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Daron J, Bouafou L, Tennessen JA, Rahola N, Makanga B, Akone-Ella O, Ngangue MF, Longo Pendy NM, Paupy C, Neafsey DE, Fontaine MC, Ayala D. Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Along an Anthropogenic Gradient in Gabon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594472. [PMID: 38798379 PMCID: PMC11118577 DOI: 10.1101/2024.05.16.594472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Species distributed across heterogeneous environments often evolve locally adapted populations, but understanding how these persist in the presence of homogenizing gene flow remains puzzling. In Gabon, Anopheles coluzzii, a major African malaria mosquito is found along an ecological gradient, including a sylvatic population, away of any human presence. This study identifies into the genomic signatures of local adaptation in populations from distinct environments including the urban area of Libreville, and two proximate sites 10km apart in the La Lopé National Park (LLP), a village and its sylvatic neighborhood. Whole genome re-sequencing of 96 mosquitoes unveiled ∼ 5.7millions high-quality single nucleotide polymorphisms. Coalescent-based demographic analyses suggest an ∼ 8,000-year-old divergence between Libreville and La Lopé populations, followed by a secondary contact ( ∼ 4,000 ybp) resulting in asymmetric effective gene flow. The urban population displayed reduced effective size, evidence of inbreeding, and strong selection pressures for adaptation to urban settings, as suggested by the hard selective sweeps associated with genes involved in detoxification and insecticide resistance. In contrast, the two geographically proximate LLP populations showed larger effective sizes, and distinctive genomic differences in selective signals, notably soft-selective sweeps on the standing genetic variation. Although neutral loci and chromosomal inversions failed to discriminate between LLP populations, our findings support that microgeographic adaptation can swiftly emerge through selection on standing genetic variation despite high gene flow. This study contributes to the growing understanding of evolution of populations in heterogeneous environments amid ongoing gene flow and how major malaria mosquitoes adapt to human. Significance Anopheles coluzzii , a major African malaria vector, thrives from humid rainforests to dry savannahs and coastal areas. This ecological success is linked to its close association with domestic settings, with human playing significant roles in driving the recent urban evolution of this mosquito. Our research explores the assumption that these mosquitoes are strictly dependent on human habitats, by conducting whole-genome sequencing on An. coluzzii specimens from urban, rural, and sylvatic sites in Gabon. We found that urban mosquitoes show de novo genetic signatures of human-driven vector control, while rural and sylvatic mosquitoes exhibit distinctive genetic evidence of local adaptations derived from standing genetic variation. Understanding adaptation mechanisms of this mosquito is therefore crucial to predict evolution of vector control strategies.
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Dennis TPW, Essandoh J, Mable BK, Viana MS, Yawson AE, Weetman D. Signatures of adaptation at key insecticide resistance loci in Anopheles gambiae in Southern Ghana revealed by reduced-coverage WGS. Sci Rep 2024; 14:8650. [PMID: 38622230 PMCID: PMC11018624 DOI: 10.1038/s41598-024-58906-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Resistance to insecticides and adaptation to a diverse range of environments present challenges to Anopheles gambiae s.l. mosquito control efforts in sub-Saharan Africa. Whole-genome-sequencing is often employed for identifying the genomic basis underlying adaptation in Anopheles, but remains expensive for large-scale surveys. Reduced coverage whole-genome-sequencing can identify regions of the genome involved in adaptation at a lower cost, but is currently untested in Anopheles mosquitoes. Here, we use reduced coverage WGS to investigate population genetic structure and identify signatures of local adaptation in Anopheles mosquitoes across southern Ghana. In contrast to previous analyses, we find no structuring by ecoregion, with Anopheles coluzzii and Anopheles gambiae populations largely displaying the hallmarks of large, unstructured populations. However, we find signatures of selection at insecticide resistance loci that appear ubiquitous across ecoregions in An. coluzzii, and strongest in forest ecoregions in An. gambiae. Our study highlights resistance candidate genes in this region, and validates reduced coverage WGS, potentially to very low coverage levels, for population genomics and exploratory surveys for adaptation in Anopheles taxa.
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Affiliation(s)
- Tristan P W Dennis
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - John Essandoh
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Conservation Biology and Entomology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Barbara K Mable
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Mafalda S Viana
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Alexander E Yawson
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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Pichler V, Sanou A, Love RR, Caputo B, Pombi M, Toe KH, Guelbeogo MW, Sagnon N, Ferguson HM, Ranson H, Torre AD, Besansky NJ. A novel tetra-primer ARMS-PCR approach for the molecular karyotyping of chromosomal inversion 2Ru in the main malaria vectors Anopheles gambiae and Anopheles coluzzii. Parasit Vectors 2023; 16:388. [PMID: 37891582 PMCID: PMC10605393 DOI: 10.1186/s13071-023-06014-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Chromosomal inversion polymorphisms have been associated with adaptive behavioral, physiological, morphological and life history traits in the two main Afrotropical malaria vectors, Anopheles coluzzii and Anopheles gambiae. The understanding of the adaptive value of chromosomal inversion systems is constrained by the feasibility of cytological karyotyping. In recent years in silico and molecular approaches have been developed for the genotyping of most widespread inversions (2La, 2Rb and 2Rc). The 2Ru inversion, spanning roughly 8% of chromosome 2R, is commonly polymorphic in West African populations of An. coluzzii and An. gambiae and shows clear increases in frequency with increasing rainfall seasonally and geographically. The aim of this work was to overcome the constraints of currently available cytological and high-throughput molecular assays by developing a simple PCR assay for genotyping the 2Ru inversion in individual specimens of both mosquito species. METHODS We designed tetra-primer amplification refractory mutation system (ARMS)-PCR assays based on five tag single-nucleotide polymorphisms (SNPs) previously shown to be strongly correlated with 2Ru inversion orientation. The most promising assay was validated against laboratory and field samples of An. coluzzii and An. gambiae karyotyped either cytogenetically or molecularly using a genotyping-in-thousands by sequencing (GT-seq) high-throughput approach that employs targeted sequencing of multiplexed PCR amplicons. RESULTS A successful assay was designed based on the tag SNP at position 2R, 31710303, which is highly predictive of the 2Ru genotype. The assay, which requires only one PCR, and no additional post-PCR processing other than electrophoresis, produced a clear banding pattern for 98.5% of the 454 specimens tested, which is a 96.7% agreement with established karyotyping methods. Sequences were obtained for nine of the An. coluzzii specimens manifesting 2Ru genotype discrepancies with GT-seq. Possible sources of these discordances are discussed. CONCLUSIONS The tetra-primer ARMS-PCR assay represents an accurate, streamlined and cost-effective method for the molecular karyotyping of the 2Ru inversion in An. coluzzii and An. gambiae. Together with approaches already available for the other common polymorphic inversions, 2La, 2Rb and 2Rc, this assay will allow investigations of the adaptive value of the complex set of inversion systems observed in the two major malaria vectors in the Afrotropical region.
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Affiliation(s)
- Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy.
| | - Antoine Sanou
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
- Institute of Biodiversity, Animal Health & Comparative Medicine, Glasgow University, Glasgow, G128QQ, UK
| | - R Rebecca Love
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
- Entomology Branch, Division of Parasitic Diseases and Malaria, U.S. Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30333, USA
| | - Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy
| | - Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy
| | - Kobie Hyacinth Toe
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
| | - Moussa W Guelbeogo
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation Sur le Paludisme, Ouagadougou, Burkina Faso
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health & Comparative Medicine, Glasgow University, Glasgow, G128QQ, UK
| | - Hilary Ranson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur-Fondazione Cenci-Bolognetti, Università "La Sapienza", 00185, Rome, Italy
| | - Nora J Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
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Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Mol Ecol 2023. [PMID: 37843465 DOI: 10.1111/mec.17160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.
