1
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Di C, Lohmueller KE. Revisiting Dominance in Population Genetics. Genome Biol Evol 2024; 16:evae147. [PMID: 39114967 PMCID: PMC11306932 DOI: 10.1093/gbe/evae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2024] [Indexed: 08/11/2024] Open
Abstract
Dominance refers to the effect of a heterozygous genotype relative to that of the two homozygous genotypes. The degree of dominance of mutations for fitness can have a profound impact on how deleterious and beneficial mutations change in frequency over time as well as on the patterns of linked neutral genetic variation surrounding such selected alleles. Since dominance is such a fundamental concept, it has received immense attention throughout the history of population genetics. Early work from Fisher, Wright, and Haldane focused on understanding the conceptual basis for why dominance exists. More recent work has attempted to test these theories and conceptual models by estimating dominance effects of mutations. However, estimating dominance coefficients has been notoriously challenging and has only been done in a few species in a limited number of studies. In this review, we first describe some of the early theoretical and conceptual models for understanding the mechanisms for the existence of dominance. Second, we discuss several approaches used to estimate dominance coefficients and summarize estimates of dominance coefficients. We note trends that have been observed across species, types of mutations, and functional categories of genes. By comparing estimates of dominance coefficients for different types of genes, we test several hypotheses for the existence of dominance. Lastly, we discuss how dominance influences the dynamics of beneficial and deleterious mutations in populations and how the degree of dominance of deleterious mutations influences the impact of inbreeding on fitness.
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Affiliation(s)
- Chenlu Di
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA, USA
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2
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Claret JL, Di-Liegro M, Namias A, Assogba B, Makoundou P, Koffi A, Pennetier C, Weill M, Milesi P, Labbé P. Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes. Heredity (Edinb) 2024; 132:179-191. [PMID: 38280976 PMCID: PMC10997782 DOI: 10.1038/s41437-024-00670-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/29/2024] Open
Abstract
Anopheles gambiae s.l. has been the target of intense insecticide treatment since the mid-20th century to try and control malaria. A substitution in the ace-1 locus has been rapidly selected for, allowing resistance to organophosphate and carbamate insecticides. Since then, two types of duplication of the ace-1 locus have been found in An. gambiae s.l. populations: homogeneous duplications that are composed of several resistance copies, or heterogeneous duplications that contain both resistance and susceptible copies. The substitution induces a trade-off between resistance in the presence of insecticides and disadvantages in their absence: the heterogeneous duplications allow the fixation of the intermediate heterozygote phenotype. So far, a single heterogeneous duplication has been described in An. gambiae s.l. populations (in contrast with the multiple duplicated alleles found in Culex pipiens mosquitoes). We used a new approach, combining long and short-read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications, in two populations of An. gambiae s.l. We show that these alleles share the same structure as the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds new light on the origin and maintenance of these alleles in An. gambiae s.l. populations, and their role in mosquito adaptation.
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Affiliation(s)
| | | | - Alice Namias
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Benoit Assogba
- Medical Research Council, Unit The Gambia at London School of Hygiene and Tropical Medicine, London, UK
| | | | - Alphonsine Koffi
- National Institute of Public Health/Pierre Richet Institute, Bouake, Côte d'Ivoire
| | | | - Mylène Weill
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237, Uppsala, Sweden
| | - Pierrick Labbé
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France.
- Institut Universitaire de France (IUF), Paris, France.
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3
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Haberkorn C, David J, Henri H, Delpuech J, Lasseur R, Vavre F, Varaldi J. A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius. Evol Appl 2023; 16:1012-1028. [PMID: 37216030 PMCID: PMC10197226 DOI: 10.1111/eva.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
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Affiliation(s)
- Chloé Haberkorn
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
- IZInovationLyonFrance
| | - Jean‐Philippe David
- Laboratoire d'Écologie AlpineUMR UGA‐USMB‐CNRS 5553 Université Grenoble Alpes CS 40700Grenoble cedex 9France
| | - Hélène Henri
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Jean‐Marie Delpuech
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | | | - Fabrice Vavre
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Julien Varaldi
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
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4
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Milesi P, Claret JL, Unal S, Weill M, Labbé P. Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes. Parasit Vectors 2022; 15:484. [PMID: 36550589 PMCID: PMC9783466 DOI: 10.1186/s13071-022-05599-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Organophosphate and carbamate insecticides have largely been used worldwide to control mosquito populations. As a response, the same amino acid substitution in the ace-1 gene (G119S), conferring resistance to both insecticides, has been selected independently in many mosquito species. In Anopheles gambiae, it has recently been shown that the G119S mutation is actually part of homogeneous duplications that associate multiple resistance copies of the ace-1 gene. In this study, we showed that duplications of resistance copies of the ace-1 gene also exist in the Culex pipiens species complex. The number of copies is variable, and different numbers of copies are associated with different phenotypic trade-offs: we used a combination of bioassays and competition in population cages to show that having more resistance copies conferred higher resistance levels, but was also associated with higher selective disadvantage (or cost) in the absence of insecticide. These results further show the versatility of the genetic architecture of resistance to organophosphate and carbamate insecticides around the ace-1 locus and its role in fine-tuned adaptation to insecticide treatment variations.
