Patterns of Genome-Wide Variation, Population Differentiation and SNP Discovery of the Red Banded Stink Bug (Piezodorus guildinii)

Abstract Unravelling the details of range expansion and ecological dominance shifts of insect pests has been challenging due to the lack of basic knowledge about population structure, gene flow, and most importantly, how natural selection is affecting the adaptive process. Piezodous guildinii is an emerging pest of soybean in the southern region of the United States, and increasingly important in Brazil in recent years. However, the reasons P. guildinii is gradually becoming more of a problem are questions still mostly unanswered. Here, we have genotyped P. guildinii samples and discovered 1,337 loci containing 4,083 variant sites SNPs that were used to estimate genetic structure and to identify gene candidates under natural selection. Our results revealed the existence of a significant genetic structure separating populations according to their broad geographic origin, i.e., U.S. and Brazil, supported by AMOVA (FGT = 0.26), STRUCTURE, PCA, and FST analyses. High levels of gene flow or coancestry within groups (i.e., within countries) can be inferred from the data, and no spatial pattern was apparent at the finer scale in Brazil. Samples from different seasons show more heterogeneous compositions suggesting mixed ancestry and a more complex dynamic. Lastly, we were able to detect and successfully annotated 123 GBS loci (10.5%) under positive selection. The gene ontology (GO) analysis implicated candidate genes under selection with genome reorganization, neuropeptides, and energy mobilization. We discuss how these findings could be related to recent outbreaks and suggest how new efforts directed to better understand P. guildinii population dynamics.

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The genetic structure of populations of orchids and its evolutionary importance: understanding processes from patterns

Lankesteriana ◽

10.15517/lank.v3i2.23024 ◽

2016 ◽

Vol 3 (2) ◽

Author(s):

Raymond L. Tremblay

Keyword(s):

Gene Flow ◽

Natural Selection ◽

Genetic Structure ◽

Population Size ◽

Effective Population Size ◽

Genetic Drift ◽

Mating Systems ◽

Mutation Rates ◽

Effective Population ◽

Genetic Structure Of Populations

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>Evolution through either natural selection or genetic drift is dependent on variation at the genetic and mor- phological levels. Processes that influence the genetic structure of populations include mating systems, effective population size, mutation rates and gene flow among populations. </span></p></div></div></div>

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The Genetic Structure of Pseudoperonospora cubensis Populations

Plant Disease ◽

10.1094/pdis-11-11-0943-re ◽

2012 ◽

Vol 96 (10) ◽

pp. 1459-1470 ◽

Cited By ~ 37

Author(s):

L. M. Quesada-Ocampo ◽

L. L. Granke ◽

J. Olsen ◽

H. C. Gutting ◽

F. Runge ◽

...

Keyword(s):

United States ◽

Population Structure ◽

Genetic Structure ◽

Geographic Origin ◽

The United States ◽

Diagnostic Tools ◽

Pseudoperonospora Cubensis ◽

Genetic Structuring ◽

Genetic Clusters ◽

Global Population

Pseudoperonospora cubensis is a destructive foliar pathogen of economically important cucurbitaceous crops in the United States and worldwide. In this study, we investigated the genetic structure of 465 P. cubensis isolates from three continents, 13 countries, 19 states of the United States, and five host species using five nuclear and two mitochondrial loci. Bayesian clustering resolved six genetic clusters and suggested some population structure by geographic origin and host, because some clusters occurred more or less frequently in particular categories. All of the genetic clusters were present in the sampling from North America and Europe. Differences in cluster occurrence were observed by country and state. Isolates from cucumber had different cluster composition and lower genetic diversity than isolates from other cucurbits. Because genetic structuring was detected, isolates that represent the genetic variation in P. cubensis should be used when developing diagnostic tools, fungicides, and resistant host varieties. Although this study provides an initial map of global population structure of P. cubensis, future genotyping of isolates could reveal population structure within specific geographic regions, across a wider range of hosts, or during different time points during the growing season.

