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Craig S. Wilding

Bio: Craig S. Wilding is an academic researcher from Liverpool John Moores University. The author has contributed to research in topics: Anopheles gambiae & Population. The author has an hindex of 29, co-authored 67 publications receiving 3469 citations. Previous affiliations of Craig S. Wilding include Bangor University & University of Leeds.


Papers
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Journal ArticleDOI
Daniel E. Neafsey1, Robert M. Waterhouse, Mohammad Reza Abai2, Sergey Aganezov3, Max A. Alekseyev3, James E. Allen4, James Amon, Bruno Arcà5, Peter Arensburger6, Gleb N. Artemov7, Lauren A. Assour8, Hamidreza Basseri2, Aaron M. Berlin1, Bruce W. Birren1, Stéphanie Blandin9, Stéphanie Blandin10, Andrew I. Brockman11, Thomas R. Burkot12, Austin Burt11, Clara S. Chan13, Cedric Chauve14, Joanna C. Chiu15, Mikkel B. Christensen4, Carlo Costantini16, Victoria L.M. Davidson17, Elena Deligianni18, Tania Dottorini11, Vicky Dritsou19, Stacey Gabriel1, Wamdaogo M. Guelbeogo, Andrew Brantley Hall20, Mira V. Han21, Thaung Hlaing, Daniel S.T. Hughes4, Daniel S.T. Hughes22, Adam M. Jenkins23, Xiaofang Jiang20, Irwin Jungreis13, Evdoxia G. Kakani24, Evdoxia G. Kakani19, Maryam Kamali20, Petri Kemppainen25, Ryan C. Kennedy26, Ioannis K. Kirmitzoglou11, Ioannis K. Kirmitzoglou27, Lizette L. Koekemoer28, Njoroge Laban, Nicholas Langridge4, Mara K. N. Lawniczak11, Manolis Lirakis29, Neil F. Lobo8, Ernesto Lowy4, Robert M. MacCallum11, Chunhong Mao20, Gareth Maslen4, Charles Mbogo30, Jenny McCarthy6, Kristin Michel17, Sara N. Mitchell24, Wendy Moore31, Katherine A. Murphy15, Anastasia N. Naumenko20, Tony Nolan11, Eva Maria Novoa13, Samantha M. O’Loughlin11, Chioma Oringanje31, Mohammad Ali Oshaghi2, Nazzy Pakpour15, Philippos Aris Papathanos11, Philippos Aris Papathanos19, Ashley Peery20, Michael Povelones32, Anil Prakash33, David P. Price34, Ashok Rajaraman14, Lisa J. Reimer35, David C. Rinker36, Antonis Rokas37, Tanya L. Russell12, N’Fale Sagnon, Maria V. Sharakhova20, Terrance Shea1, Felipe A. Simão38, Felipe A. Simão39, Frédéric Simard16, Michel A. Slotman40, Pradya Somboon41, V. N. Stegniy7, Claudio J. Struchiner42, Claudio J. Struchiner43, Gregg W.C. Thomas44, Marta Tojo45, Pantelis Topalis18, Jose M. C. Tubio46, Maria F. Unger8, John Vontas29, Catherine Walton25, Craig S. Wilding47, Judith H. Willis48, Yi-Chieh Wu49, Yi-Chieh Wu13, Guiyun Yan50, Evgeny M. Zdobnov38, Evgeny M. Zdobnov39, Xiaofan Zhou37, Flaminia Catteruccia24, Flaminia Catteruccia19, George K. Christophides11, Frank H. Collins8, Robert S. Cornman48, Andrea Crisanti19, Andrea Crisanti11, Martin J. Donnelly35, Martin J. Donnelly46, Scott J. Emrich8, Michael C. Fontaine51, Michael C. Fontaine8, William M. Gelbart24, Matthew W. Hahn44, Immo A. Hansen34, Paul I. Howell52, Fotis C. Kafatos11, Manolis Kellis13, Daniel Lawson4, Christos Louis18, Shirley Luckhart15, Marc A. T. Muskavitch23, Marc A. T. Muskavitch53, José M. C. Ribeiro, Michael A. Riehle31, Igor V. Sharakhov20, Zhijian Tu20, Laurence J. Zwiebel37, Nora J. Besansky8 
Broad Institute1, Tehran University of Medical Sciences2, George Washington University3, European Bioinformatics Institute4, Sapienza University of Rome5, Temple University6, Tomsk State University7, University of Notre Dame8, French Institute of Health and Medical Research9, Centre national de la recherche scientifique10, Imperial College London11, James Cook University12, Massachusetts Institute of Technology13, Simon Fraser University14, University of California, Davis15, Institut de recherche pour le développement16, Kansas State University17, Foundation for Research & Technology – Hellas18, University of Perugia19, Virginia Tech20, University of Nevada, Las Vegas21, Baylor College of Medicine22, Boston College23, Harvard University24, University of Manchester25, University of California, San Francisco26, University of Cyprus27, National Health Laboratory Service28, University of Crete29, Kenya Medical Research Institute30, University of Arizona31, University of Pennsylvania32, Indian Council of Medical Research33, New Mexico State University34, Liverpool School of Tropical Medicine35, Vanderbilt University Medical Center36, Vanderbilt University37, University of Geneva38, Swiss Institute of Bioinformatics39, Texas A&M University40, Chiang Mai University41, Rio de Janeiro State University42, Oswaldo Cruz Foundation43, Indiana University44, University of Santiago de Compostela45, Wellcome Trust Sanger Institute46, Liverpool John Moores University47, University of Georgia48, Harvey Mudd College49, University of California, Irvine50, University of Groningen51, Centers for Disease Control and Prevention52, Biogen Idec53
02 Jan 2015-Science
TL;DR: The authors investigated the genomic basis of vectorial capacity and explore new avenues for vector control, sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila.
Abstract: Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts