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Affiliation(s)
- Pascal Milesi
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen, 18D, SE-752 36, Uppsala, Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory (SciLifeLab), Uppsala, Sweden
| | - Jean-Loup Claret
- grid.121334.60000 0001 2097 0141Institut Des Sciences de L’Évolution de Montpellier (UMR 5554, CNRS-UM-IRD- EPHE), Université de Montpellier, Cedex 05, Montpellier, France
| | - Sandra Unal
- grid.121334.60000 0001 2097 0141Institut Des Sciences de L’Évolution de Montpellier (UMR 5554, CNRS-UM-IRD- EPHE), Université de Montpellier, Cedex 05, Montpellier, France
| | - Mylène Weill
- grid.121334.60000 0001 2097 0141Institut Des Sciences de L’Évolution de Montpellier (UMR 5554, CNRS-UM-IRD- EPHE), Université de Montpellier, Cedex 05, Montpellier, France
| | - Pierrick Labbé
- grid.121334.60000 0001 2097 0141Institut Des Sciences de L’Évolution de Montpellier (UMR 5554, CNRS-UM-IRD- EPHE), Université de Montpellier, Cedex 05, Montpellier, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, 1 Rue Descartes Cedex 05, 75231 Paris, France
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5
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Harris M, Garud NR. Enrichment of Hard Sweeps on the X Chromosome in Drosophila melanogaster. Mol Biol Evol 2022; 40:6955808. [PMID: 36546413 PMCID: PMC9825254 DOI: 10.1093/molbev/msac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The characteristic properties of the X chromosome, such as male hemizygosity and its unique inheritance pattern, expose it to natural selection in a way that can be different from the autosomes. Here, we investigate the differences in the tempo and mode of adaptation on the X chromosome and autosomes in a population of Drosophila melanogaster. Specifically, we test the hypothesis that due to hemizygosity and a lower effective population size on the X, the relative proportion of hard sweeps, which are expected when adaptation is gradual, compared with soft sweeps, which are expected when adaptation is rapid, is greater on the X than on the autosomes. We quantify the incidence of hard versus soft sweeps in North American D. melanogaster population genomic data with haplotype homozygosity statistics and find an enrichment of the proportion of hard versus soft sweeps on the X chromosome compared with the autosomes, confirming predictions we make from simulations. Understanding these differences may enable a deeper understanding of how important phenotypes arise as well as the impact of fundamental evolutionary parameters on adaptation, such as dominance, sex-specific selection, and sex-biased demography.
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Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA
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6
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Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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7
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Muralidhar P, Veller C. Dominance shifts increase the likelihood of soft selective sweeps. Evolution 2022; 76:966-984. [PMID: 35213740 PMCID: PMC9928167 DOI: 10.1111/evo.14459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/04/2022] [Indexed: 01/21/2023]
Abstract
Genetic models of adaptation to a new environment have typically assumed that the alleles involved maintain a constant fitness dominance across the old and new environments. However, theories of dominance suggest that this should often not be the case. Instead, the alleles involved should frequently shift from recessive deleterious in the old environment to dominant beneficial in the new environment. Here, we study the consequences of these expected dominance shifts for the genetics of adaptation to a new environment. We find that dominance shifts increase the likelihood that adaptation occurs from standing variation, and that multiple alleles from the standing variation are involved (a soft selective sweep). Furthermore, we find that expected dominance shifts increase the haplotypic diversity of selective sweeps, rendering soft sweeps more detectable in small genomic samples. In cases where an environmental change threatens the viability of the population, we show that expected dominance shifts of newly beneficial alleles increase the likelihood of evolutionary rescue and the number of alleles involved. Finally, we apply our results to a well-studied case of adaptation to a new environment: the evolution of pesticide resistance at the Ace locus in Drosophila melanogaster. We show that, under reasonable demographic assumptions, the expected dominance shift of resistant alleles causes soft sweeps to be the most frequent outcome in this case, with the primary source of these soft sweeps being the standing variation at the onset of pesticide use, rather than recurrent mutation thereafter.
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Affiliation(s)
- Pavitra Muralidhar
- Center for Population Biology, University of California,
Davis, CA 95616,Department of Evolution and Ecology, University of
California, Davis, CA 95616,corresponding author:
| | - Carl Veller
- Center for Population Biology, University of California,
Davis, CA 95616,Department of Evolution and Ecology, University of
California, Davis, CA 95616
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8
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Freeman JC, Smith LB, Silva JJ, Fan Y, Sun H, Scott JG. Fitness studies of insecticide resistant strains: lessons learned and future directions. PEST MANAGEMENT SCIENCE 2021; 77:3847-3856. [PMID: 33506993 DOI: 10.1002/ps.6306] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/02/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
The evolution of insecticide resistance is generally thought to be associated with a fitness cost in the absence of insecticide exposure. However, it is not clear how these fitness costs manifest or how universal this phenomenon is. To investigate this, we conducted a literature review of publications that studied fitness costs of insecticide resistance, selected papers that met our criteria for scientific rigor, and analyzed each class of insecticides separately as well as in aggregate. The more than 170 publications on fitness costs of insecticide resistance show that in 60% of the experiments there is a cost to having resistance, particularly for measurements of reversion of resistance and reproduction. There were differences between classes of insecticides, with fitness costs seen less commonly for organochlorines. There was considerable variation in the experiments performed. We suggest that future papers will have maximum value to the community if they quantitatively determine resistance levels, identify the resistance mechanisms present (and the associated mutations), have replicated experiments, use related strains (optimally congenic with the resistance mutation introgressed into different genetic backgrounds) and measure fitness by multiple metrics. Studies on the fitness costs of insecticide resistance will continue to enlighten our understanding of the evolutionary process and provide valuable information for resistance management. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Jamie C Freeman
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA
| | - Letícia B Smith
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Juan J Silva
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA
| | - Yinjun Fan
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA
| | - Haina Sun
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA
| | - Jeffrey G Scott
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA
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9
