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Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Van Rij RP, Robertson DL, Schwemmle M, Stern-Ginossar N, Marz M. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses 2021; 13:v13050766. [PMID: 33925452 PMCID: PMC8145447 DOI: 10.3390/v13050766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.
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Affiliation(s)
- Winfried Goettsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland;
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Max von Kleist
- MF1 Bioinformatics, Robert Koch-Institute, 13353 Berlin, Germany;
| | - Roland Marquet
- CNRS, Architecture et Réactivité de l’ARN, Université de Strasbourg, UPR 9002 Strasbourg, France;
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Herestraat 49 Box 1040, 3000 Leuven, Belgium;
| | - Shawna McCallin
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, Forchstrasse 340, 8008 Zürich, Switzerland;
| | - Dino McMahon
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195 Berlin, Germany;
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Ronald P. Van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
| | - David L. Robertson
- MRC, University of Glasgow Centre for Virus Research (CVR), 464 Bearsden Road, Glasgow G61 1QH, UK;
| | - Martin Schwemmle
- Institute of Virology, Medical Center—University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany;
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
- Correspondence: ; Tel.: +49-3641-9-46480
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Lazzaro BP. Detecting Adaptation with Genome-Scale Molecule Evolutionary Analysis: An Educational Primer for Use with "RNA Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates". Genetics 2018; 210:773-80. [PMID: 30401763 DOI: 10.1534/genetics.118.301453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/30/2018] [Indexed: 11/18/2022] Open
Abstract
Hosts and pathogens impose coevolutionary pressure on each other as pathogens strive to establish themselves and hosts seek to suppress infection. RNA interference (RNAi) is a mechanism by which cells repress viruses and transposable elements, thereby serving as a form of immune defense. Previous studies have shown that antiviral RNAi genes evolve extraordinarily quickly in the fruit fly Drosophila melanogaster, suggesting that they may adaptively coevolve with viruses and transposable elements. An article by Palmer and colleagues extends this observation to nematodes and multiple insects. Their article can be combined with this Primer to demonstrate the use of comparative genomics and molecular evolutionary analyses in the measurement of natural selection.
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Palmer WH, Hadfield JD, Obbard DJ. RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates. Genetics 2018; 208:1585-99. [PMID: 29437826 DOI: 10.1534/genetics.117.300567] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races.
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Riehle MM, Bukhari T, Gneme A, Guelbeogo WM, Coulibaly B, Fofana A, Pain A, Bischoff E, Renaud F, Beavogui AH, Traore SF, Sagnon N, Vernick KD. The Anopheles gambiae 2La chromosome inversion is associated with susceptibility to Plasmodium falciparum in Africa. eLife 2017. [PMID: 28643631 PMCID: PMC5482571 DOI: 10.7554/elife.25813] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome inversions suppress genetic recombination and establish co-adapted gene complexes, or supergenes. The 2La inversion is a widespread polymorphism in the Anopheles gambiae species complex, the major African mosquito vectors of human malaria. Here we show that alleles of the 2La inversion are associated with natural malaria infection levels in wild-captured vectors from West and East Africa. Mosquitoes carrying the more-susceptible allele (2L+a) are also behaviorally less likely to be found inside houses. Vector control tools that target indoor-resting mosquitoes, such as bednets and insecticides, are currently the cornerstone of malaria control in Africa. Populations with high levels of the 2L+a allele may form reservoirs of persistent outdoor malaria transmission requiring novel measures for surveillance and control. The 2La inversion is a major and previously unappreciated component of the natural malaria transmission system in Africa, influencing both malaria susceptibility and vector behavior.
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Affiliation(s)
- Michelle M Riehle
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, United States
| | - Tullu Bukhari
- Department of Zoology, Maseno University, Maseno, Kenya
| | - Awa Gneme
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Boubacar Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Abdrahamane Fofana
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Adrien Pain
- Department of Parasites and Insect Vectors, Unit of Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Hosts, Vectors and Pathogens, Paris, France.,Bioinformatics and Biostatistics Hub (C3BI), USR 3756 IP CNRS, Institut Pasteur, Paris, France
| | - Emmanuel Bischoff
- Department of Parasites and Insect Vectors, Unit of Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Hosts, Vectors and Pathogens, Paris, France
| | - Francois Renaud
- Laboratoire Maladies Infectieuses et Vecteurs: Ecologie Génétique, Evolution et Contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD), Montpellier, France.,UMR 224-5290, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Abdoul H Beavogui
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Sekou F Traore
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Kenneth D Vernick
- Department of Parasites and Insect Vectors, Unit of Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Hosts, Vectors and Pathogens, Paris, France
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Simões ML, Dong Y, Hammond A, Hall A, Crisanti A, Nolan T, Dimopoulos G. The Anopheles FBN9 immune factor mediates Plasmodium species-specific defense through transgenic fat body expression. Dev Comp Immunol 2017; 67:257-265. [PMID: 27667688 DOI: 10.1016/j.dci.2016.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Mosquitoes have a multifaceted innate immune system that is actively engaged in warding off various pathogens, including the protozoan malaria parasite Plasmodium. Various immune signaling pathways and effectors have been shown to mediate a certain degree of defense specificity against different Plasmodium species. A key pattern recognition receptor of the Anopheles gambiae immune system is the fibrinogen domain-containing immunolectin FBN9, which has been shown to be transcriptonally induced by Plasmodium infection, and to mediate defense against both rodent and human malaria parasites and bacteria. Here we have further studied the defense specificity of FBN9 using a transgenic approach, in which FBN9 is overexpressed in the fat body tissue after a blood meal through a vitellogenin promoter. Interestingly, the Vg-FBN9 transgenic mosquitoes showed increased resistance only to the rodent parasite P. berghei, and not to the human parasite P. falciparum, pointing to differences in the mosquito's defense mechanisms against the two parasite species. The Vg-FBN9 transgenic mosquitoes were also more resistant to infection with both Gram-positive and Gram-negative bacteria and showed increased longevity when infected with P. berghei. Our study points to the importance of both experimentally depleting and enriching candidate anti-Plasmodium effectors in functional studies in order to ascertain their suitability for the development of transgenic mosquito-based malaria control strategies.