476 citations

Journal ArticleDOI
TL;DR: This work applies the technique of amplified fragment length polymorphism (AFLP) analysis to an intertidal snail whose populations display a cline in shell shape across vertical gradients on rocky shores and finds that about 5% of these loci show greater differentiation than expected, providing evidence of the effects of selection across the cline.
Abstract: Speciation requires the acquisition of reproductive isolation, and the circumstances under which this could evolve are of great interest. Are new species formed after the acquisition of generalized incompatibility arising between physically separated populations, or may they arise as a result of the action of disruptive selection beginning with the divergence of a rather restricted set of gene loci? Here we apply the technique of amplified fragment length polymorphism (AFLP) analysis to an intertidal snail whose populations display a cline in shell shape across vertical gradients on rocky shores. We compare the FST values for 306 AFLP loci with the distribution of FST estimated from a simulation model using values of mutation and migration derived from the data. We find that about 5% of these loci show greater differentiation than expected, providing evidence of the effects of selection across the cline, either direct or indirect through linkage. This is consistent with expectations from nonallopatric speciation models that propose an initial divergence of a small part of the genome driven by strong disruptive selection while divergence at other loci is prevented by gene flow. However, the pattern could also be the result of differential introgression after secondary contact.

332 citations

Journal ArticleDOI
07 Dec 2017-Nature
TL;DR: These data revealed complex population structure and patterns of gene flow, with evidence of ancient expansions, recent bottlenecks, and local variation in effective population size.
Abstract: The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease1. To gain a deeper understanding of how mosquito populations are evolving, here we sequenced the genomes of 765 specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across Africa, and identified over 50 million single nucleotide polymorphisms within the accessible genome. These data revealed complex population structure and patterns of gene flow, with evidence of ancient expansions, recent bottlenecks, and local variation in effective population size. Strong signals of recent selection were observed in insecticide-resistance genes, with several sweeps spreading over large geographical distances and between species. The design of new tools for mosquito control using gene-drive systems will need to take account of high levels of genetic diversity in natural mosquito populations.

265 citations

Journal ArticleDOI
TL;DR: In the primary African malaria vector, Anopheles gambiae sensu stricto, a single enzyme, CYP6M2, confers resistance to two classes of insecticide, which is unique evidence in a disease vector of cross-resistance associated with a single metabolic gene that simultaneously reduces the efficacy of two of the four classes of Insecticide routinely used for malaria control.
Abstract: In the last decade there have been marked reductions in malaria incidence in sub-Saharan Africa. Sustaining these reductions will rely upon insecticides to control the mosquito malaria vectors. We report that in the primary African malaria vector, Anopheles gambiae sensu stricto, a single enzyme, CYP6M2, confers resistance to two classes of insecticide. This is unique evidence in a disease vector of cross-resistance associated with a single metabolic gene that simultaneously reduces the efficacy of two of the four classes of insecticide routinely used for malaria control. The gene-expression profile of a highly DDT-resistant population of A. gambiae s.s. from Ghana was characterized using a unique whole-genome microarray. A number of genes were significantly overexpressed compared with two susceptible West African colonies, including genes from metabolic families previously linked to insecticide resistance. One of the most significantly overexpressed probe groups (false-discovery rate-adjusted P < 0.0001) belonged to the cytochrome P450 gene CYP6M2. This gene is associated with pyrethroid resistance in wild A. gambiae s.s. populations) and can metabolize both type I and type II pyrethroids in recombinant protein assays. Using in vitro assays we show that recombinant CYP6M2 is also capable of metabolizing the organochlorine insecticide DDT in the presence of solubilizing factor sodium cholate.