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Arich S, Assaid N, Taki H, Weill M, Labbé P, Sarih M. Distribution of insecticide resistance and molecular mechanisms involved in the West Nile vector Culex pipiens in Morocco. PEST MANAGEMENT SCIENCE 2021; 77:1178-1186. [PMID: 33009878 DOI: 10.1002/ps.6127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/03/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Mosquitoes of the Culex pipiens complex are the vectors of several arboviruses and are thus subjected to insecticide control worldwide. However, overuse of insecticides selects for resistance. While assessing the resistance status of the vectors is required for effective and sustainable disease control, resistance has so far only been sparsely studied in Morocco. In this study, we establish a first countrywide assessment of the levels of resistance to various insecticides and the potential responsible mechanisms involved. Cx. pipiens larvae were collected from natural populations of five regions of Morocco, and their taxonomic status was determined (molecular forms). The level of their susceptibility to insecticides was assessed by single-diagnostic-dose bioassays. Molecular identification of known resistance alleles was investigated to determine the frequency of target-site mutations. RESULTS This study confirms that Moroccan populations are an interbreeding mix of pipiens and molestus forms, with large gene flow for the resistance alleles. We also found that Cx. pipiens mosquitoes are resistant to all insecticide families, all over Morocco: resistance is high for insecticides used in mosquito control, but also present for other pesticides. Resistance alleles are similarly more frequent for mosquito control insecticides. However, their distribution is heterogeneous in the five regions, with significant genetic differentiation between populations, revealing the crucial role of local insecticide treatment practices. CONCLUSION This study provides reference countrywide data that highlight the need for further research to refine the distribution of resistance in Morocco and to understand the role of agriculture/urban residuals in its spread. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Soukaina Arich
- Laboratory of Biology and Health, Faculty of Sciences Ben M'Sik, URAC 34, Hassan II University-Casablanca, Casablanca, Morocco
- Laboratoire des Maladies Vectorielles (LMV), Institut Pasteur du Maroc, Casablanca, Morocco
| | - Najlaa Assaid
- Laboratoire des Maladies Vectorielles (LMV), Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hassan Taki
- Laboratory of Biology and Health, Faculty of Sciences Ben M'Sik, URAC 34, Hassan II University-Casablanca, Casablanca, Morocco
| | - Mylène Weill
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Montpellier, CEDEX 5, France
| | - Pierrick Labbé
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Montpellier, CEDEX 5, France
| | - M'hammed Sarih
- Laboratoire des Maladies Vectorielles (LMV), Institut Pasteur du Maroc, Casablanca, Morocco
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Grau-Bové X, Lucas E, Pipini D, Rippon E, van ‘t Hof AE, Constant E, Dadzie S, Egyir-Yawson A, Essandoh J, Chabi J, Djogbénou L, Harding NJ, Miles A, Kwiatkowski D, Donnelly MJ, Weetman D. Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus. PLoS Genet 2021; 17:e1009253. [PMID: 33476334 PMCID: PMC7853456 DOI: 10.1371/journal.pgen.1009253] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 02/02/2021] [Accepted: 11/03/2020] [Indexed: 12/30/2022] Open
Abstract
Vector population control using insecticides is a key element of current strategies to prevent malaria transmission in Africa. The introduction of effective insecticides, such as the organophosphate pirimiphos-methyl, is essential to overcome the recurrent emergence of resistance driven by the highly diverse Anopheles genomes. Here, we use a population genomic approach to investigate the basis of pirimiphos-methyl resistance in the major malaria vectors Anopheles gambiae and A. coluzzii. A combination of copy number variation and a single non-synonymous substitution in the acetylcholinesterase gene, Ace1, provides the key resistance diagnostic in an A. coluzzii population from Côte d'Ivoire that we used for sequence-based association mapping, with replication in other West African populations. The Ace1 substitution and duplications occur on a unique resistance haplotype that evolved in A. gambiae and introgressed into A. coluzzii, and is now common in West Africa primarily due to selection imposed by other organophosphate or carbamate insecticides. Our findings highlight the predictive value of this complex resistance haplotype for phenotypic resistance and clarify its evolutionary history, providing tools to for molecular surveillance of the current and future effectiveness of pirimiphos-methyl based interventions.
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Affiliation(s)
- Xavier Grau-Bové
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Eric Lucas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Dimitra Pipini
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Emily Rippon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Arjèn E. van ‘t Hof
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edi Constant
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Samuel Dadzie
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - John Essandoh
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Joseph Chabi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Luc Djogbénou
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Institut Régional de Santé Publique, Université d’Abomey-Calavi, Benin
| | - Nicholas J. Harding
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Alistair Miles
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Dominic Kwiatkowski
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Martin J. Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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11
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Bkhache M, Tmimi FZ, Charafeddine O, Filali OB, Lemrani M, Labbé P, Sarih M. G119S ace-1 mutation conferring insecticide resistance detected in the Culex pipiens complex in Morocco. PEST MANAGEMENT SCIENCE 2019; 75:286-291. [PMID: 29885052 DOI: 10.1002/ps.5114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Arboviruses are controlled through insecticide control of their mosquito vector. However, inconsiderate use of insecticides often results in the selection of resistance in treated populations, so that monitoring is required to optimize their usage. Here, Culex pipiens (West Nile and Rift Valley Fever virus vector) specimens were collected from four Moroccan cities. Levels of susceptibility to the organophosphate (OP) insecticide malathion were assessed using World Health Organization (WHO)-recommended bioassays. Individual mosquitoes were tested for the presence of the G119S mutation in the ace-1 gene, the main OP-target resistance mutation. RESULTS Bioassays showed that mosquitoes from Mohammedia were significantly more resistant to malathion than those from Marrakech. Analyzing the ace-1 genotypes in dead and surviving individuals suggested that other resistance mechanisms may be present in Mohammedia. The ace-1 resistance allele frequencies were relatively moderate (< 0.4). Their analyses in three Moroccan cities (Tangier, Casablanca and Marrakech) however showed disparities between two coexisting Cx. pipiens forms and revealed that the G119S mutation tends to be more frequent in urban than in rural collection sites. CONCLUSION These findings provide a reference assessment of OP resistance in Morocco and should help the health authorities to develop informed and sustainable vector control programs. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Meriem Bkhache
- Institut Pasteur du Maroc, Service de Parasitologie et des Maladies Vectorielles, Casablanca, Morocco
- Faculté des Sciences et Techniques de Mohammedia, Laboratoire de Virologie Microbiologie & Qualité et Biotechnologies / Eco-toxicologie & Biodiversité, Université Hassan II de Casablanca, Casablanca, Morocco
| | - Fatim-Zohra Tmimi
- Institut Pasteur du Maroc, Service de Parasitologie et des Maladies Vectorielles, Casablanca, Morocco
| | - Omar Charafeddine
- Faculté des Sciences et Techniques de Mohammedia, Laboratoire de Virologie Microbiologie & Qualité et Biotechnologies / Eco-toxicologie & Biodiversité, Université Hassan II de Casablanca, Casablanca, Morocco
| | | | - Meryem Lemrani
- Institut Pasteur du Maroc, Service de Parasitologie et des Maladies Vectorielles, Casablanca, Morocco