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Affiliation(s)
- Maria L Simões
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Ann Hall
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St., Baltimore, MD 21205, USA.
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Salgueiro P, Lopes AS, Mendes C, Charlwood JD, Arez AP, Pinto J, Silveira H. Molecular evolution and population genetics of a Gram-negative binding protein gene in the malaria vector Anopheles gambiae (sensu lato). Parasit Vectors 2016; 9:515. [PMID: 27658383 PMCID: PMC5034674 DOI: 10.1186/s13071-016-1800-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/14/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Clarifying the role of the innate immune system of the malaria vector Anopheles gambiae is a potential way to block the development of the Plasmodium parasites. Pathogen recognition is the first step of innate immune response, where pattern recognition proteins like GNBPs play a central role. RESULTS We analysed 70 sequences of the protein coding gene GNBPB2 from two species, Anopheles gambiae (s.s.) and An. coluzzii, collected in six African countries. We detected 135 segregating sites defining 63 distinct haplotypes and 30 proteins. Mean nucleotide diversity (π) was 0.014 for both species. We found no significant genetic differentiation between species, but a significant positive correlation between genetic differentiation and geographical distance among populations. CONCLUSIONS Species status seems to contribute less for the molecular differentiation in GNBPB2 than geographical region in the African continent (West and East). Purifying selection was found to be the most common form of selection, as in many other immunity-related genes. Diversifying selection may be also operating in the GNBPB2 gene.
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Affiliation(s)
- Patrícia Salgueiro
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ana Sofia Lopes
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Cristina Mendes
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jacques Derek Charlwood
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
- London School of Hygiene and Tropical Medicine, London, UK
| | - Ana Paula Arez
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - João Pinto
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
| | - Henrique Silveira
- Global Health and Tropical Medicine Centre (GHTM), Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisboa, Portugal
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Coulibaly B, Kone R, Barry MS, Emerson B, Coulibaly MB, Niare O, Beavogui AH, Traore SF, Vernick KD, Riehle MM. Malaria vector populations across ecological zones in Guinea Conakry and Mali, West Africa. Malar J 2016; 15:191. [PMID: 27059057 PMCID: PMC4826509 DOI: 10.1186/s12936-016-1242-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/30/2016] [Indexed: 11/12/2022] Open
Abstract
Background Malaria remains a pervasive public health problem in sub-Saharan West Africa. Here mosquito vector populations were explored across four sites in Mali and the Republic of Guinea (Guinea Conakry). The study samples the major ecological zones of malaria-endemic regions in West Africa within a relatively small distance. Methods Mosquito vectors were sampled from larval pools, adult indoor resting sites, and indoor and outdoor human-host seeking adults. Mosquitoes were collected at sites spanning 350 km that represented arid savannah, humid savannah, semi-forest and deep forest ecological zones, in areas where little was previously known about malaria vector populations. 1425 mosquito samples were analysed by molecular assays to determine species, genetic attributes, blood meal sources and Plasmodium infection status. Results Anopheles gambiae and Anopheles coluzzii were the major anophelines represented in all collections across the ecological zones, with A. coluzzii predominant in the arid savannah and A. gambiae in the more humid sites. The use of multiple collection methodologies across the sampling sites allows assessment of potential collection bias of the different methods. The L1014F kdr insecticide resistance mutation (kdr-w) is found at high frequency across all study sites. This mutation appears to have swept almost to fixation, from low frequencies 6 years earlier, despite the absence of widespread insecticide use for vector control. Rates of human feeding are very high across ecological zones, with only small fractions of animal derived blood meals in the arid and humid savannah. About 30 % of freshly blood-fed mosquitoes were positive for Plasmodium falciparum presence, while the rate of mosquitoes with established infections was an order of magnitude lower. Conclusions The study represents detailed vector characterization from an understudied area in West Africa with endemic malaria transmission. The deep forest study site includes the epicenter of the 2014 Ebola virus epidemic. With new malaria control interventions planned in Guinea, these data provide a baseline measure and an opportunity to assess the outcome of future interventions. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1242-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Boubacar Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Raymond Kone
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Republic of Guinea
| | - Mamadou S Barry
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Republic of Guinea
| | - Becky Emerson
- Department of Microbiology, University of Minnesota, Minneapolis, MN, USA
| | - Mamadou B Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Oumou Niare
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Abdoul H Beavogui
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Republic of Guinea
| | - Sekou F Traore
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Kenneth D Vernick
- Department of Microbiology, University of Minnesota, Minneapolis, MN, USA. .,Department of Parasites and Insect Vectors, Unit of Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France. .,CNRS Unit of Hosts, Vectors and Pathogens (URA3012), Paris, France.
| | - Michelle M Riehle
- Department of Microbiology, University of Minnesota, Minneapolis, MN, USA
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Abstract
Immune memory is a central feature of the mammalian adaptive immune system. The more primitive innate immune system of insects has also been shown to comprise memory, or immune priming. A recent study has shed new light on how Plasmodium primes the mosquito immune system for greater resistance to a subsequent infection with the same pathogen.
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Affiliation(s)
- Maria L Simões
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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9
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Rottschaefer SM, Crawford JE, Riehle MM, Guelbeogo WM, Gneme A, Sagnon N, Vernick KD, Lazzaro BP. Population genetics of Anopheles coluzzii immune pathways and genes. G3 (Bethesda) 2014; 5:329-39. [PMID: 25552603 DOI: 10.1534/g3.114.014845] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Natural selection is expected to drive adaptive evolution in genes involved in host–pathogen interactions. In this study, we use molecular population genetic analyses to understand how natural selection operates on the immune system of Anopheles coluzzii (formerly A. gambiae “M form”). We analyzed patterns of intraspecific and interspecific genetic variation in 20 immune-related genes and 17 nonimmune genes from a wild population of A. coluzzii and asked if patterns of genetic variation in the immune genes are consistent with pathogen-driven selection shaping the evolution of defense. We found evidence of a balanced polymorphism in CTLMA2, which encodes a C-type lectin involved in regulation of the melanization response. The two CTLMA2 haplotypes, which are distinguished by fixed amino acid differences near the predicted peptide cleavage site, are also segregating in the sister species A. gambiae (“S form”) and A. arabiensis. Comparison of the two haplotypes between species indicates that they were not shared among the species through introgression, but rather that they arose before the species divergence and have been adaptively maintained as a balanced polymorphism in all three species. We additionally found that STAT-B, a retroduplicate of STAT-A, shows strong evidence of adaptive evolution that is consistent with neofunctionalization after duplication. In contrast to the striking patterns of adaptive evolution observed in these Anopheles-specific immune genes, we found no evidence of adaptive evolution in the Toll and Imd innate immune pathways that are orthologously conserved throughout insects. Genes encoding the Imd pathway exhibit high rates of amino acid divergence between Anopheles species but also display elevated amino acid diversity that is consistent with relaxed purifying selection. These results indicate that adaptive coevolution between A. coluzzii and its pathogens is more likely to involve novel or lineage-specific molecular mechanisms than the canonical humoral immune pathways.