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Investigating the Genetic Structure of Phytophthora capsici Populations

Phytopathology ◽

10.1094/phyto-11-10-0325 ◽

2011 ◽

Vol 101 (9) ◽

pp. 1061-1073 ◽

Cited By ~ 32

Author(s):

L. M. Quesada-Ocampo ◽

L. L. Granke ◽

M. R. Mercier ◽

J. Olsen ◽

M. K. Hausbeck

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Genetic Structure ◽

Association Studies ◽

Phytophthora Capsici ◽

Geographic Origin ◽

The United States ◽

Diagnostic Tools ◽

Bayesian Clustering ◽

Genetic Structuring

Phytophthora capsici Leonian is a destructive soilborne pathogen that infects economically important solanaceous, cucurbitaceous, fabaceous, and other crops in the United States and worldwide. The objective of this study was to investigate the genetic structure of 255 P. capsici isolates assigned to predefined host, geographical, mefenoxam-sensitivity, and mating-type categories. Isolates from six continents, 21 countries, 19 U.S. states, and 26 host species were genotyped for four mitochondrial and six nuclear loci. Bayesian clustering revealed some population structure by host, geographic origin, and mefenoxam sensitivity, with some clusters occurring more or less frequently in particular categories. Bayesian clustering, split networks, and statistical parsimony genealogies also detected the presence of non-P. capsici individuals in our sample corresponding to P. tropicalis (n = 9) and isolates of a distinct cluster closely related to P. capsici and P. tropicalis (n = 10). Our findings of genetic structuring in P. capsici populations highlight the importance of including isolates from all detected clusters that represent the genetic variation in P. capsici for development of diagnostic tools, fungicides, and host resistance. The population structure detected will also impact the design and interpretation of association studies in P. capsici. This study provides an initial map of global population structure of P. capsici but continued genotyping of isolates will be necessary to expand our knowledge of genetic variation in this important plant pathogen.

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Hierarchical Analysis of Genetic Structure in Native Fire Ant Populations: Results From Three Classes of Molecular Markers

Genetics ◽

10.1093/genetics/147.2.643 ◽

1997 ◽

Vol 147 (2) ◽

pp. 643-655 ◽

Cited By ~ 3

Author(s):

Kenneth G Ross ◽

Michael J B Krieger ◽

D DeWayne Shoemaker ◽

Edward L Vargo ◽

Laurent Keller

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Solenopsis Invicta ◽

Large Scale ◽

Fire Ant ◽

Nuclear Markers ◽

Social Forms ◽

Native Populations ◽

Nest Level ◽

Nuclear Differentiation

We describe genetic structure at various scales in native populations of the fire ant Solenopsis invicta using two classes of nuclear markers, allozymes and microsatellites, and markers of the mitochondrial genome. Strong structure was found at the nest level in both the monogyne (single queen) and polygyne (multiple queen) social forms using allozymes. Weak but significant microgeographic structure was detected above the nest level in polygyne populations but not in monogyne populations using both classes of nuclear markers. Pronounced mitochondrial DNA (mtDNA) differentiation was evident also at this level in the polygyne form only. These microgeographic patterns are expected because polygyny in ants is associated with restricted local gene flow due mainly to limited vagility of queens. Weak but significant nuclear differentiation was detected between sympatric social forms, and strong mtDNA differentiation also was found at this level. Thus, queens of each form seem unable to establish themselves in nests of the alternate type, and some degree of assortative mating by form may exist as well. Strong differentiation was found between the two study regions usinga all three sets of markers. Phylogeographic analyses of the mtDNA suggest that recent limitations on gene flow rather than longstanding barriers to dispersal are responsible for this large-scale structure.

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Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽

10.1093/genetics/147.4.1843 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1843-1854 ◽

Cited By ~ 8

Author(s):

Nancy N FitzSimmons ◽

Craig Moritz ◽

Colin J Limpus ◽

Lisa Pope ◽

Robert Prince

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Green Turtle ◽

Nuclear Dna ◽

Nuclear Gene ◽

Chelonia Mydas ◽

Single Copy ◽

Microsatellite Data ◽

Ecological Data ◽

Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

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Prevalence of systemic lupus erythematosus in Spain: higher than previously reported in other countries?

Rheumatology ◽

10.1093/rheumatology/kez668 ◽

2020 ◽

Vol 59 (9) ◽

pp. 2556-2562 ◽

Cited By ~ 4

Author(s):

Raúl Cortés Verdú ◽

José M Pego-Reigosa ◽

Daniel Seoane-Mato ◽

Mercedes Morcillo Valle ◽

Deseada Palma Sánchez ◽

...