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Affiliation(s)
- James Reeve
- Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger K Butlin
- Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Eva L Koch
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Sean Stankowski
- Institute of Science and Technology - Austria, Klosterneuburg, Austria
| | - Rui Faria
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Brusentsov II, Gordeev MI, Yurchenko AA, Karagodin DA, Moskaev AV, Hodge JM, Burlak VA, Artemov GN, Sibataev AK, Becker N, Sharakhov IV, Baricheva EM, Sharakhova MV. Patterns of genetic differentiation imply distinct phylogeographic history of the mosquito species Anopheles messeae and Anopheles daciae in Eurasia. Mol Ecol 2023; 32:5609-5625. [PMID: 37702976 DOI: 10.1111/mec.17127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
Abstract
Detailed knowledge of phylogeography is important for control of mosquito species involved in the transmission of human infectious diseases. Anopheles messeae is a geographically widespread and genetically diverse dominant vector of malaria in Eurasia. A closely related species, An. daciae, was originally distinguished from An. messeae based on five nucleotide substitutions in its ribosomal DNA (rDNA). However, the patterns of phylogeographic history of these species in Eurasia remain poorly understood. Here, using internal transcribed spacer 2 (ITS2) of rDNA and karyotyping for the species identification we determined the composition of five Anopheles species in 28 locations in Eurasia. Based on the frequencies of 11 polymorphic chromosomal inversions used as genetic markers, a large-scale population genetics analysis was performed of 1932 mosquitoes identified as An. messeae, An. daciae and their hybrids. The largest genetic differences between the species were detected in the X sex chromosome suggesting a potential involvement of this chromosome in speciation. The frequencies of autosomal inversions in the same locations differed by 13%-45% between the species demonstrating a restricted gene flow between the species. Overall, An. messeae was identified as a diverse species with a more complex population structure than An. daciae. The clinal gradients in frequencies of chromosomal inversions were determined in both species implicating their possible involvement in climate adaptations. The frequencies of hybrids were low ~1% in northern Europe but high up to 50% in south-eastern populations. Thus, our study revealed critical differences in patterns of phylogeographic history between An. messeae and An. daciae in Eurasia. This knowledge will help to predict the potential of the malaria transmission in the northern territories of the continent.
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Affiliation(s)
- Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | | | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dimitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | | | - James M Hodge
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
| | - Vladimir A Burlak
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Gleb N Artemov
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Anuarbek K Sibataev
- Department of General Biology and Genomics, L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
- Department of Agricultural Biology, Tomsk State University, Tomsk, Russia
| | - Norbert Becker
- Center for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- German Mosquito Control Association, Speyer, Germany
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
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Small ST, Costantini C, Sagnon N, Guelbeogo MW, Emrich SJ, Kern AD, Fontaine MC, Besansky NJ. Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito. Proc Natl Acad Sci U S A 2023; 120:e2219835120. [PMID: 36881629 PMCID: PMC10089221 DOI: 10.1073/pnas.2219835120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 y ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 y ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variations implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes by suppressing recombination between opposing chromosomal orientations of the two ecotypes, while permitting free recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.
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Affiliation(s)
- Scott T. Small
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
| | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Scott J. Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Andrew D. Kern
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Michael C. Fontaine
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
| | - Nora J. Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
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Pollegioni P, Persampieri T, Minuz RL, Bucci A, Trusso A, Martino SD, Leo C, Bruttini M, Ciolfi M, Waldvogel A, Tripet F, Simoni A, Crisanti A, Müller R. Introgression of a synthetic sex ratio distortion transgene into different genetic backgrounds of Anopheles coluzzii. INSECT MOLECULAR BIOLOGY 2023; 32:56-68. [PMID: 36251429 PMCID: PMC10092091 DOI: 10.1111/imb.12813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The development of genetically modified mosquitoes (GMM) and their subsequent field release offers innovative approaches for vector control of malaria. A non-gene drive self-limiting male-bias Ag(PMB)1 strain has been developed in a 47-year-old laboratory G3 strain of Anopheles gambiae s.l. When Ag(PMB)1 males are crossed to wild-type females, expression of the endonuclease I-PpoI during spermatogenesis causes the meiotic cleavage of the X chromosome in sperm cells, leading to fertile offspring with a 95% male bias. However, World Health Organization states that the functionality of the transgene could differ when inserted in different genetic backgrounds of Anopheles coluzzii which is currently a predominant species in several West-African countries and thus a likely recipient for a potential release of self-limiting GMMs. In this study, we introgressed the transgene from the donor Ag(PMB)1 by six serial backcrosses into two recipient colonies of An. coluzzii that had been isolated in Mali and Burkina Faso. Scans of informative Single Nucleotide Polymorphism (SNP) markers and whole-genome sequencing analysis revealed a nearly complete introgression of chromosomes 3 and X, but a remarkable genomic divergence in a large region of chromosome 2 between the later backcrossed (BC6) transgenic offspring and the recipient paternal strains. These findings suggested to extend the backcrossing breeding strategy beyond BC6 generation and increasing the introgression efficiency of critical regions that have ecological and epidemiological implications through the targeted selection of specific markers. Disregarding differential introgression efficiency, we concluded that the phenotype of the sex ratio distorter is stable in the BC6 introgressed An. coluzzii strains.
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Affiliation(s)
- Paola Pollegioni
- Research Institute on Terrestrial EcosystemsNational Research CouncilTerniItaly
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Tania Persampieri
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Roxana L. Minuz
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Alessandro Bucci
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Alessandro Trusso
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Salvatore Di Martino
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Chiara Leo
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Marco Bruttini
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
- Tuscan Centre of Precision Medicine, Department of Medicine, Surgery and NeurosciencesUniversity of SienaSienaItaly
| | - Marco Ciolfi
- Research Institute on Terrestrial EcosystemsNational Research CouncilTerniItaly
| | | | - Frédéric Tripet
- Centre for Applied Entomology and ParasitologyKeele UniversityNewcastle‐under‐LymeUK
| | - Alekos Simoni
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
| | - Andrea Crisanti
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | - Ruth Müller
- Genetics and Ecology Research CentrePolo d'Innovazione di Genomica, Genetica e BiologiaTerniItaly
- Unit Entomology, Department of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
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8
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Sangbakembi-Ngounou C, Ngoagouni C, Akone-Ella O, Kengne P, Costantini C, Nakouné E, Ayala D. Temporal and biting dynamics of the chromosomal inversion 2La in the malaria vectors Anopheles gambiae and Anopheles coluzzii in Bangui, Central African Republic. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.986925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The chromosomal rearrangement 2La has been directly involved in the ecological and deadly epidemiological success of the malaria mosquitoes Anopheles gambiae and Anopheles coluzzii in sub-Saharan Africa. However, little is known about the biological and ecological factors that drive the local and temporal dynamics of this inversion in both species. Here, we performed a year-round longitudinal survey in Bangui, Central African Republic. We monthly sampled A. gambiae and A. coluzzii mosquitoes indoor and outdoor using human landing catches (HLC) for 48 h non-stop. We molecularly karyotyped all specimens to study the 2La inversion frequency variations, and monitored the mosquito spatial and temporal biting behavior throughout the year. In total, we successfully karyotyped 5121 A. gambiae and 986 A. coluzzii specimens. The 2La inversion frequency was higher in A. coluzzii than in A. gambiae across the year. In A. gambiae and A. coluzzii, the inversion frequency or karyotypes did not influence the biting behavior, either location or time. Moreover, the inversion frequency variation in both species was also independent of local climatic changes. Overall, our results revealed that in Bangui, the 2La inversion segregates at different frequency in each species, but this is not influenced by their trophic behavior. Studying the impact of urban settings and the population genetic structure of these two A. gambiae complex members could bring insights into the intrinsic relationship between 2La inversion and local conditions. More studies are needed to understand the polymorphic equilibrium of this inversion in Bangui.