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O'Loughlin SM, Magesa S, Mbogo C, Mosha F, Midega J, Lomas S, Burt A. Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories. Mol Biol Evol 2014; 31:889-902. [PMID: 24408911 PMCID: PMC3969563 DOI: 10.1093/molbev/msu040] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Anopheles gambiae s.l. are important malaria vectors, but little is known about their genomic variation in the wild. Here, we present inter- and intraspecies analysis of genome-wide RADseq data, in three Anopheles gambiae s.l. species collected from East Africa. The mosquitoes fall into three genotypic clusters representing described species (A. gambiae, A. arabiensis, and A. merus) with no evidence of cryptic breeding units. Anopheles merus is the most divergent of the three species, supporting a recent new phylogeny based on chromosomal inversions. Even though the species clusters are well separated, there is extensive shared polymorphism, particularly between A. gambiae and A. arabiensis. Divergence between A. gambiae and A. arabiensis does not vary across the autosomes but is higher in X-linked inversions than elsewhere on X or on the autosomes, consistent with the suggestion that this inversion (or a gene within it) is important in reproductive isolation between the species. The 2La/2L+(a) inversion shows no more evidence of introgression between A. gambiae and A. arabiensis than the rest of the autosomes. Population differentiation within A. gambiae and A. arabiensis is weak over approximately 190-270 km, implying no strong barriers to dispersal. Analysis of Tajima's D and the allele frequency spectrum is consistent with modest population increases in A. arabiensis and A. merus, but a more complex demographic history of expansion followed by contraction in A. gambiae. Although they are less than 200 km apart, the two A. gambiae populations show evidence of different demographic histories.
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Affiliation(s)
- Samantha M O'Loughlin
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
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Sanford MR, Ramsay S, Cornel AJ, Marsden CD, Norris LC, Patchoke S, Fondjo E, Lanzaro GC, Lee Y. A preliminary investigation of the relationship between water quality and Anopheles gambiae larval habitats in Western Cameroon. Malar J 2013; 12:225. [PMID: 23819866 PMCID: PMC3704728 DOI: 10.1186/1475-2875-12-225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/24/2013] [Indexed: 11/16/2022] Open
Abstract
Background Water quality and anopheline habitat have received increasing attention due to the possibility that challenges during larval life may translate into adult susceptibility to malaria parasite infection and/or insecticide resistance. Methods A preliminary study of Anopheles gambiae s.s. larval habitats in the north-west and south-west regions of Cameroon was conducted in order to detect associations between An. gambiae s.s. molecular form and 2La inversion distributions with basic water quality parameters. Water quality was measured by temperature, pH, conductivity, total dissolved solids (TDS) at seven sites in Cameroon and one site in Selinkenyi, Mali. Results Principal components and correlation analyses indicated a complex relationship between 2La polymorphism, temperature, conductivity and TDS. Cooler water sites at more inland locations yielded more S form larvae with higher 2La inversion polymorphism while warmer water sites yielded more M form larvae with rare observations of the 2La inversion. Discussion More detailed studies that take into account the population genetics but also multiple life stages, environmental data relative to these life stages and interactions with both humans and the malaria parasite may help us to understand more about how and why this successful mosquito is able to adapt and diverge, and how it can be successfully managed.
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12
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Parmakelis A, Kotsakiozi P, Rand D. Animal mitochondria, positive selection and cyto-nuclear coevolution: insights from pulmonates. PLoS One 2013; 8:e61970. [PMID: 23620797 PMCID: PMC3631144 DOI: 10.1371/journal.pone.0061970] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/15/2013] [Indexed: 01/06/2023] Open
Abstract
Pulmonate snails have remarkably high levels of mtDNA polymorphism within species and divergence between species, making them an interesting group for the study of mutation and selection on mitochondrial genomes. The availability of sequence data from most major lineages – collected largely for studies of phylogeography - provides an opportunity to perform several tests of selection that may provide general insights into the evolutionary forces that have produced this unusual pattern. Several protein coding mtDNA datasets of pulmonates were analyzed towards this direction. Two different methods for the detection of positive selection were used, one based on phylogeny, and the other on the McDonald-Kreitman test. The cyto-nuclear coevolution hypothesis, often implicated to account for the high levels of mtDNA divergence of some organisms, was also addressed by assessing the divergence pattern exhibited by a nuclear gene. The McDonald-Kreitman test indicated multiple signs of positive selection in the mtDNA genes, but was significantly biased when sequence divergence was high. The phylogenetic method identified five mtDNA datasets as affected by positive selection. In the nuclear gene, the McDonald-Kreitman test provided no significant results, whereas the phylogenetic method identified positive selection as likely present. Overall, our findings indicate that: 1) slim support for the cyto-nuclear coevolution hypothesis is present, 2) the elevated rates of mtDNA polymorphims and divergence in pulmonates do not appear to be due to pervasive positive selection, 3) more stringent tests show that spurious positive selection is uncovered when distant taxa are compared and 4) there are significant examples of positive selection acting in some cases, so it appears that mtDNA evolution in pulmonates can escape from strict deleterious evolution suggested by the Muller’s ratchet effect.
