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Apte RA, Smidler AL, Pai JJ, Chow ML, Chen S, Mondal A, Sánchez C. HM, Antoshechkin I, Marshall JM, Akbari OS. Eliminating malaria vectors with precision-guided sterile males. Proc Natl Acad Sci U S A 2024; 121:e2312456121. [PMID: 38917000 PMCID: PMC11228498 DOI: 10.1073/pnas.2312456121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 05/03/2024] [Indexed: 06/27/2024] Open
Abstract
Controlling the principal African malaria vector, the mosquito Anopheles gambiae, is considered essential to curtail malaria transmission. However, existing vector control technologies rely on insecticides, which are becoming increasingly ineffective. Sterile insect technique (SIT) is a powerful suppression approach that has successfully eradicated a number of insect pests, yet the A. gambiae toolkit lacks the requisite technologies for its implementation. SIT relies on iterative mass releases of nonbiting, nondriving, sterile males which seek out and mate with monandrous wild females. Once mated, females are permanently sterilized due to mating-induced refractoriness, which results in population suppression of the subsequent generation. However, sterilization by traditional methods renders males unfit, making the creation of precise genetic sterilization methods imperative. Here, we introduce a vector control technology termed precision-guided sterile insect technique (pgSIT), in A. gambiae for inducible, programmed male sterilization and female elimination for wide-scale use in SIT campaigns. Using a binary CRISPR strategy, we cross separate engineered Cas9 and gRNA strains to disrupt male-fertility and female-essential genes, yielding >99.5% male sterility and >99.9% female lethality in hybrid progeny. We demonstrate that these genetically sterilized males have good longevity, are able to induce sustained population suppression in cage trials, and are predicted to eliminate wild A. gambiae populations using mathematical models, making them ideal candidates for release. This work provides a valuable addition to the malaria genetic biocontrol toolkit, enabling scalable SIT-like confinable, species-specific, and safe suppression in the species.
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Affiliation(s)
- Reema A. Apte
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Andrea L. Smidler
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - James J. Pai
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Martha L. Chow
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Sanle Chen
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Agastya Mondal
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA94720
| | - Héctor M. Sánchez C.
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA94720
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - John M. Marshall
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA94720
- Innovative Genomics Institute, University of California, Berkeley, CA94720
| | - Omar S. Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
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Smidler AL, Apte RA, Pai JJ, Chow ML, Chen S, Mondal A, Sánchez C. HM, Antoshechkin I, Marshall JM, Akbari OS. Eliminating Malaria Vectors with Precision Guided Sterile Males. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549947. [PMID: 37503146 PMCID: PMC10370176 DOI: 10.1101/2023.07.20.549947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Controlling the principal African malaria vector, the mosquito Anopheles gambiae, is considered essential to curtail malaria transmission. However existing vector control technologies rely on insecticides, which are becoming increasingly ineffective. Sterile insect technique (SIT) is a powerful suppression approach that has successfully eradicated a number of insect pests, yet the A. gambiae toolkit lacks the requisite technologies for its implementation. SIT relies on iterative mass-releases of non-biting, non-driving, sterile males which seek out and mate with monandrous wild females. Once mated, females are permanently sterilized due to mating-induced refractoriness, which results in population suppression of the subsequent generation. However, sterilization by traditional methods renders males unfit, making the creation of precise genetic sterilization methods imperative. Here we develop precision guided Sterile Insect Technique (pgSIT) in the mosquito A. gambiae for inducible, programmed male-sterilization and female-elimination for wide scale use in SIT campaigns. Using a binary CRISPR strategy, we cross separate engineered Cas9 and gRNA strains to disrupt male-fertility and female-essential genes, yielding >99.5% male-sterility and >99.9% female-lethality in hybrid progeny. We demonstrate that these genetically sterilized males have good longevity, are able to induce population suppression in cage trials, and are predicted to eliminate wild A. gambiae populations using mathematical models, making them ideal candidates for release. This work provides a valuable addition to the malaria genetic biocontrol toolkit, for the first time enabling scalable SIT-like confinable suppression in the species.