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Graboyes M, Meta J, Clarke R. Mazingira and the malady of malaria: Perceptions of malaria as an environmental disease in contemporary Zanzibar. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2022; 95:134-144. [PMID: 36027656 DOI: 10.1016/j.shpsa.2022.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 02/25/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
This paper addresses how contemporary Zanzibaris perceive the relationship between the mazingira (roughly translated as "environment") and the malady of malaria. More broadly, this article presents data exploring Zanzibari conceptions of the mazingira, the relationship between the mazingira and malaria, and who Zanzibaris believe are responsible for acting on, or for, the mazingira in regards to malaria. We use the biomedical disease malaria-and the local syncretic understanding of it, which we recognize by referring to it as the "malady of malaria"-as a lens to investigate Zanzibari conceptions of the mazingira. We highlight the need to integrate local forms of knowledge, which we refer to as vernacular knowledge. 50 interviews show that Zanzibaris believe the mazingira can be modified in positive ways to cleaner, safer spaces that will also reduce malaria levels. People expressed widespread agreement that there is a clear relationship between the mazingira and the malady of malaria, though they differed in what exactly the relationship was.
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10
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Ayala D, Akone-Ella O, Kengne P, Johnson H, Heaton H, Collins J, Krasheninnikova K, Pelan S, Pointon DL, Sims Y, Torrance J, Tracey A, Uliano-Silva M, von Wyschetzki K, Wood J, McCarthy S, Neafsey D, Makunin A, Lawniczak M. The genome sequence of the malaria mosquito, Anopheles funestus, Giles, 1900. Wellcome Open Res 2022; 7:287. [PMID: 36874567 PMCID: PMC9975407.2 DOI: 10.12688/wellcomeopenres.18445.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
We present a genome assembly from an individual female Anopheles funestus (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 251 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
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Affiliation(s)
- Diego Ayala
- MIVEGEC, IRD, Montpellier, 34394, France
- ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Ousman Akone-Ella
- ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Pierre Kengne
- MIVEGEC, IRD, Montpellier, 34394, France
- ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Harriet Johnson
- Scientific Operations, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - James Torrance
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | | | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Shane McCarthy
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Daniel Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Alex Makunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Mara Lawniczak
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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Ayala D, Akone-Ella O, Kengne P, Johnson H, Heaton H, Collins J, Krasheninnikova K, Pelan S, Pointon DL, Sims Y, Torrance J, Tracey A, Uliano-Silva M, von Wyschetzki K, Wood J, McCarthy S, Neafsey D, Makunin A, Lawniczak M. The genome sequence of the malaria mosquito, Anopheles funestus, Giles, 1900. Wellcome Open Res 2022; 7:287. [PMID: 36874567 PMCID: PMC9975407 DOI: 10.12688/wellcomeopenres.18445.1] [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] [Accepted: 10/20/2022] [Indexed: 11/27/2022] Open
Abstract
We present a genome assembly from an individual female Anopheles funestus (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 251 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
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Affiliation(s)
- Diego Ayala
- MIVEGEC, IRD, Montpellier, 34394, France.,ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Ousman Akone-Ella
- ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Pierre Kengne
- MIVEGEC, IRD, Montpellier, 34394, France.,ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Harriet Johnson
- Scientific Operations, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - James Torrance
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | | | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Shane McCarthy
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Daniel Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Alex Makunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Mara Lawniczak
- Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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12
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Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Res 2021; 32:189-202. [PMID: 34965939 PMCID: PMC8744685 DOI: 10.1101/gr.275761.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has spread into the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments partly results from an increased tolerance to organic pollution and insecticides. Some of the molecular mechanisms for ecological adaptation are known, but the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. As a first step toward assessing the role of TEs in rapid urban adaptation, we sequenced using long reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated TEs in these genomes and in an additional high-quality An. coluzzii genome, and we identified 64 new TE families. TEs were nonrandomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity, and several TEs that may provide promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Overall, the analysis of multiple high-quality genomes allowed us to generate the most comprehensive TE annotation in this species to date and identify several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.
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Affiliation(s)
- Carlos Vargas-Chavez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Neil Michel Longo Pendy
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,École Doctorale Régional (EDR) en Infectiologie Tropicale d'Afrique Centrale, BP 876, Franceville, Gabon
| | - Sandrine E Nsango
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de Douala, BP 2701, Douala, Cameroun
| | - Laura Aguilera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Diego Ayala
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université Montpellier, CNRS, IRD, 64501 Montpellier, France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
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13
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Jayaswal V, Ndo C, Ma HC, Clifton BD, Pombi M, Cabrera K, Couhet A, Mouline K, Diabaté A, Dabiré R, Ayala D, Ranz JM. Intraspecific Transcriptome Variation and Sex-Biased Expression in Anopheles arabiensis. Genome Biol Evol 2021; 13:6357708. [PMID: 34432020 PMCID: PMC8449828 DOI: 10.1093/gbe/evab199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 01/17/2023] Open
Abstract
The magnitude and functional patterns of intraspecific transcriptional variation in the anophelines, including those of sex-biased genes underlying sex-specific traits relevant for malaria transmission, remain understudied. As a result, how changes in expression levels drive adaptation in these species is poorly understood. We sequenced the female, male, and larval transcriptomes of three populations of Anopheles arabiensis from Burkina Faso. One-third of the genes were differentially expressed between populations, often involving insecticide resistance-related genes in a sample type-specific manner, and with the females showing the largest number of differentially expressed genes. At the genomic level, the X chromosome appears depleted of differentially expressed genes compared with the autosomes, chromosomes harboring inversions do not exhibit evidence for enrichment of such genes, and genes that are top contributors to functional enrichment patterns of population differentiation tend to be clustered in the genome. Further, the magnitude of variation for the sex expression ratio across populations did not substantially differ between male- and female-biased genes, except for some populations in which male-limited expressed genes showed more variation than their female counterparts. In fact, female-biased genes exhibited a larger level of interpopulation variation than male-biased genes, both when assayed in males and females. Beyond uncovering the extensive adaptive potential of transcriptional variation in An. Arabiensis, our findings suggest that the evolutionary rate of changes in expression levels on the X chromosome exceeds that on the autosomes, while pointing to female-biased genes as the most variable component of the An. Arabiensis transcriptome.