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Affiliation(s)
- Aristeidis Parmakelis
- Department of Ecology and Taxonomy, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
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Crawford JE, Rottschaefer SM, Coulibaly B, Sacko M, Niaré O, Riehle MM, Traore SF, Vernick KD, Lazzaro BP. No evidence for positive selection at two potential targets for malaria transmission-blocking vaccines in Anopheles gambiae s.s. Infect Genet Evol 2013; 16:87-92. [PMID: 23357581 DOI: 10.1016/j.meegid.2013.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/04/2013] [Accepted: 01/05/2013] [Indexed: 12/27/2022]
Abstract
Human malaria causes nearly a million deaths in sub-Saharan Africa each year. The evolution of drug-resistance in the parasite and insecticide resistance in the mosquito vector has complicated control measures and made the need for new control strategies more urgent. Anopheles gambiae s.s. is one of the primary vectors of human malaria in Africa, and parasite-transmission-blocking vaccines targeting Anopheles proteins have been proposed as a possible strategy to control the spread of the disease. However, the success of these hypothetical technologies would depend on the successful ability to broadly target mosquito populations that may be genetically heterogeneous. Understanding the evolutionary pressures shaping genetic variation among candidate target molecules offers a first step towards evaluating the prospects of successfully deploying such technologies. We studied the population genetics of genes encoding two candidate target proteins, the salivary gland protein saglin and the basal lamina structural protein laminin, in wild populations of the M and S molecular forms of A. gambiae in Mali. Through analysis of intraspecific genetic variation and interspecific comparisons, we found no evidence of positive natural selection at the genes encoding these proteins. On the contrary, we found evidence for particularly strong purifying selection at the laminin gene. These results provide insight into the patterns of genetic diversity of saglin and laminin, and we discuss these findings in relation to the potential development of these molecules as vaccine targets.
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Crawford JE, Bischoff E, Garnier T, Gneme A, Eiglmeier K, Holm I, Riehle MM, Guelbeogo WM, Sagnon N, Lazzaro BP, Vernick KD. Evidence for population-specific positive selection on immune genes of Anopheles gambiae. G3 (Bethesda) 2012; 2:1505-19. [PMID: 23275874 DOI: 10.1534/g3.112.004473] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/22/2012] [Indexed: 12/16/2022]
Abstract
Host-pathogen interactions can be powerful drivers of adaptive evolution, shaping the patterns of molecular variation at the genes involved. In this study, we sequenced alleles from 28 immune-related loci in wild samples of multiple genetic subpopulations of the African malaria mosquito Anopheles gambiae, obtaining unprecedented sample sizes and providing the first opportunity to contrast patterns of molecular evolution at immune-related loci in the recently discovered GOUNDRY population to those of the indoor-resting M and S molecular forms. In contrast to previous studies that focused on immune genes identified in laboratory studies, we centered our analysis on genes that fall within a quantitative trait locus associated with resistance to Plasmodium falciparum in natural populations of A. gambiae. Analyses of haplotypic and genetic diversity at these 28 loci revealed striking differences among populations in levels of genetic diversity and allele frequencies in coding sequence. Putative signals of positive selection were identified at 11 loci, but only one was shared by two subgroups of A. gambiae. Striking patterns of linkage disequilibrium were observed at several loci. We discuss these results with respect to ecological differences among these strata as well as potential implications for disease transmission.
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Lee Y, Seifert SN, Fornadel CM, Norris DE, Lanzaro GC. Single-nucleotide polymorphisms for high-throughput genotyping of Anopheles arabiensis in East and southern Africa. J Med Entomol 2012; 49:307-15. [PMID: 22493848 PMCID: PMC4089035 DOI: 10.1603/me11113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Anopheles arabiensis Patton is one of the principal vectors of malaria in sub-Saharan Africa, occupying a wide variety of ecological zones. This species is increasingly responsible for malaria transmission in Africa and is becoming the dominant vector species in some localities. Despite its growing importance, little is known about genetic polymorphisms in this species. Multiple sequences of various gene fragments from An. arabiensis isolates from Cameroon were obtained from GenBank. In total, 20 gene fragments containing single-nucleotide polymorphisms (SNPs) at moderate density were selected for direct sequencing from field collected specimens from Tanzania and Zambia. We obtained 301 SNPs in total from the 20 gene fragments, 60 of which were suitable for Illumina GoldenGate SNP genotyping. A greater number of SNPs (n = 185) was suitable for analysis using Sequenom iPLEX, an alternative high-throughput genotyping technology using mass spectrometry. An SNP was present every 59 (+/- 44.5) bases on average. Overall, An. arabiensis from Tanzania and Zambia are genetically closer (mean F(ST) = 0.075) than either is to populations in Cameroon (F(ST, TZ-CM) = 0.250, F(ST,ZA-CM) = 0.372). A fixed polymorphism between East/southern and Central Africa was identified on AGAP000574, a gene on the X chromosome. We have identified SNPs in natural populations of An. arabiensis. SNP densities in An. arabiensis were higher than Anopheles gambiae s.s., suggesting a greater challenge in the development of high-throughput SNP analysis for this species. The SNP markers provided in this study are suitable for a high-throughput genotyping analysis and can be used for population genetic studies and association mapping efforts.
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Affiliation(s)
- Yoosook Lee
- School of Veterinary Medicine, Department of Pathology, Microbiology and Immunology, University of California-Davis, Davis, CA 95616, USA.
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Abstract
The closely related and morphologically indistinguishable mosquito species in the Afrotropical Anopheles gambiae complex differ dramatically in their contribution to malaria transmission, ranging from major vectors through minor or locally important vectors and nonvectors. Radiation of the A. gambiae complex and ongoing diversification within its nominal species appears to be a product of recent and rapid adaptation to environmental heterogeneities, notably those of anthropogenic origin. Polytene chromosome and genomic analyses suggest that paracentric chromosomal inversions and possibly other low-recombination regions have played instrumental roles in this process by facilitating ecotypic differentiation both within and across semipermeable species boundaries. Forthcoming complete genome sequences from several members of the A. gambiae complex will provide powerful tools to accelerate ongoing investigation of how genetic diversification of populations and species has shaped behavioral and physiological traits, such as vector competence, that bear on vectorial importance.