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Affiliation(s)
- Andrea L. Smidler
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Reema A. Apte
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - James J. Pai
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Martha L. Chow
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Sanle Chen
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Agastya Mondal
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Héctor M. Sánchez C.
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA91125, USA
| | - John M. Marshall
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Omar S. Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
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Gene drive in species complexes: defining target organisms. Trends Biotechnol 2023; 41:154-164. [PMID: 35868886 DOI: 10.1016/j.tibtech.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 01/24/2023]
Abstract
Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.
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Onyango SA, Ochwedo KO, Machani MG, Olumeh JO, Debrah I, Omondi CJ, Ogolla SO, Lee MC, Zhou G, Kokwaro E, Kazura JW, Afrane YA, Githeko AK, Zhong D, Yan G. Molecular characterization and genotype distribution of thioester-containing protein 1 gene in Anopheles gambiae mosquitoes in western Kenya. Malar J 2022; 21:235. [PMID: 35948910 PMCID: PMC9364548 DOI: 10.1186/s12936-022-04256-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Evolutionary pressures lead to the selection of efficient malaria vectors either resistant or susceptible to Plasmodium parasites. These forces may favour the introduction of species genotypes that adapt to new breeding habitats, potentially having an impact on malaria transmission. Thioester-containing protein 1 (TEP1) of Anopheles gambiae complex plays an important role in innate immune defenses against parasites. This study aims to characterize the distribution pattern of TEP1 polymorphisms among populations of An. gambiae sensu lato (s.l.) in western Kenya. METHODS Anopheles gambiae adult and larvae were collected using pyrethrum spray catches (PSC) and plastic dippers respectively from Homa Bay, Kakamega, Bungoma, and Kisumu counties between 2017 and 2020. Collected adults and larvae reared to the adult stage were morphologically identified and then identified to sibling species by PCR. TEP1 alleles were determined in 627 anopheles mosquitoes using restriction fragment length polymorphisms-polymerase chain reaction (RFLP-PCR) and to validate the TEP1 genotyping results, a representative sample of the alleles was sequenced. RESULTS Two TEP1 alleles (TEP1*S1 and TEP1*R2) and three corresponding genotypes (*S1/S1, *R2/S1, and *R2/R2) were identified. TEP1*S1 and TEP1*R2 with their corresponding genotypes, homozygous *S1/S1 and heterozygous *R2/S1 were widely distributed across all sites with allele frequencies of approximately 80% and 20%, respectively both in Anopheles gambiae and Anopheles arabiensis. There was no significant difference detected among the populations and between the two mosquito species in TEP1 allele frequency and genotype frequency. The overall low levels in population structure (FST = 0.019) across all sites corresponded to an effective migration index (Nm = 12.571) and low Nei's genetic distance values (< 0.500) among the subpopulation. The comparative fixation index values revealed minimal genetic differentiation between species and high levels of gene flow among populations. CONCLUSION Genotyping TEP1 has identified two common TEP1 alleles (TEP1*S1 and TEP1*R2) and three corresponding genotypes (*S1/S1, *R2/S1, and *R2/R2) in An. gambiae s.l. The TEP1 allele genetic diversity and population structure are low in western Kenya.
