artificial Neural

AbstractVenous thromboembolism is the third common cardiovascular disease and is composed of two entities, deep vein thrombosis (DVT) and its potential fatal form, pulmonary embolism (PE). While PE is observed in ~ 40% of patients with documented DVT, there is limited biomarkers that can help identifying patients at high PE risk. To fill this need, we implemented a two hidden-layers artificial neural networks (ANN) on 376 antibodies and 19 biological traits measured in the plasma of 1388 DVT patients, with or without PE, of the MARTHA study. We used the LIME algorithm to obtain a linear approximate of the resulting ANN prediction model. As MARTHA patients were typed for genotyping DNA arrays, a genome wide association study (GWAS) was conducted on the LIME estimate. Detected single nucleotide polymorphisms (SNPs) were tested for association with PE risk in MARTHA. Main findings were replicated in the EOVT study composed of 143 PE patients and 196 DVT only patients. The derived ANN model for PE achieved an accuracy of 0.89 and 0.79 in our training and testing sets, respectively. A GWAS on the LIME approximate identified a strong statistical association peak (rs1424597: p = 5.3 × 10–7) at the PLXNA4 locus. Homozygote carriers for the rs1424597-A allele were then more frequently observed in PE than in DVT patients from the MARTHA (2% vs. 0.4%, p = 0.005) and the EOVT (3% vs. 0%, p = 0.013) studies. In a sample of 112 COVID-19 patients known to have endotheliopathy leading to acute lung injury and an increased risk of PE, decreased PLXNA4 levels were associated (p = 0.025) with worsened respiratory function. Using an original integrated proteomics and genetics strategy, we identified PLXNA4 as a new susceptibility gene for PE whose exact role now needs to be further elucidated.

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Eucalyptus cladocalyx Trees under Arid Conditions

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 148
Author(s):  
Camilo E. Valenzuela ◽  
Paulina Ballesta ◽  
Sunny Ahmar ◽  
Sajid Fiaz ◽  
Parviz Heidari ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Wood Quality ◽  
Tree Height ◽  
Mediterranean Ecosystems ◽  
Primary Metabolism ◽  
Arid Environments ◽  
Nucleotide Polymorphisms ◽  
Haplotype Blocks ◽  
A Genome ◽  
Stem Straightness

The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and haplotype blocks associated with the growth and wood quality of Eucalyptus cladocalyx, a tree species suitable for low-rainfall sites. The study was conducted in a progeny-provenance trial established in an arid site with Mediterranean patterns located in the southern Atacama Desert, Chile. A total of 87 SNPs and 3 haplotype blocks were significantly associated with the 6 traits under study (tree height, diameter at breast height, slenderness coefficient, first bifurcation height, stem straightness, and pilodyn penetration). In addition, 11 loci were identified as pleiotropic through Bayesian multivariate regression and were mainly associated with wood hardness, height, and diameter. In general, the GWAS revealed associations with genes related to primary metabolism and biosynthesis of cell wall components. Additionally, associations coinciding with stress response genes, such as GEM-related 5 and prohibitin-3, were detected. The findings of this study provide valuable information regarding genetic control of morphological traits related to adaptation to arid environments.

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