| | - Pierrick Labbé
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Montpellier, Cedex 5, France
| | - M'hammed Sarih
- Institut Pasteur du Maroc, Service de Parasitologie et des Maladies Vectorielles, Casablanca, Morocco
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12
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Assogba BS, Alout H, Koffi A, Penetier C, Djogbénou LS, Makoundou P, Weill M, Labbé P. Adaptive deletion in resistance gene duplications in the malaria vector Anopheles gambiae. Evol Appl 2018; 11:1245-1256. [PMID: 30151037 PMCID: PMC6099818 DOI: 10.1111/eva.12619] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/15/2018] [Indexed: 12/11/2022] Open
Abstract
While gene copy-number variations play major roles in long-term evolution, their early dynamics remains largely unknown. However, examples of their role in short-term adaptation are accumulating: identical repetitions of a locus (homogeneous duplications) can provide a quantitative advantage, while the association of differing alleles (heterogeneous duplications) allows carrying two functions simultaneously. Such duplications often result from rearrangements of sometimes relatively large chromosome fragments, and even when adaptive, they can be associated with deleterious side effects that should, however, be reduced by subsequent evolution. Here, we took advantage of the unique model provided by the malaria mosquito Anopheles gambiae s.l. to investigate the early evolution of several duplications, heterogeneous and homogeneous, segregating in natural populations from West Africa. These duplications encompass ~200 kb and 11 genes, including the adaptive insecticide resistance ace-1 locus. Through the survey of several populations from three countries over 3-4 years, we showed that an internal deletion of all coamplified genes except ace-1 is currently spreading in West Africa and introgressing from An. gambiae s.s. to An. coluzzii. Both observations provide evidences of its selection, most likely due to reducing the gene-dosage disturbances caused by the excessive copies of the nonadaptive genes. Our study thus provides a unique example of the early adaptive trajectory of duplications and underlines the role of the environmental conditions (insecticide treatment practices and species ecology). It also emphasizes the striking diversity of adaptive responses in these mosquitoes and reveals a worrisome process of resistance/cost trade-off evolution that could impact the control of malaria vectors in Africa.
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Affiliation(s)
- Benoît S. Assogba
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐UM‐IRD‐EPHE)Université de MontpellierMontpellierFrance
- Disease Control and Elimination DepartmentMedical Research Council, Unit The GambiaBanjulThe Gambia
- Institut Régional de Santé PubliqueUniversité d'Abomey CalaviCotonouBenin
- Faculté des Sciences et TechniquesLaboratoire de Biologie et de Typage Moléculaire en MicrobiologieUniversité d'Abomey CalaviCotonouBénin
| | - Haoues Alout
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐UM‐IRD‐EPHE)Université de MontpellierMontpellierFrance
| | - Alphonsine Koffi
- Institut Pierre Richet (IPR)/Institut National de Santé Publique (INSP)BouakéCôte d'Ivoire
| | - Cédric Penetier
- Institut de Recherche pour le Développement (IRD)UMR MIVEGECMontpellierFrance
| | - Luc S. Djogbénou
- Institut Régional de Santé PubliqueUniversité d'Abomey CalaviCotonouBenin
- Faculté des Sciences et TechniquesLaboratoire de Biologie et de Typage Moléculaire en MicrobiologieUniversité d'Abomey CalaviCotonouBénin
| | - Patrick Makoundou
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐UM‐IRD‐EPHE)Université de MontpellierMontpellierFrance
| | - Mylène Weill
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐UM‐IRD‐EPHE)Université de MontpellierMontpellierFrance
| | - Pierrick Labbé
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐UM‐IRD‐EPHE)Université de MontpellierMontpellierFrance
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13
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Weetman D, Djogbenou LS, Lucas E. Copy number variation (CNV) and insecticide resistance in mosquitoes: evolving knowledge or an evolving problem? CURRENT OPINION IN INSECT SCIENCE 2018; 27:82-88. [PMID: 30025639 PMCID: PMC6056009 DOI: 10.1016/j.cois.2018.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/21/2018] [Accepted: 04/09/2018] [Indexed: 05/10/2023]
Abstract
Copy number variation (CNV) in insect genomes is a rich source of potentially adaptive polymorphism which may help overcome the constraints of purifying selection on conserved genes and/or permit elevated transcription. Classic studies of amplified esterases and acetylcholinesterase duplication in Culex pipiens quantified evolutionary dynamics of CNV driven by insecticidal selection. A more complex and potentially medically impactful form of CNV is found in Anopheles gambiae, with both heterogeneous duplications and homogeneous amplifications strongly linked with insecticide resistance. Metabolic gene amplification, revealed by shotgun sequencing, appears common in Aedes aegypti, but poorly understood in other mosquito species. Many methodologies have been used to detect CNV in mosquitoes, but relatively few can detect both duplications and amplifications, and contrasting methods should be combined. Genome scans for CNV have been rare to date in mosquitoes, but offer immense potential to determine the overall role of CNV as a component of resistance mechanisms.
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Affiliation(s)
- David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.
| | - Luc S Djogbenou
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; Institut Régional de Santé Publique/Université d'Abomey-Calavi, Ouidah, Benin
| | - Eric Lucas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
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14
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Milesi P, Assogba BS, Atyame CM, Pocquet N, Berthomieu A, Unal S, Makoundou P, Weill M, Labbé P. The evolutionary fate of heterogeneous gene duplications: A precarious overdominant equilibrium between environment, sublethality and complementation. Mol Ecol 2017; 27:493-507. [PMID: 29230902 DOI: 10.1111/mec.14463] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/08/2017] [Accepted: 11/25/2017] [Indexed: 11/30/2022]
Abstract
Gene duplications occur at a high rate. Although most appear detrimental, some homogeneous duplications (identical gene copies) can be selected for beneficial increase in produced proteins. Heterogeneous duplications, which combine divergent alleles of a single locus, are seldom studied due to the paucity of empirical data. We investigated their role in an ongoing adaptive process at the ace-1 locus in Culex pipiens mosquitoes. We assessed the worldwide diversity of the ace-1 alleles (single-copy, susceptible S and insecticide-resistant R, and duplicated D that pair one S and one R copy), analysed their phylogeography and measured their fitness to understand their early dynamics using population genetics models. It provides a coherent and comprehensive evolutionary scenario. We show that D alleles are present in most resistant populations and display a higher diversity than R alleles (27 vs. 4). Most appear to result from independent unequal crossing-overs between local single-copy alleles, suggesting a recurrent process. Most duplicated alleles have a limited geographic distribution, probably resulting from their homozygous sublethality (HS phenotype). In addition, heterozygotes carrying different HS D alleles showed complementation, indicating different recessive lethal mutations. Due to mosaic insecticide control practices, balancing selection (overdominance) plays a key role in the early dynamics of heterogeneous duplicated alleles; it also favours a high local polymorphism of HS D alleles in natural populations (overdominance reinforced by complementation). Overall, our study shows that the evolutionary fate of heterogeneous duplications (and their long-term role) depends on finely balanced selective pressures due to the environment and to their genomic structure.