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Affiliation(s)
- Shirley A. Onyango
- Department of Zoological Sciences, School of Science and Technology, Kenyatta University, Nairobi, Kenya
- Sub-Saharan Africa International Centre of Excellence for Malaria Research, Homa bay, Kenya
| | - Kevin O. Ochwedo
- Sub-Saharan Africa International Centre of Excellence for Malaria Research, Homa bay, Kenya
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Maxwell G. Machani
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Julius O. Olumeh
- Sub-Saharan Africa International Centre of Excellence for Malaria Research, Homa bay, Kenya
| | - Isaiah Debrah
- Sub-Saharan Africa International Centre of Excellence for Malaria Research, Homa bay, Kenya
- Department of Biochemistry, Cell and Molecular Biology, West Africa Centre for Cell Biology of Infectious Pathogen, University of Ghana, Accra, Ghana
| | - Collince J. Omondi
- Sub-Saharan Africa International Centre of Excellence for Malaria Research, Homa bay, Kenya
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Sidney O. Ogolla
- Department of Zoological Sciences, School of Science and Technology, Kenyatta University, Nairobi, Kenya
- Sub-Saharan Africa International Centre of Excellence for Malaria Research, Homa bay, Kenya
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology, Medical School, University of Ghana, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West Africa Centre for Cell Biology of Infectious Pathogen, University of Ghana, Accra, Ghana
- Center for Global Health and Diseases, Case Western Reserve University, LC 4983, Cleveland, OH 44106 USA
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Guofa Zhou
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Elizabeth Kokwaro
- Department of Zoological Sciences, School of Science and Technology, Kenyatta University, Nairobi, Kenya
| | - James W. Kazura
- Center for Global Health and Diseases, Case Western Reserve University, LC 4983, Cleveland, OH 44106 USA
| | - Yaw A. Afrane
- Department of Medical Microbiology, Medical School, University of Ghana, University of Ghana, Accra, Ghana
| | - Andrew K. Githeko
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
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The origin of island populations of the African malaria mosquito, Anopheles coluzzii. Commun Biol 2021; 4:630. [PMID: 34040154 PMCID: PMC8155153 DOI: 10.1038/s42003-021-02168-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/21/2021] [Indexed: 11/09/2022] Open
Abstract
Anopheles coluzzii is a major malaria vector throughout its distribution in west-central Africa. Here we present a whole-genome study of 142 specimens from nine countries in continental Africa and three islands in the Gulf of Guinea. This sample set covers a large part of this species' geographic range. Our population genomic analyses included a description of the structure of mainland populations, island populations, and connectivity between them. Three genetic clusters are identified among mainland populations and genetic distances (FST) fits an isolation-by-distance model. Genomic analyses are applied to estimate the demographic history and ancestry for each island. Taken together with the unique biogeography and history of human occupation for each island, they present a coherent explanation underlying levels of genetic isolation between mainland and island populations. We discuss the relationship of our findings to the suitability of São Tomé and Príncipe islands as candidate sites for potential field trials of genetic-based malaria control strategies.
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Courtier‐Orgogozo V, Danchin A, Gouyon P, Boëte C. Evaluating the probability of CRISPR-based gene drive contaminating another species. Evol Appl 2020; 13:1888-1905. [PMID: 32908593 PMCID: PMC7463340 DOI: 10.1111/eva.12939] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = h y b + t r a n s f × e x p r e s s × c u t × f l a n k × i m m u n e × n o n e x t i n c t with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9-expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.
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Affiliation(s)
| | - Antoine Danchin
- Institut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris DescartesParisFrance
| | - Pierre‐Henri Gouyon
- Institut de Systématique, Évolution, BiodiversitéMuséum National d'Histoire NaturelleCNRSSorbonne UniversitéEPHEUAParisFrance
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7
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Corrêa AS, Cordeiro EM, Omoto C. Agricultural insect hybridization and implications for pest management. PEST MANAGEMENT SCIENCE 2019; 75:2857-2864. [PMID: 31124266 DOI: 10.1002/ps.5495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Biological invasions, the expansion of agricultural frontiers, and climate change favor encounters of divergent lineages of animals and plants, increasing the likelihood of hybridization. However, hybridization of insect species and its consequences for agroecosystems have not received sufficient attention. Gene exchange between distinct and distant genetic pools can improve the survival and reproduction of insect pests, and threaten beneficial insects in disturbed agricultural environments. Hybridization may be the underlying explanation for the recurrent pest outbreaks and control failures in putative hybrid zones, as suspected for bollworm, corn borer, whiteflies, and stink bugs. Reliable predictions of the types of changes that can be expected in pest insect genomes and fitness, and of their impacts on the fate of species and populations remain elusive. Typical steps in pest management, such as insect identification, pest monitoring, and control are likely affected by gene flow and adaptive introgression mediated by hybridization, and we do not have ways to respond to or mitigate the problem. To address the adverse effects of farming intensification and global trade, we must ensure that current integrated pest management programs incorporate up-to-date monitoring and diagnostic tools. The rapid identification of hybrids, quantification of levels of introgression, and in-depth knowledge of what genes have been transferred may help to explain and predict insect population outbreaks and control failures in the future. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Alberto S Corrêa
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Erick Mg Cordeiro
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Celso Omoto
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
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Seixas FA, Boursot P, Melo-Ferreira J. The genomic impact of historical hybridization with massive mitochondrial DNA introgression. Genome Biol 2018; 19:91. [PMID: 30056805 PMCID: PMC6065068 DOI: 10.1186/s13059-018-1471-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. RESULTS Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. CONCLUSIONS General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.