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Affiliation(s)
- Vivek Jayaswal
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Cyrille Ndo
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Hsiu-Ching Ma
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, University of Rome "Sapienza", Rome, Italy
| | - Kevin Cabrera
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Anna Couhet
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - Karine Mouline
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Roch Dabiré
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Diego Ayala
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
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14
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da Silva SAS, de Lima-Filho PA, da Motta-Neto CC, da Costa GWWF, Cioffi MDB, Bertollo LAC, Molina WF. High chromosomal evolutionary dynamics in sleeper gobies (Eleotridae) and notes on disruptive biological factors in Gobiiformes karyotypes (Osteichthyes, Teleostei). MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:293-302. [PMID: 37073290 PMCID: PMC10077260 DOI: 10.1007/s42995-020-00084-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/15/2020] [Indexed: 05/03/2023]
Abstract
The order Gobiiformes is made up of more than 2200 species, representing one of the most diverse groups among teleost fishes. The biological causes for the tachytelic karyotype evolution of the gobies have not yet been fully studied. Here we expanded cytogenetic data for the Eleotridae family, analyzing the neotropical species Dormitator maculatus, Eleotris pisonis, Erotelis smaragdus, and Guavina guavina. In addition, a meta-analytical approach was followed for elucidating the karyotype diversification versus biological aspects (habitat and egg type) of the Gobiiformes. The species E. smaragdus and E. pisonis present 2n = 46 acrocentric chromosomes (NF = 46), D. maculatus 2n = 46 (36sm + 4st + 6a; NF = 86), and G. guavina, the most divergent karyotype, with 2n = 52 acrocentric chromosomes (NF = 52). Besides numeric and structural diversification in the karyotypes, the mapping of rDNAs and microsatellites also showed noticeable numerical and positional variation, supporting the high chromosomal evolutionary dynamism of these species. In Gobiiformes, karyotype patterns which are more divergent from the basal karyotype (2n = 46a) are associated with characteristics less effective to dispersion, such as the benthic habit. These adaptive characteristics, connected with the organization of the repetitive DNA content in the chromosomes, likely play a synergistic role in the remarkable karyotype diversification of this group.
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Affiliation(s)
- Simião Alefe Soares da Silva
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59.078-970 Brazil
| | | | - Clóvis Coutinho da Motta-Neto
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59.078-970 Brazil
| | | | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13.565-905 Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, SP 13.565-905 Brazil
| | - Wagner Franco Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59.078-970 Brazil
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15
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Maney DL, Merritt JR, Prichard MR, Horton BM, Yi SV. Inside the supergene of the bird with four sexes. Horm Behav 2020; 126:104850. [PMID: 32937166 PMCID: PMC7725849 DOI: 10.1016/j.yhbeh.2020.104850] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023]
Abstract
The white-throated sparrow (Zonotrichia albicollis) offers unique opportunities to understand the adaptive value of supergenes, particularly their role in alternative phenotypes. In this species, alternative plumage morphs segregate with a nonrecombining segment of chromosome 2, which has been called a 'supergene'. The species mates disassortatively with respect to the supergene; that is, each breeding pair consists of one individual with it and one without it. This species has therefore been called the "bird with four sexes". The supergene segregates with a behavioral phenotype; birds with it are more aggressive and less parental than birds without it. Here, we review our efforts to identify the genes inside the supergene that are responsible for the behavioral polymorphism. The gene ESR1, which encodes estrogen receptor α, differs between the morphs and predicts both territorial and parental behavior. Variation in the regulatory regions of ESR1 causes an imbalance in expression of the two alleles, and the degree to which this imbalance favors the supergene allele predicts territorial singing. In heterozygotes, knockdown of ESR1 causes a phenotypic switch, from more aggressive to less aggressive. We recently showed that another gene important for social behavior, vasoactive intestinal peptide (VIP), is differentially expressed between the morphs and predicts territorial singing. We hypothesize that ESR1 and VIP contribute to behavior in a coordinated way and could represent co-adapted alleles. Because the supergene contains more than 1000 individual genes, this species provides rich possibilities for discovering alleles that work together to mediate life-history trade-offs and maximize the fitness of alternative complex phenotypes.
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Affiliation(s)
- Donna L Maney
- Department of Psychology, Emory University, Atlanta, GA, USA.
| | | | | | - Brent M Horton
- Department of Biology, Millersville University, Millersville, PA, USA
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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16
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Nowling RJ, Manke KR, Emrich SJ. Detecting inversions with PCA in the presence of population structure. PLoS One 2020; 15:e0240429. [PMID: 33119626 PMCID: PMC7595445 DOI: 10.1371/journal.pone.0240429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI
| | - Krystal R. Manke
- Physics and Chemistry, Milwaukee School of Engineering, Milwaukee, WI
| | - Scott J. Emrich
- Electrical Engineering and Computer Science, University of Tennessee–Knoxville, Knoxville, TN
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17
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Lukindu M, Love RR, Guelbeogo MW, Small ST, Stephens MT, Campbell NR, Sagnon N, Costantini C, Besansky NJ. High-Throughput Genotyping of Common Chromosomal Inversions in the Afrotropical Malaria Mosquito Anopheles Funestus. INSECTS 2020; 11:E693. [PMID: 33065978 PMCID: PMC7650614 DOI: 10.3390/insects11100693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022]
Abstract
Polymorphic chromosomal inversions have been implicated in local adaptation. In anopheline mosquitoes, inversions also contribute to epidemiologically relevant phenotypes such as resting behavior. Progress in understanding these phenotypes and their mechanistic basis has been hindered because the only available method for inversion genotyping relies on traditional cytogenetic karyotyping, a rate-limiting and technically difficult approach that is possible only for the fraction of the adult female population at the correct gonotrophic stage. Here, we focus on an understudied malaria vector of major importance in sub-Saharan Africa, Anopheles funestus. We ascertain and validate tag single nucleotide polymorphisms (SNPs) using high throughput molecular assays that allow rapid inversion genotyping of the three most common An. funestus inversions at scale, overcoming the cytogenetic karyotyping barrier. These same inversions are the only available markers for distinguishing two An. funestus ecotypes that differ in indoor resting behavior, Folonzo and Kiribina. Our new inversion genotyping tools will facilitate studies of ecotypic differentiation in An. funestus and provide a means to improve our understanding of the roles of Folonzo and Kiribina in malaria transmission.
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Affiliation(s)
- Martin Lukindu
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - R. Rebecca Love
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
| | - Scott T. Small
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - Melissa T. Stephens
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | | | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
- 5 MIVEGEC, University of Montpellier, CNRS 5290, IRD 224, F-34394 Montpellier, France
| | - Nora J. Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
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18
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Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms. G3-GENES GENOMES GENETICS 2020; 10:3299-3307. [PMID: 32680855 PMCID: PMC7467005 DOI: 10.1534/g3.120.401418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs using two alternative high throughput molecular genotyping approaches vs. traditional cytogenetic karyotyping of the same 960 individual An. gambiae and An. coluzzii mosquitoes sampled from Burkina Faso, West Africa. We show that both molecular approaches yield comparable results, and that either one performs as well or better than cytogenetics in terms of genotyping accuracy. Given the ability of molecular genotyping approaches to be conducted at scale and at relatively low cost without restriction on mosquito sex or developmental stage, molecular genotyping via tag SNPs has the potential to revitalize research into the role of chromosomal inversions in the behavior and ongoing adaptation of An. gambiae and An. coluzzii to environmental heterogeneities.