233 citations

Journal ArticleDOI
TL;DR: Two A. aegypti populations from Ceará are under strong selection pressure by temephos, compromising the field effectiveness of this organophosphate, and resistance to cypermethrin is shown in two of the three populations studied.
Abstract: Organophosphates and pyrethroids are used widely in Brazil to control Aedes aegypti, the main vector of dengue viruses, under the auspices of the National Programme for Dengue Control. Resistance to these insecticides is widespread throughout Brazil. In Ceara the vector is present in 98% of districts and resistance to temephos has been reported previously. Here we measure resistance to temephos and the pyrethroid cypermethrin in three populations from Ceara and use biochemical and molecular assays to characterise resistance mechanisms. Resistance to temephos varied widely across the three studied populations, with resistance ratios (RR95) of 7.2, 30 and 192.7 in Juazeiro do Norte, Barbalha and Crato respectively. The high levels of resistance detected in Barbalha and Crato (RR95 ≥ 30) imply a reduction of temephos efficacy, and indeed in simulated field tests reduced effectiveness was observed for the Barbalha population. Two populations (Crato and Barbalha) were also resistant to cypermethrin, whilst Juazeiro do Norte showed only an altered susceptibility. The Ile1011Met kdr mutation was detected in all three populations and Val1016Ile in Crato and Juazeiro do Norte. 1011Met was significantly associated with resistance to cypermethrin in the Crato population. Biochemical tests showed that only the activity of esterases and GSTs, among the tested detoxification enzymes, was altered in these populations when compared with the Rockefeller strain. Our results demonstrate that two A. aegypti populations from Ceara are under strong selection pressure by temephos, compromising the field effectiveness of this organophosphate. Our results also provide evidence that the process of reducing resistance to this larvicide in the field is difficult and slow and may require more than seven years for reversal. In addition, we show resistance to cypermethrin in two of the three populations studied, and for the first time the presence of the allele 1016Ile in mosquito populations from northeastern Brazil. A significant association between 1011M et and resistance was observed in one of the populations. Target-site mechanisms seem not to be implicated in temephos resistance, reinforcing the idea that for the studied populations, detoxification enzymes most likely play a major role in the resistance to this insecticide.

204 citations


Cited by
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01 Oct 2008-Genetics
TL;DR: It is shown that the inclusion of isolated populations that underwent a strong bottleneck can lead to a high rate of false positives, and it is demonstrated that it is possible to avoid them by carefully choosing the populations that should be included in the analysis.
Abstract: Identifying loci under natural selection from genomic surveys is of great interest in different research areas. Commonly used methods to separate neutral effects from adaptive effects are based on locus-specific population differentiation coefficients to identify outliers. Here we extend such an approach to estimate directly the probability that each locus is subject to selection using a Bayesian method. We also extend it to allow the use of dominant markers like AFLPs. It has been shown that this model is robust to complex demographic scenarios for neutral genetic differentiation. Here we show that the inclusion of isolated populations that underwent a strong bottleneck can lead to a high rate of false positives. Nevertheless, we demonstrate that it is possible to avoid them by carefully choosing the populations that should be included in the analysis. We analyze two previously published data sets: a human data set of codominant markers and a Littorina saxatilis data set of dominant markers. We also perform a detailed sensitivity study to compare the power of the method using amplified fragment length polymorphism (AFLP), SNP, and microsatellite markers. The method has been implemented in a new software available at our website (http://www-leca.ujf-grenoble.fr/logiciels.htm).

2,366 citations

Journal ArticleDOI
TL;DR: This work surveys studies of natural interspecific hybridization in plants and a variety of animals to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.
Abstract: Hybridization between species is commonplace in plants, but is often seen as unnatural and unusual in animals. Here, I survey studies of natural interspecific hybridization in plants and a variety of animals. At least 25% of plant species and 10% of animal species, mostly the youngest species, are involved in hybridization and potential introgression with other species. Species in nature are often incompletely isolated for millions of years after their formation. Therefore, much evolution of eventual reproductive isolation can occur while nascent species are in gene-flow contact, in sympatry or parapatry, long after divergence begins. Although the relative importance of geographic isolation and gene flow in the origin of species is still unknown, many key processes involved in speciation, such as 'reinforcement' of post-mating isolation by the evolution of assortative mating, will have ample opportunity to occur in the presence of continuing gene flow. Today, DNA sequence data and other molecular methods are beginning to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.

1,897 citations

Journal ArticleDOI
TL;DR: A perspective on the context and evolutionary significance of hybridization during speciation is offered, highlighting issues of current interest and debate and suggesting that the Dobzhansky–Muller model of hybrid incompatibilities requires a broader interpretation.
Abstract: Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.

1,715 citations

10 Dec 2007
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

1,528 citations

Journal ArticleDOI
TL;DR: The most useful contribution of the genomics model to population genetics will be improving inferences about population demography and evolutionary history.
Abstract: Population genomics has the potential to improve studies of evolutionary genetics, molecular ecology and conservation biology, by facilitating the identification of adaptive molecular variation and by improving the estimation of important parameters such as population size, migration rates and phylogenetic relationships. There has been much excitement in the recent literature about the identification of adaptive molecular variation using the population-genomic approach. However, the most useful contribution of the genomics model to population genetics will be improving inferences about population demography and evolutionary history.

1,276 citations