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Affiliation(s)
- Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France.
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
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Pombi M, Kengne P, Gimonneau G, Tene-Fossog B, Ayala D, Kamdem C, Santolamazza F, Guelbeogo WM, Sagnon N, Petrarca V, Fontenille D, Besansky NJ, Antonio-Nkondjio C, Dabiré RK, Della Torre A, Simard F, Costantini C. Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex. Evol Appl 2017; 10:1102-1120. [PMID: 29151864 PMCID: PMC5680640 DOI: 10.1111/eva.12517] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/10/2017] [Indexed: 01/10/2023] Open
Abstract
Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms. Here, we studied patterns of reproductive isolation among three taxa, Anopheles coluzzii, An. gambiae s.s. and Anopheles arabiensis, to compare its strength at different spatial scales, to dissect the relative contribution of pre‐ versus postmating isolation, and to infer the involvement of ecological divergence on hybridization. Because F1 hybrids are viable, fertile and not uncommon, understanding the dynamics of hybridization in this trio of major malaria vectors has important implications for how adaptations arise and spread across the group, and in planning studies of the safety and efficacy of gene drive as a means of malaria control. We first performed a systematic review and meta‐analysis of published surveys reporting on hybrid prevalence, showing strong reproductive isolation at a continental scale despite geographically restricted exceptions. Second, we exploited our own extensive field data sets collected at a regional scale in two contrasting environmental settings, to assess: (i) levels of premating isolation; (ii) spatio/temporal and frequency‐dependent dynamics of hybridization, (iii) relationship between reproductive isolation and ecological divergence and (iv) hybrid viability penalty. Results are in accordance with ecological speciation theory predicting a positive association between the strength of reproductive isolation and degree of ecological divergence, and indicate that postmating isolation does contribute to reproductive isolation among these species. Specifically, only postmating isolation was positively associated with ecological divergence, whereas premating isolation was correlated with phylogenetic distance.
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Affiliation(s)
- Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | - Pierre Kengne
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon
| | | | - Billy Tene-Fossog
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon
| | - Diego Ayala
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Centre International de Recherches Médicales de Franceville Franceville Gabon
| | - Colince Kamdem
- Department of Entomology University of California Riverside CA USA
| | - Federica Santolamazza
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | | | - N'Falé Sagnon
- Centre National de Recherche et Formation sur le Paludisme (CNRFP) Ouagadougou Burkina Faso
| | - Vincenzo Petrarca
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | - Didier Fontenille
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Institut Pasteur du Cambodge Phnom Penh Cambodia
| | - Nora J Besansky
- Eck Institute for Global Health & Department of Biological Sciences University of Notre Dame Notre Dame IN USA
| | | | - Roch Kounbobr Dabiré
- Institut de Recherche en Sciences de la Santé (IRSS) Bobo-Dioulasso Burkina Faso
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie InfettiveUniversità di Roma "Sapienza"RomeItaly.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti Rome Italy
| | - Frédéric Simard
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon.,Institut de Recherche en Sciences de la Santé (IRSS) Bobo-Dioulasso Burkina Faso
| | - Carlo Costantini
- Institut de Recherche pour le Développement (IRD) UMR MIVEGEC (University of Montpellier, CNRS 5290 IRD 224) Centre IRD de Montpellier Montpellier France.,Organisation de Coordination pour la lutte contre les Endemies en Afrique Centrale (OCEAC) Yaoundé Cameroon.,Institut de Recherche en Sciences de la Santé (IRSS) Bobo-Dioulasso Burkina Faso