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19
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Oomen RA, Kuparinen A, Hutchings JA. Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change. J Hered 2020; 111:319-332. [PMID: 32620014 PMCID: PMC7423069 DOI: 10.1093/jhered/esaa020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Anna Kuparinen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Jeffrey A Hutchings
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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20
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McKinney G, McPhee MV, Pascal C, Seeb JE, Seeb LW. Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon. G3 (BETHESDA, MD.) 2020; 10:1553-1561. [PMID: 32165371 PMCID: PMC7202013 DOI: 10.1534/g3.119.400972] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/28/2020] [Indexed: 11/26/2022]
Abstract
Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.
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Affiliation(s)
- Garrett McKinney
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Megan V McPhee
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
| | - Carita Pascal
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
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21
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Montanez-Gonzalez R, Pichler V, Calzetta M, Love RR, Vallera A, Schaecher L, Caputo B, Pombi M, Petrarca V, Della Torre A, Besansky NJ. Highly specific PCR-RFLP assays for karyotyping the widespread 2Rb inversion in malaria vectors of the Anopheles gambiae complex. Parasit Vectors 2020; 13:16. [PMID: 31924251 PMCID: PMC6954590 DOI: 10.1186/s13071-019-3877-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/30/2019] [Indexed: 01/29/2023] Open
Abstract
Background Chromosomal inversion polymorphisms play a role in adaptation to heterogeneous environments. Inversion polymorphisms are implicated in the very high ecological flexibility of the three main malaria vector species of the Afrotropical Anopheles gambiae complex, facilitating the exploitation of anthropogenic environmental modifications and promoting a strong association with humans. In addition to extending the species’ spatial and temporal distribution, inversions are associated with epidemiologically relevant mosquito behavior and physiology, underscoring their medical importance. We here present novel PCR-RFLP based assays strongly predictive of genotype for the cosmopolitan 2Rb inversion in An. coluzzii and An. gambiae, a development which overcomes the numerous constraints inherent to traditional cytological karyotyping. Methods We designed PCR-RFLP genotyping assays based on tag SNPs previously computationally identified as strongly predictive (> 95%) of 2Rb genotype. We targeted those tags whose alternative allelic states destroyed or created the recognition site of a commercially available restriction enzyme, and designed assays with distinctive cleavage profiles for each inversion genotype. The assays were validated on 251 An. coluzzii and 451 An. gambiae cytologically karyotyped specimens from nine countries across Africa and one An. coluzzii laboratory colony. Results For three tag SNPs, PCR-RFLP assays (denoted DraIII, MspAI, and TatI) reliably produced robust amplicons and clearly distinguishable electrophoretic profiles for all three inversion genotypes. Results obtained with the DraIII assay are ≥ 95% concordant with cytogenetic assignments in both species, while MspAI and TatI assays produce patterns highly concordant with cytogenetic assignments only in An. coluzzii or An. gambiae, respectively. Joint application of species-appropriate pairs of assays increased the concordance levels to > 99% in An. coluzzii and 98% in An. gambiae. Potential sources of discordance (e.g. imperfect association between tag and inversion, allelic dropout, additional polymorphisms in the restriction target site, incomplete or failed restriction digestion) are discussed. Conclusions The availability of highly specific, cost effective and accessible molecular assays for genotyping 2Rb in An. gambiae and An. coluzzii allows karyotyping of both sexes and all developmental stages. These novel tools will accelerate deeper investigations into the role of this ecologically and epidemiologically important chromosomal inversion in vector biology.![]()
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Affiliation(s)
- Raquel Montanez-Gonzalez
- Eck Institute for Global Health, & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Università "La Sapienza", Istituto Pasteur-Fondazione Cenci-Bolognetti, 00185, Rome, Italy
| | - Maria Calzetta
- Dipartimento di Sanità Pubblica e Malattie Infettive, Università "La Sapienza", Istituto Pasteur-Fondazione Cenci-Bolognetti, 00185, Rome, Italy
| | - Rachel R Love
- Eck Institute for Global Health, & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Alexandra Vallera
- Eck Institute for Global Health, & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Lydia Schaecher
- Eck Institute for Global Health, & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Università "La Sapienza", Istituto Pasteur-Fondazione Cenci-Bolognetti, 00185, Rome, Italy
| | - Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Università "La Sapienza", Istituto Pasteur-Fondazione Cenci-Bolognetti, 00185, Rome, Italy
| | - Vincenzo Petrarca
- Dipartimento di Sanità Pubblica e Malattie Infettive, Università "La Sapienza", Istituto Pasteur-Fondazione Cenci-Bolognetti, 00185, Rome, Italy
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Università "La Sapienza", Istituto Pasteur-Fondazione Cenci-Bolognetti, 00185, Rome, Italy.
| | - Nora J Besansky
- Eck Institute for Global Health, & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
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22
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Corbett-Detig RB, Said I, Calzetta M, Genetti M, McBroome J, Maurer NW, Petrarca V, Della Torre A, Besansky NJ. Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing. Genetics 2019; 213:1495-1511. [PMID: 31666292 PMCID: PMC6893396 DOI: 10.1534/genetics.119.302385] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/21/2019] [Indexed: 11/18/2022] Open
Abstract
Chromosomal inversions are fundamental drivers of genome evolution. In the main Afrotropical malaria vector species, belonging to the Anopheles gambiae species complex, inversions play an important role in local adaptation and have a rich history of cytological study. Despite the importance and ubiquity of some chromosomal inversions across the species complex, inversion breakpoints are often challenging to map molecularly due to the presence of large repetitive regions. Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions. We demonstrate that this approach is robust and likely to be widely applicable for both identification and fine-mapping inversion breakpoints in species whose inversions have heretofore been challenging to characterize. We apply our method to interrogate the previously unknown inversion breakpoints of 2Rbc and 2Rd in An. coluzzii We found that inversion breakpoints occur in large repetitive regions, and, strikingly, among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. These breakpoint-adjacent regions are strongly enriched for the presence of a 30 bp satellite repeat sequence. Because low frequency inversion breakpoints are not correlated with genomic regions containing this satellite, we suggest that interrupting this particular repeat may result in arrangements with higher relative fitness. Additionally, we use heterozygous individuals to quantitatively investigate the impacts of somatic pairing in the regions immediately surrounding inversion breakpoints. Finally, we discuss important considerations for possible applications of this approach for inversion breakpoint identification in a range of organisms.
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Affiliation(s)
- Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
- Genomics Institute, University of California Santa Cruz, California 95064
| | - Iskander Said
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Maria Calzetta
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Max Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Vincenzo Petrarca
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Indiana 46556
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23
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Holmes CJ, Benoit JB. Biological Adaptations Associated with Dehydration in Mosquitoes. INSECTS 2019; 10:insects10110375. [PMID: 31661928 PMCID: PMC6920799 DOI: 10.3390/insects10110375] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/05/2022]
Abstract
Diseases that are transmitted by mosquitoes are a tremendous health and socioeconomic burden with hundreds of millions of people being impacted by mosquito-borne illnesses annually. Many factors have been implicated and extensively studied in disease transmission dynamics, but knowledge regarding how dehydration impacts mosquito physiology, behavior, and resulting mosquito-borne disease transmission remain underdeveloped. The lapse in understanding on how mosquitoes respond to dehydration stress likely obscures our ability to effectively study mosquito physiology, behavior, and vectorial capabilities. The goal of this review is to develop a profile of factors underlying mosquito biology that are altered by dehydration and the implications that are related to disease transmission.