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Affiliation(s)
- Pascal Milesi
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
| | - Benoît S Assogba
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
| | - Célestine M Atyame
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
| | - Nicolas Pocquet
- UMR MIVEGEC Maladies infectieuses et vecteurs: écologie, génétique, évolution et contrôle (CNRS-Université de Montpellier-IRD), Montpellier, France
| | - Arnaud Berthomieu
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
| | - Sandra Unal
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
| | - Patrick Makoundou
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
| | - Mylène Weill
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
| | - Pierrick Labbé
- ISEM Institut des Sciences de l'Evolution de Montpellier (CNRS-Université de Montpellier-IRD-EPHE), Montpellier, France
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15
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Silva Martins WF, Wilding CS, Steen K, Mawejje H, Antão TR, Donnelly MJ. Local selection in the presence of high levels of gene flow: Evidence of heterogeneous insecticide selection pressure across Ugandan Culex quinquefasciatus populations. PLoS Negl Trop Dis 2017; 11:e0005917. [PMID: 28972985 PMCID: PMC5640252 DOI: 10.1371/journal.pntd.0005917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/13/2017] [Accepted: 08/29/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Culex quinquefasciatus collected in Uganda, where no vector control interventions directly targeting this species have been conducted, was used as a model to determine if it is possible to detect heterogeneities in selection pressure driven by insecticide application targeting other insect species. METHODOLOGY/PRINCIPAL FINDINGS Population genetic structure was assessed through microsatellite analysis, and the impact of insecticide pressure by genotyping two target-site mutations, Vgsc-1014F of the voltage-gated sodium channel target of pyrethroid and DDT insecticides, and Ace1-119S of the acetylcholinesterase gene, target of carbamate and organophosphate insecticides. No significant differences in genetic diversity were observed among populations by microsatellite markers with HE ranging from 0.597 to 0.612 and low, but significant, genetic differentiation among populations (FST = 0.019, P = 0.001). By contrast, the insecticide-resistance markers display heterogeneous allelic distributions with significant differences detected between Central Ugandan (urban) populations relative to Eastern and Southwestern (rural) populations. In the central region, a frequency of 62% for Vgsc-1014F, and 32% for the Ace1-119S resistant allele were observed. Conversely, in both Eastern and Southwestern regions the Vgsc-1014F alleles were close to fixation, whilst Ace1-119S allele frequency was 12% (although frequencies may be underestimated due to copy number variation at both loci). CONCLUSIONS/SIGNIFICANCE Taken together, the microsatellite and both insecticide resistance target-site markers provide evidence that in the face of intense gene flow among populations, disjunction in resistance frequencies arise due to intense local selection pressures despite an absence of insecticidal control interventions targeting Culex.
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Affiliation(s)
- Walter Fabricio Silva Martins
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Departamento de Biologia, Universidade Estadual da Paraíba, Campina Grande, Brasil
| | - Craig Stephen Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Keith Steen
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Tiago Rodrigues Antão
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Division of Biological Science, University of Montana, Missoula, United States of America
| | - Martin James Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Malaria Programme, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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16
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Milesi P, Weill M, Lenormand T, Labbé P. Heterogeneous gene duplications can be adaptive because they permanently associate overdominant alleles. Evol Lett 2017; 1:169-180. [PMID: 30283647 PMCID: PMC6121789 DOI: 10.1002/evl3.17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/23/2017] [Indexed: 01/04/2023] Open
Abstract
Gene duplications are widespread in genomes, but their role in contemporary adaptation is not fully understood. Although mostly deleterious, homogeneous duplications that associate identical repeats of a locus often increase the quantity of protein produced, which can be selected in certain environments. However, another type exists: heterogeneous gene duplications, which permanently associate two (or more) alleles of a single locus on the same chromosome. They are far less studied, as only few examples of contemporary heterogeneous duplications are known. Haldane proposed in 1954 that they could be adaptive in situations of heterozygote advantage, or overdominance, but this hypothesis was never tested. To assess its validity, we took advantage of the well-known model of insecticide resistance in mosquitoes. We used experimental evolution to estimate the fitnesses associated with homozygous and heterozygous genotypes in different selection regimes. It first showed that balanced antagonist selective pressures frequently induce overdominance, generating stable polymorphic equilibriums. The frequency of equilibrium moreover depends on the magnitude of two antagonistic selective pressures, the survival advantage conferred by the resistant allele versus the selective costs it induces. We then showed that heterogeneous duplications are selected over single-copy alleles in such contexts. They allow the fixation of the heterozygote phenotype, providing an alternative and stable intermediate fitness trade-off. By allowing the rapid fixation of divergent alleles, this immediate advantage could contribute to the rarity of overdominance. More importantly, it also creates new material for long-term genetic innovation, making a crucial but underestimated contribution to the evolution of new genes and gene families.