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Affiliation(s)
- Bradley J. White
- Department of Entomology, University of California, Riverside, Riverside, California 92521
| | - Frank H. Collins
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
| | - Nora J. Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556
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Mancini E, Tammaro F, Baldini F, Via A, Raimondo D, George P, Audisio P, Sharakhov IV, Tramontano A, Catteruccia F, della Torre A. Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract. BMC Evol Biol 2011; 11:72. [PMID: 21418586 PMCID: PMC3068966 DOI: 10.1186/1471-2148-11-72] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 03/19/2011] [Indexed: 11/30/2022] Open
Abstract
Background Genes involved in post-mating processes of multiple mating organisms are known to evolve rapidly due to coevolution driven by sexual conflict among male-female interacting proteins. In the malaria mosquito Anopheles gambiae - a monandrous species in which sexual conflict is expected to be absent or minimal - recent data strongly suggest that proteolytic enzymes specifically expressed in the female lower reproductive tissues are involved in the processing of male products transferred to females during mating. In order to better understand the role of selective forces underlying the evolution of proteins involved in post-mating responses, we analysed a cluster of genes encoding for three serine proteases that are down-regulated after mating, two of which specifically expressed in the atrium and one in the spermatheca of A. gambiae females. Results The analysis of polymorphisms and divergence of these female-expressed proteases in closely related species of the A. gambiae complex revealed a high level of replacement polymorphisms consistent with relaxed evolutionary constraints of duplicated genes, allowing to rapidly fix novel replacements to perform new or more specific functions. Adaptive evolution was detected in several codons of the 3 genes and hints of episodic selection were also found. In addition, the structural modelling of these proteases highlighted some important differences in their substrate specificity, and provided evidence that a number of sites evolving under selective pressures lie relatively close to the catalytic triad and/or on the edge of the specificity pocket, known to be involved in substrate recognition or binding. The observed patterns suggest that these proteases may interact with factors transferred by males during mating (e.g. substrates, inhibitors or pathogens) and that they may have differently evolved in independent A. gambiae lineages. Conclusions Our results - also examined in light of constraints in the application of selection-inference methods to the closely related species of the A. gambiae complex - reveal an unexpectedly intricate evolutionary scenario. Further experimental analyses are needed to investigate the biological functions of these genes in order to better interpret their molecular evolution and to assess whether they represent possible targets for limiting the fertility of Anopheles mosquitoes in malaria vector control strategies.
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Affiliation(s)
- Emiliano Mancini
- Istituto-Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, 'Sapienza' Università di Roma, Italy
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Rottschaefer SM, Riehle MM, Coulibaly B, Sacko M, Niaré O, Morlais I, Traoré SF, Vernick KD, Lazzaro BP. Exceptional diversity, maintenance of polymorphism, and recent directional selection on the APL1 malaria resistance genes of Anopheles gambiae. PLoS Biol 2011; 9:e1000600. [PMID: 21408087 PMCID: PMC3050937 DOI: 10.1371/journal.pbio.1000600] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 01/27/2011] [Indexed: 01/17/2023] Open
Abstract
The three-gene APL1 locus encodes essential components of the mosquito immune defense against malaria parasites. APL1 was originally identified because it lies within a mapped QTL conferring the vector mosquito Anopheles gambiae natural resistance to the human malaria parasite, Plasmodium falciparum, and APL1 genes have subsequently been shown to be involved in defense against several species of Plasmodium. Here, we examine molecular population genetic variation at the APL1 gene cluster in spatially and temporally diverse West African collections of A. gambiae. The locus is extremely polymorphic, showing evidence of adaptive evolutionary maintenance of genetic variation. We hypothesize that this variability aids in defense against genetically diverse pathogens, including Plasmodium. Variation at APL1 is highly structured across geographic and temporal subpopulations. In particular, diversity is exceptionally high during the rainy season, when malaria transmission rates are at their peak. Much less allelic diversity is observed during the dry season when mosquito population sizes and malaria transmission rates are low. APL1 diversity is weakly stratified by the polymorphic 2La chromosomal inversion but is very strongly subdivided between the M and S “molecular forms.” We find evidence that a recent selective sweep has occurred at the APL1 locus in M form mosquitoes only. The independently reported observation of a similar M-form restricted sweep at the Tep1 locus, whose product physically interacts with APL1C, suggests that epistatic selection may act on these two loci causing them to sweep coordinately. Immune defense genes are sometimes highly variable in host populations, reflecting selective pressure to combat diverse pathogens. In other instances, where there are only a few dominant pathogens, natural selection may favor only one or a few defense alleles. Here, we show that both adaptive strategies can occur in the same genes under different circumstances. We examined diversity in the APL1 genes of the human malaria vector mosquito Anophleles gambiae, which play a role in defense against malaria parasites. We found that the APL1 genes are exceptionally polymorphic, being 10-fold more diverse than typical A. gambiae genes. The distribution of APL1 allelic diversity, however, is strongly structured depending on whether the genes are carried by the M or S “molecular forms” of the vector, which are thought to constitute newly forming species. We show that despite the evolutionary maintenance of APL1 diversity in the S form of A. gambiae, there is evidence of strong recent directional selection on APL1 genes in the M form. Independent research has shown that Tep1, a gene which encodes a protein that physically interacts with the APL1C protein, also harbors high allelic diversity in the S form and shows evidence of recent directional selection in the M form, suggesting that the evolutionary trajectories of the Tep1 and APL1 defense loci may be correlated.