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Sougoufara S, Sokhna C, Diagne N, Doucouré S, Sembène PMB, Harry M. The implementation of long-lasting insecticidal bed nets has differential effects on the genetic structure of the African malaria vectors in the Anopheles gambiae complex in Dielmo, Senegal. Malar J 2017; 16:337. [PMID: 28810861 PMCID: PMC5558778 DOI: 10.1186/s12936-017-1992-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mosquitoes belonging to the Anopheles gambiae complex are the main vectors of malaria in sub-Saharan Africa. Among these, An. gambiae, Anopheles coluzzii and Anopheles arabiensis are the most efficient vectors and are largely distributed in sympatric locations. However, these species present ecological and behavioural differences that impact their vectorial capacity and complicate vector-control efforts, mainly based on long-lasting insecticidal bed nets (LLINs) and indoor residual spraying (IRS). In this study, the genetic structure of these three species in a Senegalese village (Dielmo) was investigated using microsatellite data in samples collected in 2006 before implementation of LLINs, in 2008, when they were introduced, and in 2010, 2 years after the use of LLINs. RESULTS In this study 611 individuals were included, namely 136 An. coluzzii, 101 An. gambiae, 6 An. coluzzii/An. gambiae hybrids and 368 An. arabiensis. According to the species, the effect of the implementation of LLINs in Dielmo is differentiated. Populations of the sister species An. coluzzii and An. gambiae regularly experienced bottleneck events, but without significant inbreeding. The Fst values suggested in 2006 a breakdown of assortative mating resulting in hybrids, but the introduction of LLINs was followed by a decrease in the number of hybrids. This suggests a decrease in mating success of hybrids, ecological maladaptation, or a lesser probability of mating between species due to a decrease in An. coluzzii population size. By contrast, the introduction of LLINs has favoured the sibling species An. arabiensis. In this study, some spatial and temporal structuration between An. arabiensis populations were detected, especially in 2008, and the higher genetic diversity observed could result from a diversifying selection. CONCLUSIONS This work demonstrates the complexity of the malaria context and shows the need to study the genetic structure of Anopheles populations to evaluate the effectiveness of vector-control tools and successful management of malaria vector control.
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Affiliation(s)
- Seynabou Sougoufara
- URMITE (Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes), UM63, CNRS 7278, IRD 198, INSERM 1095, IHU-Méditerranée Infection, Marseille, France. .,Département de Biologie Animale, Faculté des Sciences et Techniques/Université Cheikh Anta Diop, Dakar, Senegal.
| | - Cheikh Sokhna
- URMITE (Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes), UM63, CNRS 7278, IRD 198, INSERM 1095, IHU-Méditerranée Infection, Marseille, France
| | - Nafissatou Diagne
- URMITE (Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes), UM63, CNRS 7278, IRD 198, INSERM 1095, IHU-Méditerranée Infection, Marseille, France
| | - Souleymane Doucouré
- URMITE (Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes), UM63, CNRS 7278, IRD 198, INSERM 1095, IHU-Méditerranée Infection, Marseille, France
| | - Pape MBacké Sembène
- Département de Biologie Animale, Faculté des Sciences et Techniques/Université Cheikh Anta Diop, Dakar, Senegal
| | - Myriam Harry
- UMR EGCE (Évolution, Génomes, Comportement, Écologie) CNRS, IRD-Université Paris-Sud, IDEEV, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
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11
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Vicente JL, Clarkson CS, Caputo B, Gomes B, Pombi M, Sousa CA, Antao T, Dinis J, Bottà G, Mancini E, Petrarca V, Mead D, Drury E, Stalker J, Miles A, Kwiatkowski DP, Donnelly MJ, Rodrigues A, Torre AD, Weetman D, Pinto J. Massive introgression drives species radiation at the range limit of Anopheles gambiae. Sci Rep 2017; 7:46451. [PMID: 28417969 PMCID: PMC5394460 DOI: 10.1038/srep46451] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 03/17/2017] [Indexed: 12/30/2022] Open
Abstract
Impacts of introgressive hybridisation may range from genomic erosion and species collapse to rapid adaptation and speciation but opportunities to study these dynamics are rare. We investigated the extent, causes and consequences of a hybrid zone between Anopheles coluzzii and Anopheles gambiae in Guinea-Bissau, where high hybridisation rates appear to be stable at least since the 1990s. Anopheles gambiae was genetically partitioned into inland and coastal subpopulations, separated by a central region dominated by A. coluzzii. Surprisingly, whole genome sequencing revealed that the coastal region harbours a hybrid form characterised by an A. gambiae-like sex chromosome and massive introgression of A. coluzzii autosomal alleles. Local selection on chromosomal inversions may play a role in this process, suggesting potential for spatiotemporal stability of the coastal hybrid form and providing resilience against introgression of medically-important loci and traits, found to be more prevalent in inland A. gambiae.