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Affiliation(s)
- Pascal Milesi
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐Université de Montpellier‐IRD‐EPHE)Campus Université de MontpellierPlace Eugène Bataillon34095MontpellierCEDEX 05France
| | - Mylène Weill
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐Université de Montpellier‐IRD‐EPHE)Campus Université de MontpellierPlace Eugène Bataillon34095MontpellierCEDEX 05France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175, CNRS‐Université de Montpellier‐Université Paul‐Valéry Montpellier‐EPHE) 1919 route de MendeF‐34293MontpellierCEDEX 05France
| | - Pierrick Labbé
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS‐Université de Montpellier‐IRD‐EPHE)Campus Université de MontpellierPlace Eugène Bataillon34095MontpellierCEDEX 05France
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17
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Martins WFS, Subramaniam K, Steen K, Mawejje H, Liloglou T, Donnelly MJ, Wilding CS. Detection and quantitation of copy number variation in the voltage-gated sodium channel gene of the mosquito Culex quinquefasciatus. Sci Rep 2017; 7:5821. [PMID: 28725028 PMCID: PMC5517494 DOI: 10.1038/s41598-017-06080-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/07/2017] [Indexed: 01/23/2023] Open
Abstract
Insecticide resistance is typically associated with alterations to the insecticidal target-site or with gene expression variation at loci involved in insecticide detoxification. In some species copy number variation (CNV) of target site loci (e.g. the Ace-1 target site of carbamate insecticides) or detoxification genes has been implicated in the resistance phenotype. We show that field-collected Ugandan Culex quinquefasciatus display CNV for the voltage-gated sodium channel gene (Vgsc), target-site of pyrethroid and organochlorine insecticides. In order to develop field-applicable diagnostics for Vgsc CN, and as a prelude to investigating the possible association of CN with insecticide resistance, three assays were compared for their accuracy in CN estimation in this species. The gold standard method is droplet digital PCR (ddPCR), however, the hardware is prohibitively expensive for widespread utility. Here, ddPCR was compared to quantitative PCR (qPCR) and pyrosequencing. Across all platforms, CNV was detected in ≈10% of mosquitoes, corresponding to three or four copies (per diploid genome). ddPCR and qPCR-Std-curve yielded similar predictions for Vgsc CN, indicating that the qPCR protocol developed here can be applied as a diagnostic assay, facilitating monitoring of Vgsc CN in wild populations and the elucidation of association between the Vgsc CN and insecticide resistance.
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Affiliation(s)
- Walter Fabricio Silva Martins
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Departamento de Biologia, Universidade Estadual da Paraíba, Campina Grande, Brazil
| | | | - Keith Steen
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Henry Mawejje
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Triantafillos Liloglou
- Department of Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research, Liverpool, UK
| | - Martin James Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Malaria Programme, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Craig Stephen Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.
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18
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Chatonnet A, Lenfant N, Marchot P, Selkirk ME. Natural genomic amplification of cholinesterase genes in animals. J Neurochem 2017; 142 Suppl 2:73-81. [PMID: 28382676 DOI: 10.1111/jnc.13990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 12/31/2022]
Abstract
Tight control of the concentration of acetylcholine at cholinergic synapses requires precise regulation of the number and state of the acetylcholine receptors, and of the synthesis and degradation of the neurotransmitter. In particular, the cholinesterase activity has to be controlled exquisitely. In the genome of the first experimental models used (man, mouse, zebrafish and drosophila), there are only one or two genes coding for cholinesterases, whereas there are more genes for their closest relatives the carboxylesterases. Natural amplification of cholinesterase genes was first found to occur in some cancer cells and in insect species subjected to evolutionary pressure by insecticides. Analysis of the complete genome sequences of numerous representatives of the various metazoan phyla show that moderate amplification of cholinesterase genes is not uncommon in molluscs, echinoderms, hemichordates, prochordates or lepidosauria. Amplification of acetylcholinesterase genes is also a feature of parasitic nematodes or ticks. In these parasites, over-production of cholinesterase-like proteins in secreted products and the saliva are presumed to have effector roles related to host infection. These amplification events raise questions about the role of the amplified gene products, and the adaptation processes necessary to preserve efficient cholinergic transmission. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms.
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Affiliation(s)
- Arnaud Chatonnet
- Dynamique Musculaire et Métabolisme, INRA, Université Montpellier, Place Viala, Montpellier France
| | - Nicolas Lenfant
- Dynamique Musculaire et Métabolisme, INRA, Université Montpellier, Place Viala, Montpellier France.,Aix-Marseille Université / Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques laboratory, Marseille, France
| | - Pascale Marchot
- Aix-Marseille Université / Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques laboratory, Marseille, France
| | - Murray E Selkirk
- Department of Life Sciences, Imperial College London, London, UK
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19
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Assogba BS, Milesi P, Djogbénou LS, Berthomieu A, Makoundou P, Baba-Moussa LS, Fiston-Lavier AS, Belkhir K, Labbé P, Weill M. The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications. PLoS Biol 2016; 14:e2000618. [PMID: 27918584 PMCID: PMC5137868 DOI: 10.1371/journal.pbio.2000618] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 12/21/2022] Open
Abstract
Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides' target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies. We used an integrative approach, from genome to phenotype level, to investigate the influence of duplication architecture and gene-dosage on mosquito fitness. We found that both heterogeneous (i.e., one susceptible and one resistant ace-1 copy) and homogeneous (i.e., identical resistant copies) duplications segregated in field populations. The number of copies in homogeneous duplications was variable and positively correlated with acetylcholinesterase activity and resistance level. Determining the genomic structure of the duplicated region revealed that, in both types of duplication, ace-1 and 11 other genes formed tandem 203kb amplicons. We developed a diagnostic test for duplications, which showed that ace-1 was amplified in all 173 resistant mosquitoes analyzed (field-collected in several African countries), in heterogeneous or homogeneous duplications. Each type was associated with different fitness trade-offs: heterogeneous duplications conferred an intermediate phenotype (lower resistance and fitness costs), whereas homogeneous duplications tended to increase both resistance and fitness cost, in a complex manner. The type of duplication selected seemed thus to depend on the intensity and distribution of selection pressures. This versatility of trade-offs available through gene duplication highlights the importance of large mutation events in adaptation to environmental variation. This impressive adaptability could have a major impact on vector control in Africa.