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Affiliation(s)
- Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
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24
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Antonio-Nkondjio C, Ndo C, Njiokou F, Bigoga JD, Awono-Ambene P, Etang J, Ekobo AS, Wondji CS. Review of malaria situation in Cameroon: technical viewpoint on challenges and prospects for disease elimination. Parasit Vectors 2019; 12:501. [PMID: 31655608 PMCID: PMC6815446 DOI: 10.1186/s13071-019-3753-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/18/2019] [Indexed: 11/30/2022] Open
Abstract
Malaria still has a devastating impact on public health and welfare in Cameroon. Despite the increasing number of studies conducted on disease prevalence, transmission patterns or treatment, there are to date, not enough studies summarising findings from previous works in order to identify gaps in knowledge and areas of interest where further evidence is needed to drive malaria elimination efforts. The present study seeks to address these gaps by providing a review of studies conducted so far on malaria in Cameroon since the 1940s to date. Over 250 scientific publications were consulted for this purpose. Although there has been increased scale-up of vector control interventions which significantly reduced the morbidity and mortality to malaria across the country from a prevalence of 41% of the population reporting at least one malaria case episode in 2000 to a prevalence of 24% in 2017, the situation is not yet under control. There is a high variability in disease endemicity between epidemiological settings with prevalence of Plasmodium parasitaemia varying from 7 to 85% in children aged 6 months to 15 years after long-lasting insecticidal nets (LLINs) scale-up. Four species of Plasmodium have been recorded across the country: Plasmodium falciparum, P. malariae, P. ovale and P. vivax. Several primate-infecting Plasmodium spp. are also circulating in Cameroon. A decline of artemisinin-based combinations therapeutic efficacy from 97% in 2006 to 90% in 2016 have been reported. Several mutations in the P. falciparum chloroquine resistance (Pfcrt) and P. falciparum multidrug resistance 1 (Pfmdr1) genes conferring resistance to either 4-amino-quinoleine, mefloquine, halofanthrine and quinine have been documented. Mutations in the Pfdhfr and Pfdhps genes involved in sulfadoxine-pyrimethamine are also on the rise. No mutation associated with artemisinin resistance has been recorded. Sixteen anopheline species contribute to malaria parasite transmission with six recognized as major vectors: An. gambiae, An. coluzzii, An. arabiensis, An. funestus, An. nili and An. moucheti. Studies conducted so far, indicated rapid expansion of DDT, pyrethroid and carbamate resistance in An. gambiae, An. coluzzii, An. arabiensis and An. funestus threatening the performance of LLINs. This review highlights the complex situation of malaria in Cameroon and the need to urgently implement and reinforce integrated control strategies in different epidemiological settings, as part of the substantial efforts to consolidate gains and advance towards malaria elimination in the country.
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Affiliation(s)
- Christophe Antonio-Nkondjio
- Laboratoire de Recherche sur le Paludisme, Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), B. P.288 Yaoundé, Cameroun
- Centre for Research in Infectious Disease (CRID), P.O. Box 13591, Yaoundé, Cameroon
- Vector Biology Liverpool School of Tropical medicine Pembroke Place, Liverpool, UK
| | - Cyrille Ndo
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, P.O. Box 24157, Douala, Cameroon
- Centre for Research in Infectious Disease (CRID), P.O. Box 13591, Yaoundé, Cameroon
| | - Flobert Njiokou
- Centre for Research in Infectious Disease (CRID), P.O. Box 13591, Yaoundé, Cameroon
- Faculty of Sciences, University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Jude D. Bigoga
- Laboratory for Vector Biology and control, National Reference Unit for Vector Control, The Biotechnology Center, Nkolbisson-University of Yaounde I, P.O. Box 3851, Messa, Yaounde, Cameroon
- Department of Biochemistry, Faculty of Science, University of Yaounde I, Yaounde, Cameroon
| | - Parfait Awono-Ambene
- Laboratoire de Recherche sur le Paludisme, Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), B. P.288 Yaoundé, Cameroun
| | - Josiane Etang
- Laboratoire de Recherche sur le Paludisme, Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), B. P.288 Yaoundé, Cameroun
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, P.O. Box 24157, Douala, Cameroon
- Institute for Insect Biotechnology, Justus Liebig University Gießen, Winchester Str. 2, 35394 Gießen, Germany
| | - Albert Same Ekobo
- Faculty of Sciences, University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Charles S. Wondji
- Centre for Research in Infectious Disease (CRID), P.O. Box 13591, Yaoundé, Cameroon
- Vector Biology Liverpool School of Tropical medicine Pembroke Place, Liverpool, UK
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25
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Barrón MG, Paupy C, Rahola N, Akone-Ella O, Ngangue MF, Wilson-Bahun TA, Pombi M, Kengne P, Costantini C, Simard F, González J, Ayala D. A new species in the major malaria vector complex sheds light on reticulated species evolution. Sci Rep 2019; 9:14753. [PMID: 31611571 PMCID: PMC6791875 DOI: 10.1038/s41598-019-49065-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
Complexes of closely related species provide key insights into the rapid and independent evolution of adaptive traits. Here, we described and studied Anopheles fontenillei sp.n., a new species in the Anopheles gambiae complex that we recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. Particularly, we detected recent introgression, with Anopheles gambiae and Anopheles coluzzii, of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species allowed us to clarify the evolutionary history of the 3La inversion. Overall, An. fontenillei sp.n. analysis improved our understanding of the relationship between species within the An. gambiae complex, and provided insight into the evolution of vectorial capacity traits that are relevant for the successful control of malaria in Africa.
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Affiliation(s)
| | | | - Nil Rahola
- MIVEGEC, IRD, CNRS, Univ. Montpellier, Montpellier, France.,CIRMF, Franceville, Gabon
| | | | | | | | | | - Pierre Kengne
- MIVEGEC, IRD, CNRS, Univ. Montpellier, Montpellier, France
| | | | | | | | - Diego Ayala
- MIVEGEC, IRD, CNRS, Univ. Montpellier, Montpellier, France. .,CIRMF, Franceville, Gabon.
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26
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Love RR, Redmond SN, Pombi M, Caputo B, Petrarca V, Della Torre A, Besansky NJ. In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae Complex. G3 (BETHESDA, MD.) 2019; 9:3249-3262. [PMID: 31391198 PMCID: PMC6778791 DOI: 10.1534/g3.119.400445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/30/2019] [Indexed: 01/13/2023]
Abstract
Chromosomal inversion polymorphisms play an important role in adaptation to environmental heterogeneities. For mosquito species in the Anopheles gambiae complex that are significant vectors of human malaria, paracentric inversion polymorphisms are abundant and are associated with ecologically and epidemiologically important phenotypes. Improved understanding of these traits relies on determining mosquito karyotype, which currently depends upon laborious cytogenetic methods whose application is limited both by the requirement for specialized expertise and for properly preserved adult females at specific gonotrophic stages. To overcome this limitation, we developed sets of tag single nucleotide polymorphisms (SNPs) inside inversions whose biallelic genotype is strongly correlated with inversion genotype. We leveraged 1,347 fully sequenced An. gambiae and Anopheles coluzzii genomes in the Ag1000G database of natural variation. Beginning with principal components analysis (PCA) of population samples, applied to windows of the genome containing individual chromosomal rearrangements, we classified samples into three inversion genotypes, distinguishing homozygous inverted and homozygous uninverted groups by inclusion of the small subset of specimens in Ag1000G that are associated with cytogenetic metadata. We then assessed the correlation between candidate tag SNP genotypes and PCA-based inversion genotypes in our training sets, selecting those candidates with >80% agreement. Our initial tests both in held-back validation samples from Ag1000G and in data independent of Ag1000G suggest that when used for in silico inversion genotyping of sequenced mosquitoes, these tags perform better than traditional cytogenetics, even for specimens where only a small subset of the tag SNPs can be successfully ascertained.