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Affiliation(s)
- Susan M. Rottschaefer
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
| | - Michelle M. Riehle
- Department of Microbiology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Boubacar Coulibaly
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Madjou Sacko
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Oumou Niaré
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Isabelle Morlais
- Laboratoire de Recherche sur le Paludisme, Institut de Recherche pour le Développement IRD-OCEAC, Yaoundé, Cameroun
| | - Sekou F. Traoré
- Malaria Research and Training Center, University of Bamako, Bamako, Mali
| | - Kenneth D. Vernick
- Unit of Insect Vector Genetics and Genomics, Institut Pasteur, Paris, France
| | - Brian P. Lazzaro
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Abstract
Anopheles gambiae is a primary vector of Plasmodium falciparum, a human malaria parasite that causes over a million deaths each year in sub-Saharan Africa. Population genetic tests have been employed to detect natural selection at suspected A. gambiae antimalaria genes, but these tests have generally been compromised by the lack of demographically correct null models. Here, we used a coalescent simulation approach within a maximum likelihood framework to fit population growth, bottleneck, and migration models to polymorphism data from Cameroonian A. gambiae. The best-fit models for both the "M" and the "S" molecular forms of A. gambiae included ancient population growth and a high rate of migration from an unsampled subpopulation. After correcting for differences in effective population size, our models suggest that the molecular forms expanded at different times and both expansions significantly predate the advent of agriculture. We show that correcting null models for demography increases the power to detect natural selection in A. gambiae.
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Parmakelis A, Moustaka M, Poulakakis N, Louis C, Slotman MA, Marshall JC, Awono-Ambene PH, Antonio-Nkondjio C, Simard F, Caccone A, Powell JR. Anopheles immune genes and amino acid sites evolving under the effect of positive selection. PLoS One 2010; 5:e8885. [PMID: 20126662 PMCID: PMC2811201 DOI: 10.1371/journal.pone.0008885] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 01/04/2010] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND It has long been the goal of vector biology to generate genetic knowledge that can be used to "manipulate" natural populations of vectors to eliminate or lessen disease burden. While long in coming, progress towards reaching this goal has been made. Aiming to increase our understanding regarding the interactions between Plasmodium and the Anopheles immune genes, we investigated the patterns of genetic diversity of four anti-Plasmodium genes in the Anopheles gambiae complex of species. METHODOLOGY/PRINCIPAL FINDINGS Within a comparative phylogenetic and population genetics framework, the evolutionary history of four innate immunity genes within the An. gambiae complex (including the two most important human malaria vectors, An. gambiae and An. arabiensis) is reconstructed. The effect of natural selection in shaping the genes' diversity is examined. Introgression and retention of ancestral polymorphisms are relatively rare at all loci. Despite the potential confounding effects of these processes, we could identify sites that exhibited dN/dS ratios greater than 1. CONCLUSIONS/SIGNIFICANCE In two of the studied genes, CLIPB14 and FBN8, several sites indicated evolution under positive selection, with CLIPB14 exhibiting the most consistent evidence. Considering only the sites that were consistently identified by all methods, two sites in CLIPB14 are adaptively driven. However, the analysis inferring the lineage -specific evolution of each gene was not in favor of any of the Anopheles lineages evolving under the constraints imposed by positive selection. Nevertheless, the loci and the specific amino acids that were identified as evolving under strong evolutionary pressure merit further investigation for their involvement in the Anopheles defense against microbes in general.
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Affiliation(s)
- Aristeidis Parmakelis
- Department of Ecology and Taxonomy, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, Athens, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Marina Moustaka
- Department of Ecology and Taxonomy, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, Athens, Greece
| | - Nikolaos Poulakakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Christos Louis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Heraklion, Vassilika Vouton, Heraklion, Crete, Greece
| | - Michel A. Slotman
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Jonathon C. Marshall
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Zoology, Weber State University, Ogden, Utah, United States of America
| | - Parfait H. Awono-Ambene
- Organisation de Coordination pour la Lutte Contre les Endémies en Afrique Centrale (OCEAC), Yaoundé, Cameroon
| | - Christophe Antonio-Nkondjio
- Organisation de Coordination pour la Lutte Contre les Endémies en Afrique Centrale (OCEAC), Yaoundé, Cameroon
| | - Frederic Simard
- Organisation de Coordination pour la Lutte Contre les Endémies en Afrique Centrale (OCEAC), Yaoundé, Cameroon
- Institut de Recherche pour le Développement (IRD), Bobo Dioulasso, Burkina Faso
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jeffrey R. Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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Obbard DJ, Welch JJ, Little TJ. Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors. Malar J 2009; 8:117. [PMID: 19497100 PMCID: PMC2698913 DOI: 10.1186/1475-2875-8-117] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 06/04/2009] [Indexed: 12/16/2022] Open
Abstract
Background Mosquitoes of the Anopheles gambiae species complex are the primary vectors of human malaria in sub-Saharan Africa. Many host genes have been shown to affect Plasmodium development in the mosquito, and so are expected to engage in an evolutionary arms race with the pathogen. However, there is little conclusive evidence that any of these mosquito genes evolve rapidly, or show other signatures of adaptive evolution. Methods Three serine protease inhibitors have previously been identified as candidate immune system genes mediating mosquito-Plasmodium interaction, and serine protease inhibitors have been identified as hot-spots of adaptive evolution in other taxa. Population-genetic tests for selection, including a recent multi-gene extension of the McDonald-Kreitman test, were applied to 16 serine protease inhibitors and 16 other genes sampled from the An. gambiae species complex in both East and West Africa. Results Serine protease inhibitors were found to show a marginally significant trend towards higher levels of amino acid diversity than other genes, and display extensive genetic structuring associated with the 2La chromosomal inversion. However, although serpins are candidate targets for strong parasite-mediated selection, no evidence was found for rapid adaptive evolution in these genes. Conclusion It is well known that phylogenetic and population history in the An. gambiae complex can present special problems for the application of standard population-genetic tests for selection, and this may explain the failure of this study to detect selection acting on serine protease inhibitors. The pitfalls of uncritically applying these tests in this species complex are highlighted, and the future prospects for detecting selection acting on the An. gambiae genome are discussed.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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Voordouw MJ, Anholt BR, Taylor PJ, Hurd H. Rodent malaria-resistant strains of the mosquito, Anopheles gambiae, have slower population growth than -susceptible strains. BMC Evol Biol 2009; 9:76. [PMID: 19379508 PMCID: PMC2675531 DOI: 10.1186/1471-2148-9-76] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 04/20/2009] [Indexed: 01/08/2023] Open
Abstract
Background Trade-offs between anti-parasite defence mechanisms and other life history traits limit the evolution of host resistance to parasites and have important implications for understanding diseases such as malaria. Mosquitoes have not evolved complete resistance to malaria parasites and one hypothesis is that anti-malaria defence mechanisms are costly. Results We used matrix population models to compare the population growth rates among lines of Anopheles gambiae that had been selected for resistance or high susceptibility to the rodent malaria parasite, Plasmodium yoelii nigeriensis. The population growth rate of the resistant line was significantly lower than that of the highly susceptible and the unselected control lines, regardless of whether mosquitoes were infected with Plasmodium or not. The lower population growth of malaria-resistant mosquitoes was caused by reduced post blood-feeding survival of females and poor egg hatching. Conclusion With respect to eradicating malaria, the strategy of releasing Plasmodium-resistant Anopheles mosquitoes is unlikely to be successful if the costs of Plasmodium-resistance in the field are as great as the ones measured in this study. High densities of malaria-resistant mosquitoes would have to be maintained by continuous release from captive breeding facilities.