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Affiliation(s)
- Benoît S. Assogba
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
- Institut Régional de Santé Publique, Université d’Abomey Calavi, Cotonou, Benin
- Faculté des Sciences et Techniques, Laboratoire de Biologie et de Typage Moléculaire en Microbiologie, Université d’Abomey Calavi, Cotonou, Bénin
| | - Pascal Milesi
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | - Luc S. Djogbénou
- Institut Régional de Santé Publique, Université d’Abomey Calavi, Cotonou, Benin
| | - Arnaud Berthomieu
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | - Patrick Makoundou
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | - Lamine S. Baba-Moussa
- Faculté des Sciences et Techniques, Laboratoire de Biologie et de Typage Moléculaire en Microbiologie, Université d’Abomey Calavi, Cotonou, Bénin
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | - Pierrick Labbé
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | - Mylène Weill
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
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20
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Abstract
The genetic recovery of resistant populations released from pesticide exposure is
accelerated by the presence of environmental stressors. By contrast, the
relevance of environmental stressors for the spread of resistance during
pesticide exposure has not been studied. Moreover, the consequences of
interactions between different stressors have not been considered. Here we show
that stress through intraspecific competition accelerates microevolution,
because it enhances fitness differences between adapted and non-adapted
individuals. By contrast, stress through interspecific competition or predation
reduces intraspecific competition and thereby delays microevolution. This was
demonstrated in mosquito populations (Culex quinquefasciatus)
that were exposed to the pesticide chlorpyrifos. Non-selective predation through
harvesting and interspecific competition with Daphnia magna
delayed the selection for individuals carrying the
ace-1R resistance allele. Under non-toxic
conditions, susceptible individuals without ace-1R
prevailed. Likewise, predation delayed the reverse adaptation of the populations
to a non-toxic environment, while the effect of interspecific competition was
not significant. Applying a simulation model, we further identified how
microevolution is generally determined by the type and degree of competition and
predation. We infer that interactions with other species—especially
strong in ecosystems with high biodiversity—can delay the development of
pesticide resistance.
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Affiliation(s)
- Jeremias Martin Becker
- Department System Ecotoxicology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany Department of Ecosystem Analysis, RWTH-Aachen University, Institute for Environmental Research, Worringerweg 1, 52074 Aachen, Germany
| | - Matthias Liess
- Department System Ecotoxicology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany Department of Ecosystem Analysis, RWTH-Aachen University, Institute for Environmental Research, Worringerweg 1, 52074 Aachen, Germany
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21
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Alout H, Labbé P, Berthomieu A, Makoundou P, Fort P, Pasteur N, Weill M. High chlorpyrifos resistance in Culex pipiens mosquitoes: strong synergy between resistance genes. Heredity (Edinb) 2016; 116:224-31. [PMID: 26463842 PMCID: PMC4806891 DOI: 10.1038/hdy.2015.92] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/19/2015] [Accepted: 08/18/2015] [Indexed: 02/08/2023] Open
Abstract
We investigated the genetic determinism of high chlorpyrifos resistance (HCR), a phenotype first described in 1999 in Culex pipiens mosquitoes surviving chlorpyrifos doses ⩾1 mg l(-1) and more recently found in field samples from Tunisia, Israel or Indian Ocean islands. Through chlorpyrifos selection, we selected several HCR strains that displayed over 10 000-fold resistance. All strains were homozygous for resistant alleles at two main loci: the ace-1 gene, with the resistant ace-1(R) allele expressing the insensitive G119S acetylcholinesterase, and a resistant allele of an unknown gene (named T) linked to the sex and ace-2 genes. We constructed a strain carrying only the T-resistant allele and studied its resistance characteristics. By crossing this strain with strains harboring different alleles at the ace-1 locus, we showed that the resistant ace-1(R) and the T alleles act in strong synergy, as they elicited a resistance 100 times higher than expected from a simple multiplicative effect. This effect was specific to chlorpyrifos and parathion and was not affected by synergists. We also examined how HCR was expressed in strains carrying other ace-1-resistant alleles, such as ace-1(V) or the duplicated ace-1(D) allele, currently spreading worldwide. We identified two major parameters that influenced the level of resistance: the number and the nature of the ace-1-resistant alleles and the number of T alleles. Our data fit a model that predicts that the T allele acts by decreasing chlorpyrifos concentration in the compartment targeted in insects.
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Affiliation(s)
- H Alout
- CNRS, IRD, ISEM–UMR, Montpellier, France
- University of Montpellier, Montpellier, France
- Arthropod-Borne and Infectious Diseases Laboratory, Colorado State University, Fort Collins, CO, USA
| | - P Labbé
- CNRS, IRD, ISEM–UMR, Montpellier, France
- University of Montpellier, Montpellier, France
| | - A Berthomieu
- CNRS, IRD, ISEM–UMR, Montpellier, France
- University of Montpellier, Montpellier, France
| | - P Makoundou
- CNRS, IRD, ISEM–UMR, Montpellier, France
- University of Montpellier, Montpellier, France
| | - P Fort
- University of Montpellier, Montpellier, France
- CNRS, CRBM–UMR, Montpellier, France
| | - N Pasteur
- CNRS, IRD, ISEM–UMR, Montpellier, France
- University of Montpellier, Montpellier, France
| | - M Weill
- CNRS, IRD, ISEM–UMR, Montpellier, France
- University of Montpellier, Montpellier, France
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An ace-1 gene duplication resorbs the fitness cost associated with resistance in Anopheles gambiae, the main malaria mosquito. Sci Rep 2015; 5:14529. [PMID: 26434951 PMCID: PMC4592963 DOI: 10.1038/srep14529] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/25/2015] [Indexed: 11/08/2022] Open
Abstract
Widespread resistance to pyrethroids threatens malaria control in Africa. Consequently, several countries switched to carbamates and organophophates insecticides for indoor residual spraying. However, a mutation in the ace-1 gene conferring resistance to these compounds (ace-1(R) allele), is already present. Furthermore, a duplicated allele (ace-1(D)) recently appeared; characterizing its selective advantage is mandatory to evaluate the threat. Our data revealed that a unique duplication event, pairing a susceptible and a resistant copy of the ace-1 gene spread through West Africa. Further investigations revealed that, while ace-1(D) confers less resistance than ace-1(R), the high fitness cost associated with ace-1(R) is almost completely suppressed by the duplication for all traits studied. ace-1 duplication thus represents a permanent heterozygote phenotype, selected, and thus spreading, due to the mosaic nature of mosquito control. It provides malaria mosquito with a new evolutionary path that could hamper resistance management.