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Affiliation(s)
- R Rebecca Love
- Eck Institute for Global Health & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Seth N Redmond
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142
| | - Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Vincenzo Petrarca
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Nora J Besansky
- Eck Institute for Global Health & Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
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27
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Yang Z, Ge X, Yang Z, Qin W, Sun G, Wang Z, Li Z, Liu J, Wu J, Wang Y, Lu L, Wang P, Mo H, Zhang X, Li F. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nat Commun 2019; 10:2989. [PMID: 31278252 PMCID: PMC6611876 DOI: 10.1038/s41467-019-10820-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/03/2019] [Indexed: 01/28/2023] Open
Abstract
Multiple cotton genomes (diploid and tetraploid) have been assembled. However, genomic variations between cultivars of allotetraploid upland cotton (Gossypium hirsutum L.), the most widely planted cotton species in the world, remain unexplored. Here, we use single-molecule long read and Hi-C sequencing technologies to assemble genomes of the two upland cotton cultivars TM-1 and zhongmiansuo24 (ZM24). Comparisons among TM-1 and ZM24 assemblies and the genomes of the diploid ancestors reveal a large amount of genetic variations. Among them, the top three longest structural variations are located on chromosome A08 of the tetraploid upland cotton, which account for ~30% total length of this chromosome. Haplotype analyses of the mapping population derived from these two cultivars and the germplasm panel show suppressed recombination rates in this region. This study provides additional genomic resources for the community, and the identified genetic variations, especially the reduced meiotic recombination on chromosome A08, will help future breeding.
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Affiliation(s)
- Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ji Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ye Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lili Lu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Peng Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Huijuan Mo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xueyan Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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28
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Thawornwattana Y, Dalquen D, Yang Z. Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex. Mol Biol Evol 2019; 35:2512-2527. [PMID: 30102363 PMCID: PMC6188554 DOI: 10.1093/molbev/msy158] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep coalescence and introgression make it challenging to infer phylogenetic relationships among closely related species that arose through radiative speciation events. Despite numerous phylogenetic analyses and the availability of whole genomes, the phylogeny in the Anopheles gambiae species complex has not been confidently resolved. Here we extract over 80, 000 coding and noncoding short segments (called loci) from the genomes of six members of the species complex and use a Bayesian method under the multispecies coalescent model to infer the species tree, which takes into account genealogical heterogeneity across the genome and uncertainty in the gene trees. We obtained a robust estimate of the species tree from the distal region of the X chromosome: (A. merus, ((A. melas, (A. arabiensis, A. quadriannulatus)), (A. gambiae, A. coluzzii))), with A. merus to be the earliest branching species. This species tree agrees with the chromosome inversion phylogeny and provides a parsimonious interpretation of inversion and introgression events. Simulation informed by the real data suggest that the coalescent approach is reliable while the sliding-window analysis used in a previous phylogenomic study generates artifactual species trees. Likelihood ratio test of gene flow revealed strong evidence of autosomal introgression from A. arabiensis into A. gambiae (at the average rate of ∼0.2 migrants per generation), but not in the opposite direction, and introgression of the 3 L chromosomal region from A. merus into A. quadriannulatus. Our results highlight the importance of accommodating incomplete lineage sorting and introgression in phylogenomic analyses of species that arose through recent radiative speciation events.
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Affiliation(s)
- Yuttapong Thawornwattana
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Daniel Dalquen
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Radcliffe Institute for Advanced Studies, Harvard University, Cambridge, MA
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29
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Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ. A chromosome-scale assembly of the major African malaria vector Anopheles funestus. Gigascience 2019; 8:giz063. [PMID: 31157884 PMCID: PMC6545970 DOI: 10.1093/gigascience/giz063] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/28/2019] [Accepted: 05/06/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Anopheles funestus is one of the 3 most consequential and widespread vectors of human malaria in tropical Africa. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis in this important mosquito. FINDINGS Here we present a new high-quality A. funestus reference genome (AfunF3) assembled using 240× coverage of long-read single-molecule sequencing for contigging, combined with 100× coverage of short-read Hi-C data for chromosome scaffolding. The assembled contigs total 446 Mbp of sequence and contain substantial duplication due to alternative alleles present in the sequenced pool of mosquitos from the FUMOZ colony. Using alignment and depth-of-coverage information, these contigs were deduplicated to a 211 Mbp primary assembly, which is closer to the expected haploid genome size of 250 Mbp. This primary assembly consists of 1,053 contigs organized into 3 chromosome-scale scaffolds with an N50 contig size of 632 kbp and an N50 scaffold size of 93.811 Mbp, representing a 100-fold improvement in continuity versus the current reference assembly, AfunF1. CONCLUSION This highly contiguous and complete A. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.
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Affiliation(s)
- Jay Ghurye
- Department of Computer Science, University of Maryland, 8125 Paint Branch Drive, College Park, MD 20742, USA
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Scott T Small
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Science Center, Notre Dame, IN 46556, USA
| | - Seth Redmond
- Infectious Disease and Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Paul Howell
- Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Science Center, Notre Dame, IN 46556, USA
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30
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Mérot C, Berdan EL, Babin C, Normandeau E, Wellenreuther M, Bernatchez L. Intercontinental karyotype-environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly. Proc Biol Sci 2019; 285:rspb.2018.0519. [PMID: 29925615 PMCID: PMC6030540 DOI: 10.1098/rspb.2018.0519] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialization. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic, assess which environmental conditions modulate the inversion karyotype frequencies, and document the relationship between inversion karyotype and adult size. We sampled nearly 2000 flies from 20 populations along several environmental gradients to quantify associations of inversion frequencies to heterogeneous environmental variables. Genotyping and phenotyping showed a widespread and conserved inversion polymorphism between Europe and America. Variation in inversion frequency was significantly associated with environmental factors, with parallel patterns between continents, indicating that the inversion may play a role in local adaptation. The three karyotypes of the inversion are differently favoured across micro-habitats and represent life-history strategies likely to be maintained by the collective action of several mechanisms of balancing selection. Our study adds to the mounting evidence that inversions are facilitators of adaptation and enhance within-species diversity.