Keyword(s):

Lupus Erythematosus ◽

Adult Population ◽

Geographical Area ◽

Geographic Origin ◽

The United States ◽

Epidemiological Studies ◽

Population Based ◽

Cross Sectional Study ◽

Medical Visit ◽

Cross Sectional

Abstract Objectives Prevalence of SLE varies among studies, being influenced by study design, geographical area and ethnicity. Data about the prevalence of SLE in Spain are scarce. In the EPISER2016 study, promoted by the Spanish Society of Rheumatology, the prevalence estimate of SLE in the general adult population in Spain has been updated and its association with sociodemographic, anthropometric and lifestyle variables has been explored. Methods Population-based multicentre cross-sectional study, with multistage stratified and cluster random sampling. Participants were contacted by telephone to carry out a questionnaire for the screening of SLE. Investigating rheumatologists evaluated positive results (review of medical records and/or telephone interview, with medical visit if needed) to confirm the diagnosis. To calculate the prevalence and its 95% CI, the sample design was taken into account and weighing was calculated considering age, sex and geographic origin. Multivariate logistic regression models were defined to analyse which sociodemographic, anthropometric and lifestyle variables included in the telephone questionnaire were associated with the presence of SLE. Results 4916 subjects aged 20 years or over were included. 16.52% (812/4916) had a positive screening result for SLE. 12 cases of SLE were detected. The estimated prevalence was 0.21% (95% CI: 0.11, 0.40). SLE was more prevalent in the rural municipalities, with an odds ratio (OR) = 4.041 (95% CI: 1.216, 13.424). Conclusion The estimated prevalence of SLE in Spain is higher than that described in most international epidemiological studies, but lower than that observed in ethnic minorities in the United States or the United Kingdom.

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Population genetic structure and gene flow in the Japanese sea cucumber Apostichopus japonicus across Toyama Bay, Japan

Fisheries Science ◽

10.1007/s12562-012-0509-1 ◽

2012 ◽

Vol 78 (4) ◽

pp. 775-783 ◽

Cited By ~ 1

Author(s):

Taha Soliman ◽

Manami Kanno ◽

Akihiro Kijima ◽

Yuji Yamazaki

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Sea Cucumber ◽

Apostichopus Japonicus ◽

Toyama Bay ◽

Japanese Sea Cucumber

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Effects from Early Planting of Late-Maturing Sunflowers on Damage from Primary Insect Pests in the United States

Helia ◽

10.1515/helia-2015-0016 ◽

2016 ◽

Vol 39 (64) ◽

pp. 45-56 ◽

Cited By ~ 1

Author(s):

J. R. Prasifka ◽

L. F. Marek ◽

D. K. Lee ◽

S. B. Thapa ◽

V. Hahn ◽

...

Keyword(s):

United States ◽

North Dakota ◽

Sunflower Seed ◽

Insect Pests ◽

The United States ◽

Total Percentage ◽

History Of ◽

Smicronyx Fulvus ◽

Sunflower Moth ◽

Homoeosoma Electellum

AbstractDelayed planting is recommended to reduce damage from sunflower insect pests in the United States, including the sunflower moth, Homoeosoma electellum (Hulst) and banded sunflower moth, Cochylis hospes Walsingham. However, in some locations, planting earlier or growing later-maturing hybrids could improve yield or oil content of sunflowers which would partially offset any added costs from insect pests or their management. Because the abundance and distribution of some sunflower insects have changed since recommendations for delayed planting were developed, experimental plots were grown in 2012 and 2013 at sites in North Dakota, Nebraska, Iowa, and Illinois. Sunflowers were planted two to four weeks earlier than normal, including hybrids that flower two to three weeks later than elite commercial hybrids. The sum of seed damaged by sunflower moth, banded sunflower moth, and red sunflower seed weevil, Smicronyx fulvus LeConte, (i. e., total percentage) was influenced by location, but not the relative maturity of tested entries. However, when damage attributed solely to the red sunflower seed weevil was analyzed, more damaged seed were found for late-maturing entries in North Dakota and Nebraska. In addition to the trial data, current pest populations are lower than when delayed planting was first recommended and insecticide use during sunflower bloom is both common and effective. Together, these observations suggest factoring insect pests into planting time decisions may be unnecessary, except for areas with a history of problems with severe pests that cannot be managed using insecticides (e. g., sunflower midge, Contarinia schulzi Gagné).

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