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Affiliation(s)
- José L Vicente
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Christopher S Clarkson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Beniamino Caputo
- Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università di Roma "Sapienza", Rome, Italy
| | - Bruno Gomes
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Marco Pombi
- Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università di Roma "Sapienza", Rome, Italy
| | - Carla A Sousa
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Tiago Antao
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - João Dinis
- Instituto Nacional de Saúde Pública, Ministério da Saúde Pública, Bissau, Guiné-Bissau
| | - Giordano Bottà
- Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università di Roma "Sapienza", Rome, Italy.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Emiliano Mancini
- Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università di Roma "Sapienza", Rome, Italy
| | - Vincenzo Petrarca
- Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università di Roma "Sapienza", Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma "Sapienza", Rome, Italy
| | - Daniel Mead
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | - Alistair Miles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.,Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, UK.,Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Amabélia Rodrigues
- Instituto Nacional de Saúde Pública, Ministério da Saúde Pública, Bissau, Guiné-Bissau
| | - Alessandra Della Torre
- Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università di Roma "Sapienza", Rome, Italy
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - João Pinto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
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12
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Salvadori A, Del Frate G, Pagliai M, Mancini G, Barone V. Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2016; 116:1731-1746. [PMID: 27867214 PMCID: PMC5101850 DOI: 10.1002/qua.25207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 05/31/2023]
Abstract
The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.
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Affiliation(s)
- Andrea Salvadori
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | | | - Marco Pagliai
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
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13
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Caputo B, Pichler V, Mancini E, Pombi M, Vicente JL, Dinis J, Steen K, Petrarca V, Rodrigues A, Pinto J, Della Torre A, Weetman D. The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate 'genomic island of speciation'. Mol Ecol 2016; 25:5719-5731. [PMID: 27661465 DOI: 10.1111/mec.13840] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 07/19/2016] [Accepted: 09/01/2016] [Indexed: 01/19/2023]
Abstract
Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a 'genomic island of divergence' spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X-island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X-island despite a lack of autosomal divergence; (ii) individuals with multiple-recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination-driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.
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Affiliation(s)
- Beniamino Caputo
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Verena Pichler
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Emiliano Mancini
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Marco Pombi
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - José L Vicente
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua daJunqueira, 100, 1349-008, Lisboa, Portugal
| | - Joao Dinis
- Instituto Nacional de Saúde Pública, Ministério da Saúde Pública, Avenida Combatentes da Liberdade da Pátria, Apartado 861, 1004, Bissau Codex, Guinea Bissau
| | - Keith Steen
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Pl, Liverpool, Merseyside, L3 5QA, UK
| | - Vincenzo Petrarca
- Istituto Pasteur-Fondazione Cenci-Bolognetti, Dipartimento di Biologia e Biotecnologie Charles Darwin, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Amabelia Rodrigues
- Instituto Nacional de Saúde Pública, Ministério da Saúde Pública, Avenida Combatentes da Liberdade da Pátria, Apartado 861, 1004, Bissau Codex, Guinea Bissau
| | - Joao Pinto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua daJunqueira, 100, 1349-008, Lisboa, Portugal
| | - Alessandra Della Torre
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Università 'Sapienza', Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - David Weetman
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Pl, Liverpool, Merseyside, L3 5QA, UK
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14
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King KC, Stelkens RB, Webster JP, Smith DF, Brockhurst MA. Hybridization in Parasites: Consequences for Adaptive Evolution, Pathogenesis, and Public Health in a Changing World. PLoS Pathog 2015; 11:e1005098. [PMID: 26336070 PMCID: PMC4559376 DOI: 10.1371/journal.ppat.1005098] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Joanne P. Webster
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases (CEEED), Royal Veterinary College, University of London, London, United Kingdom
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