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Affiliation(s)
- Maarten J Voordouw
- Department of Biology, University of Victoria, PO Box 3020, Station CSC, Victoria, British Columbia, V8W 3N5, Canada.
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Lehmann T, Hume JCC, Licht M, Burns CS, Wollenberg K, Simard F, Ribeiro JMC. Molecular evolution of immune genes in the malaria mosquito Anopheles gambiae. PLoS One 2009; 4:e4549. [PMID: 19234606 PMCID: PMC2642720 DOI: 10.1371/journal.pone.0004549] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 12/31/2008] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND As pathogens that circumvent the host immune response are favoured by selection, so are host alleles that reduce parasite load. Such evolutionary processes leave their signature on the genes involved. Deciphering modes of selection operating on immune genes might reveal the nature of host-pathogen interactions and factors that govern susceptibility in host populations. Such understanding would have important public health implications. METHODOLOGY/FINDINGS We analyzed polymorphisms in four mosquito immune genes (SP14D1, GNBP, defensin, and gambicin) to decipher selection effects, presumably mediated by pathogens. Using samples of Anopheles arabiensis, An. quadriannulatus and four An. gambiae populations, as well as published sequences from other Culicidae, we contrasted patterns of polymorphisms between different functional units of the same gene within and between populations. Our results revealed selection signatures operating on different time scales. At the most recent time scale, within-population diversity revealed purifying selection. Between populations and between species variation revealed reduced differentiation (GNBP and gambicin) at coding vs. noncoding- regions, consistent with balancing selection. McDonald-Kreitman tests between An. quadriannulatus and both sibling species revealed higher fixation rate of synonymous than nonsynonymous substitutions (GNBP) in accordance with frequency dependent balancing selection. At the longest time scale (>100 my), PAML analysis using distant Culicid taxa revealed positive selection at one codon in gambicin. Patterns of genetic variation were independent of exposure to human pathogens. SIGNIFICANCE AND CONCLUSIONS Purifying selection is the most common form of selection operating on immune genes as it was detected on a contemporary time scale on all genes. Selection for "hypervariability" was not detected, but negative balancing selection, detected at a recent evolutionary time scale between sibling species may be rather common. Detection of positive selection at the deepest evolutionary time scale suggests that it occurs infrequently, possibly in association with speciation events. Our results provided no evidence to support the hypothesis that selection was mediated by pathogens that are transmitted to humans.
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Affiliation(s)
- Tovi Lehmann
- Division of Parasitic Diseases, Entomology Branch, Centers for Disease Control & Prevention, Chamblee, Georgia, United States of America.
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Ng'habi KR, Meneses CR, Cornel AJ, Slotman MA, Knols BG, Ferguson HM, Lanzaro GC. Clarification of anomalies in the application of a 2La molecular karyotyping method for the malaria vector Anopheles gambiae. Parasit Vectors 2008; 1:45. [PMID: 19091112 PMCID: PMC2628339 DOI: 10.1186/1756-3305-1-45] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 12/17/2008] [Indexed: 11/15/2022] Open
Abstract
Background Chromosomal inversions have been considered to be potentially important barriers to gene flow in many groups of animals through their effect on recombination suppression in heterokaryotypic individuals. Inversions can also enhance local adaptation in different groups of organisms and may often represent species-specific differences among closely related taxa. We conducted a study to characterize the 2La inversion karyotypes of An. gambiae sensu stricto mosquitoes sampled from the Kilombero Valley (Tanzania) using a newly designed PCR assay. Results We frequently encountered a (687 bp) fragment which was only present in the Kilombero Valley populations. Laboratory crossing between An. gambiae s.s. from Njage (Tanzania) and Kisumu (Western Kenya) populations resulted in F1 offspring carrying the observed fragment. Karyotype analysis did not indicate differences in 2La region chromosome morphology between individuals carrying the PCR fragments, the 207 bp fragment, or the 687 bp fragement. Conclusion The observed insertion/deletion polymorphism within the region amplified by the 2La PCR diagnostic test may confound the interpretation of this assay and should be well considered in order to maintain an acceptable level of reliability in studies using this assay to describe the distribution and frequency of the 2La inversion among natural populations of An. gambiae s.s.
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Affiliation(s)
- Kija R Ng'habi
- Ifakara Health Institute, Mlabani Passage, Ifakara, Tanzania.
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Boëte C. Anopheles mosquitoes: not just flying malaria vectors... especially in the field. Trends Parasitol 2008; 25:53-5. [PMID: 19095498 DOI: 10.1016/j.pt.2008.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 10/07/2008] [Accepted: 10/27/2008] [Indexed: 01/23/2023]
Abstract
The polymorphism of genes involved in the immunity of malaria vectors has been the subject of several recent studies with mosquitoes from natural populations. Most of the genes examined are known for their role against Plasmodium berghei and not necessarily for their role against Plasmodium falciparum. It seems, therefore, to be highly important not only to be cautious when linking natural selection with malaria epidemiology but also to consider the importance of other parasites and the environment on the mosquito genome.
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Affiliation(s)
- Christophe Boëte
- Institut de Recherche pour le Développement (IRD), Structure Gestion des Personnels, 44 bd de Dunkerque, 13572 Marseille, Cedex 02, France.