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Abstract
In response to the widespread use of control strategies such as Insecticide Treated Nets (ITN), Anopheles mosquitoes have evolved various resistance mechanisms. Kdr is a mutation that provides physiological resistance to the pyrethroid insecticides family (PYR). In the present study, we investigated the effect of the Kdr mutation on the ability of female An. gambiae to locate and penetrate a 1cm-diameter hole in a piece of netting, either treated with insecticide or untreated, to reach a bait in a wind tunnel. Kdr homozygous, PYR-resistant mosquitoes were the least efficient at penetrating an untreated damaged net, with about 51% [39-63] success rate compared to 80% [70-90] and 78% [65-91] for homozygous susceptible and heterozygous respectively. This reduced efficiency, likely due to reduced host-seeking activity, as revealed by mosquito video-tracking, is evidence of a recessive behavioral cost of the mutation. Kdr heterozygous mosquitoes were the most efficient at penetrating nets treated with PYR insecticide, thus providing evidence for overdominance, the rarely-described case of heterozygote advantage conveyed by a single locus. The study also highlights the remarkable capacity of female mosquitoes, whether PYR-resistant or not, to locate holes in bed-nets.
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Assogba BS, Djogbénou LS, Saizonou J, Milesi P, Djossou L, Djegbe I, Oumbouke WA, Chandre F, Baba-Moussa L, Weill M, Makoutodé M. Phenotypic effects of concomitant insensitive acetylcholinesterase (ace-1(R)) and knockdown resistance (kdr(R)) in Anopheles gambiae: a hindrance for insecticide resistance management for malaria vector control. Parasit Vectors 2014; 7:548. [PMID: 25471264 PMCID: PMC4265331 DOI: 10.1186/s13071-014-0548-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/19/2014] [Indexed: 01/29/2023] Open
Abstract
Background Malaria is endemic in sub-Saharan Africa with considerable burden for human health. Major insecticide resistance mechanisms such as kdrR and ace-1Ralleles constitute a hindrance to malaria vector control programs. Anopheles gambiae bearing both kdr and ace-1 resistant alleles are increasingly recorded in wild populations. In order to maintain the efficacy of vector control strategies, the characterization of concomitant kdr and ace-1 resistance, and their pleiotropic effects on malaria vector phenotype on insecticide efficacy are important. Methods Larval and adult bioassays were performed with different insecticide classes used in public health following WHO standard guidelines on four laboratory Anopheles gambiae strains, sharing the same genetic background but harboring distinct resistance status: KISUMU with no resistance allele; ACERKIS with ace-1R allele; KISKDR with kdrR allele and ACERKDRKIS with both resistance alleles’ ace-1R and kdrR. Results Larval bioassays indicate that the homozygote resistant strain harboring both alleles (ACERKDRKIS) displayed slightly but significantly higher resistance level to various insecticides like carbamates (bendiocarb, p < 0.001; propoxur, p = 0.02) and organophosphates (chlorpyriphos-methyl, p = 0.002; fenitrothion, p < 0.001) when compared to ACERKIS strain. However, no differences were recorded between ACERKDRKIS and KISKDR resistance level against permethrin (Pyrethroid, p = 0.7) and DDT (Organochlorine, p = 0.24). For adult bioassays, the percentages of mosquitoes knocked down were significantly lower for ACERKDRKIS than for KISKDR with permethrin (p = 0.003) but not with deltamethrin. The percentage of mortality from adult bioassays was similar between ACERKDRKIS and ACERKIS with carbamates and organophosphates, or between ACERKDRKIS and KISKDR with pyrethroid and DDT. Concerning acetylcholinesterase enzyme, ACERKDRKIS strain showed similarAChE1 activity than that of ACERKIS. Conclusion The presence of both kdrR and ace-1R alleles seems to increase the resistance levels to both carbamate and organophosphate insecticides and at operational level, may represent an important threat to malaria vector control programs in West Africa.
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Affiliation(s)
- Benoît S Assogba
- Institut Régional de Santé Publique, Université d'Abomey Calavi, 01BP918, Cotonou, Benin. .,Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM2-IRD), Université Montpellier 2, Montpellier, France.
| | - Luc S Djogbénou
- Institut Régional de Santé Publique, Université d'Abomey Calavi, 01BP918, Cotonou, Benin.
| | - Jacques Saizonou
- Institut Régional de Santé Publique, Université d'Abomey Calavi, 01BP918, Cotonou, Benin.
| | - Pascal Milesi
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM2-IRD), Université Montpellier 2, Montpellier, France.
| | - Laurette Djossou
- Institut Régional de Santé Publique, Université d'Abomey Calavi, 01BP918, Cotonou, Benin.
| | - Innocent Djegbe
- Institut de Recherche pour le Développement (IRD), MIVEGEC (UMR 224-CNRS 5290-UM1-UM2), Centre de Recherche Entomologique de Cotonou (CREC), Cotonou, Benin.
| | - Welbeck A Oumbouke
- Centre de Recherche Entomologique de Cotonou (CREC), Health Ministry, Cotonou, Bénin.
| | - Fabrice Chandre
- Institut de recherche pour le développement, Unité Mixte de Recherche MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France.
| | - Lamine Baba-Moussa
- Faculté des Sciences et Techniques, Laboratoire de Biologie et de Typage Moléculaire en Microbiologie, Université d'Abomey Calavi, 05 BP 1604, Cotonou, Benin.
| | - Mylene Weill
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM2-IRD), Université Montpellier 2, Montpellier, France.
| | - Michel Makoutodé
- Institut Régional de Santé Publique, Université d'Abomey Calavi, 01BP918, Cotonou, Benin.
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Posavi M, Gelembiuk GW, Larget B, Lee CE. Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation. Evolution 2014; 68:3166-83. [PMID: 25135455 DOI: 10.1111/evo.12502] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 07/08/2014] [Indexed: 01/21/2023]
Abstract
Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the saltwater-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions.
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Affiliation(s)
- Marijan Posavi
- Center of Rapid Evolution (CORE), University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706
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