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Affiliation(s)
- Claire Mérot
- Département de biologie, Université Laval, Quebec, Canada
| | - Emma L Berdan
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Charles Babin
- Département de biologie, Université Laval, Quebec, Canada
| | | | - Maren Wellenreuther
- School of Biological Sciences, University of Auckland, New Zealand.,Seafood Research Unit, Port Nelson, Nelson, New Zealand
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31
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Batista MRD, Penha RES, Sofia SH, Klaczko LB. Comparative analysis of adaptive and neutral markers of Drosophila mediopunctata populations dispersed among forest fragments. Ecol Evol 2018; 8:12681-12693. [PMID: 30619573 PMCID: PMC6308856 DOI: 10.1002/ece3.4696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 11/26/2022] Open
Abstract
Comparison of adaptive and neutral genetic markers is a valuable approach to characterize the evolutionary consequences of populations living in environments threatened by anthropogenic disturbances, such as forest fragmentation. Shifts in allele frequencies, low genetic variability, and a small effective population size can be considered clear signs of forest fragmentation effects (due to genetic drift) over natural populations, while adaptive responses correlate with environmental variables. Brazilian Atlantic Forest had its landscape drastically reduced and fragmented. Now, several forest remnants are isolated from each other by urban and crop areas. We sampled Drosophila mediopunctata populations from eight forest remnants dispersed on two adjacent geomorphological regions, which are physiognomic and climatically quite distinct. Microsatellite data of inversion-free chromosomes (neutral genetic marker) indicate low structuration among populations suggesting that they were panmictic and greatly influenced by gene flow. Moreover, significant differences in chromosomal inversion frequencies (adaptive genetic marker) among populations and their correlations with climatic and geographical variables indicate that genetic divergence among populations could be an adaptive response to their environment. Nonetheless, we observed a significant difference in inversion frequencies of a population in two consecutive years that may be associated with edge and demographic effects. Also, it may be reflecting seasonal changes of inversion frequencies influenced by great temperature variation due to edge effects. Moreover, the forest fragment size does not affect genetic variation of neutral markers. Our data indicate that despite oscillations in chromosomal inversion frequencies, D. mediopunctata populations from Brazilian Atlantic Forest and their divergence may be driven by adaptive factors to local differences, perhaps because it is a small flying insect easily carried by the wind increasing its migration rates.
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Affiliation(s)
- Marcos R. D. Batista
- Departamento de Genética, Evolução, Microbiologia e ImunologiaInstituto de Biologia, Universidade Estadual de Campinas – UnicampCampinasSPBrasil
| | - Rafael E. S. Penha
- Departamento de Genética, Evolução, Microbiologia e ImunologiaInstituto de Biologia, Universidade Estadual de Campinas – UnicampCampinasSPBrasil
| | - Silvia H. Sofia
- Departamento de Biologia Geral, Centro de Ciências BiológicasUniversidade Estadual de LondrinaLondrinaPRBrasil
| | - Louis B. Klaczko
- Departamento de Genética, Evolução, Microbiologia e ImunologiaInstituto de Biologia, Universidade Estadual de Campinas – UnicampCampinasSPBrasil
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Pombi M, Calzetta M, Guelbeogo WM, Manica M, Perugini E, Pichler V, Mancini E, Sagnon N, Ranson H, Della Torre A. Unexpectedly high Plasmodium sporozoite rate associated with low human blood index in Anopheles coluzzii from a LLIN-protected village in Burkina Faso. Sci Rep 2018; 8:12806. [PMID: 30143698 PMCID: PMC6109043 DOI: 10.1038/s41598-018-31117-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 08/10/2018] [Indexed: 12/27/2022] Open
Abstract
Despite the effectiveness of mass distribution of long-lasting insecticidal nets (LLINs) in reducing malaria transmission in Africa, in hyperendemic areas such as Burkina Faso the burden of malaria remains high. We here report the results of a 4-month survey on the feeding habits and Plasmodium infection in malaria vectors from a village in Burkina Faso one year following a national LLIN distribution programme. Low values of human blood index (HBI) observed in the major malaria vectors in the area (Anopheles coluzzii: N = 263, 20.1%; An. arabiensis: 5.8%, N = 103) are consistent with the hypothesis that LLINs reduced the availability of human hosts to mosquitoes. A regression meta-analysis of data from a systematic review of published studies reporting HBI and sporozoite rates (SR) for An. gambiae complex revealed that the observed SR values (An. coluzzii: 7.6%, N = 503; An. arabiensis: 5.3%, N = 225) are out of the ranges expected based on the low HBI observed. We hypothesize that a small fraction of inhabitants unprotected by bednets acts as a "core group" repeatedly exposed to mosquito bites, representing the major Plasmodium reservoir for the vectors, able to maintain a high risk of transmission even in a village protected by LLINs.
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Affiliation(s)
- Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, 00185, Italy.
| | - Maria Calzetta
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, 00185, Italy
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, 01 BP 2208, Burkina Faso
| | - Mattia Manica
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, 00185, Italy
- Dipartimento di Biodiversità ed Ecologia Molecolare, Centro Ricerca e Innovazione, Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Eleonora Perugini
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, 00185, Italy
| | - Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, 00185, Italy
| | - Emiliano Mancini
- Università di "Roma Tre", Dipartimento di Scienze, Rome, 00154, Italy
| | - N'Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, 01 BP 2208, Burkina Faso
| | - Hilary Ranson
- Liverpool School of Tropical Medicine, Department of Vector Biology, Liverpool, L3 5QA, UK
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, 00185, Italy
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33
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Cheng C, Tan JC, Hahn MW, Besansky NJ. Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae. Proc Natl Acad Sci U S A 2018; 115:E7005-E7014. [PMID: 29987007 PMCID: PMC6064990 DOI: 10.1073/pnas.1806760115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inversion polymorphisms in the African malaria vector Anopheles gambiae segregate along climatic gradients of aridity. Despite indirect evidence of their adaptive significance, little is known of the phenotypic targets of selection or the underlying genetic mechanisms. Here we adopt a systems genetics approach to explore the interaction of two inversions on opposite arms of chromosome 2 with gender, climatic conditions, and one another. We measure organismal traits and transcriptional profiles in 8-d-old adults of both sexes and four alternative homokaryotypic classes reared under two alternative climatic regimes. We show that karyotype strongly influences both organismal traits and transcriptional profiles but that the strength and direction of the effects depend upon complex interactions with gender and environmental conditions and between inversions on independent arms. Our data support the suppressed recombination model for the role of inversions in local adaptation, and-supported by transcriptional and physiological measurements following perturbation with the drug rapamycin-suggest that one mechanism underlying their adaptive role may be the maintenance of energy homeostasis.
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Affiliation(s)
- Changde Cheng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - John C Tan
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Computer Science, Indiana University, Bloomington, IN 47405
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556;
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
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34
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Eco-Evolutionary Genomics of Chromosomal Inversions. Trends Ecol Evol 2018; 33:427-440. [DOI: 10.1016/j.tree.2018.04.002] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/17/2023]
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35
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Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes. BMC Genomics 2018; 19:96. [PMID: 29764366 PMCID: PMC5954271 DOI: 10.1186/s12864-018-4466-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. Results We present a computational method, ADseq, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADseq provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADseq to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. Conclusions We demonstrate the method’s ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression. Electronic supplementary material The online version of this article (10.1186/s12864-018-4466-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoann Anselmetti
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France
| | - Wandrille Duchemin
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.,INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France
| | - Eric Tannier
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.,INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, V5A1S6, BC, Canada
| | - Sèverine Bérard
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.
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36
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Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements inDrosophila pseudoobscura. Mol Ecol 2017; 26:6539-6562. [DOI: 10.1111/mec.14381] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/04/2017] [Accepted: 10/07/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Zachary L. Fuller
- Department of Biology; 208 Erwin W. Mueller Laboratory; The Pennsylvania State University; University Park PA USA
| | - Gwilym D. Haynes
- Department of Biology; 208 Erwin W. Mueller Laboratory; The Pennsylvania State University; University Park PA USA
| | - Stephen Richards
- Human Genome Sequencing Center; Baylor College of Medicine; Houston TX USA
| | - Stephen W. Schaeffer
- Department of Biology; 208 Erwin W. Mueller Laboratory; The Pennsylvania State University; University Park PA USA
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