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Obbard DJ, Callister DM, Jiggins FM, Soares DC, Yan G, Little TJ. The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae. BMC Evol Biol 2008; 8:274. [PMID: 18840262 PMCID: PMC2576239 DOI: 10.1186/1471-2148-8-274] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 10/07/2008] [Indexed: 01/20/2023] Open
Abstract
Background Host-parasite coevolution can result in balancing selection, which maintains genetic variation in the susceptibility of hosts to parasites. It has been suggested that variation in a thioester-containing protein called TEP1 (AGAP010815) may alter the ability of Anopheles mosquitoes to transmit Plasmodium parasites, and high divergence between alleles of this gene suggests the possible action of long-term balancing selection. We studied whether TEP1 is a case of an ancient balanced polymorphism in an animal immune system. Results We found evidence that the high divergence between TEP1 alleles is the product of genetic exchange between TEP1 and other TEP loci, i.e. gene conversion. Additionally, some TEP1 alleles showed unexpectedly low variability. Conclusion The TEP1 gene appears to be a chimera produced from at least two other TEP loci, and the divergence between TEP1 alleles is probably not caused by long-term balancing selection, but is instead due to two independent gene conversion events from one of these other genes. Nevertheless, TEP1 still shows evidence of natural selection, in particular there appears to have been recent changes in the frequency of alleles that has diminished polymorphism within each allelic class. Although the selective force driving this dynamic was not identified, given that susceptibility to Plasmodium parasites is known to be associated with allelic variation in TEP1, these changes in allele frequencies could alter the vectoring capacity of populations.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Rd, Edinburgh EH9 3JT, UK.
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Cohuet A, Krishnakumar S, Simard F, Morlais I, Koutsos A, Fontenille D, Mindrinos M, Kafatos FC. SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system. BMC Genomics 2008; 9:227. [PMID: 18489733 PMCID: PMC2405807 DOI: 10.1186/1471-2164-9-227] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 05/19/2008] [Indexed: 01/10/2023] Open
Abstract
Background Anopheles innate immunity affects Plasmodium development and is a potential target of innovative malaria control strategies. The extent and distribution of nucleotide diversity in immunity genes might provide insights into the evolutionary forces that condition pathogen-vector interactions. The discovery of polymorphisms is an essential step towards association studies of susceptibility to infection. Results We sequenced coding fragments of 72 immune related genes in natural populations of Anopheles gambiae and of 37 randomly chosen genes to provide a background measure of genetic diversity across the genome. Mean nucleotide diversity (π) was 0.0092 in the A. gambiae S form, 0.0076 in the M form and 0.0064 in A. arabiensis. Within each species, no statistically significant differences in mean nucleotide diversity were detected between immune related and non immune related genes. Strong purifying selection was detected in genes of both categories, presumably reflecting strong functional constraints. Conclusion Our results suggest similar patterns and rates of molecular evolution in immune and non-immune genes in A. gambiae. The 3,214 Single Nucleotide Polymorphisms (SNPs) that we identified are the first large set of Anopheles SNPs from fresh, field-collected material and are relevant markers for future phenotype-association studies.
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Affiliation(s)
- Anna Cohuet
- Institut de Recherche pour le Développement, UR 016, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France.
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28
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Parmakelis A, Slotman MA, Marshall JC, Awono-Ambene PH, Antonio-Nkondjio C, Simard F, Caccone A, Powell JR. The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex. BMC Evol Biol 2008; 8:79. [PMID: 18325105 PMCID: PMC2288592 DOI: 10.1186/1471-2148-8-79] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 03/06/2008] [Indexed: 12/14/2022] Open
Abstract
Background If the insect innate immune system is to be used as a potential blocking step in transmission of malaria, then it will require targeting one or a few genes with highest relevance and ease of manipulation. The problem is to identify and manipulate those of most importance to malaria infection without the risk of decreasing the mosquito's ability to stave off infections by microbes in general. Molecular evolution methodologies and concepts can help identify such genes. Within the setting of a comparative molecular population genetic and phylogenetic framework, involving six species of the Anopheles gambiae complex, we investigated whether a set of four pre-selected immunity genes (gambicin, NOS, Rel2 and FBN9) might have evolved under selection pressure imposed by the malaria parasite. Results We document varying levels of polymorphism within and divergence between the species, in all four genes. Introgression and the sharing of ancestral polymorphisms, two processes that have been documented in the past, were verified in this study in all four studied genes. These processes appear to affect each gene in different ways and to different degrees. However, there is no evidence of positive selection acting on these genes. Conclusion Considering the results presented here in concert with previous studies, genes that interact directly with the Plasmodium parasite, and play little or no role in defense against other microbes, are probably the most likely candidates for a specific adaptive response against P. falciparum. Furthermore, since it is hard to establish direct evidence linking the adaptation of any candidate gene to P. falciparum infection, a comparative framework allowing at least an indirect link should be provided. Such a framework could be achieved, if a similar approach like the one involved here, was applied to all other anopheline complexes that transmit P. falciparum malaria.
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Affiliation(s)
- Aristeidis Parmakelis
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, 06511, New Haven, CT, USA.
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Abstract
BACKGROUND Some cancers are mediated by an interplay between tissue damage, pathogens and localised innate immune responses, but the mechanisms that underlie these linkages are only beginning to be unravelled. METHODS AND PRINCIPAL FINDINGS Here we identify a strong signature of adaptive evolution on the DNA sequence of the mammalian stress response gene SEP53, a member of the epidermal differentiation complex fused-gene family known for its role in suppressing cancers. The SEP53 gene appears to have been subject to adaptive evolution of a type that is commonly (though not exclusively) associated with coevolutionary arms races. A similar pattern of molecular evolution was not evident in the p53 cancer-suppressing gene. CONCLUSIONS Our data thus raises the possibility that SEP53 is a component of the mucosal/epithelial innate immune response engaged in an ongoing interaction with a pathogen. Although the pathogenic stress mediating adaptive evolution of SEP53 is not known, there are a number of well-known candidates, in particular viruses with established links to carcinoma.
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Affiliation(s)
- Tom J Little
- Institute of Evolutionary Biology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom.
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