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Keven JB, Vinit R, Katusele M, Reimer LJ, Zimmerman PA, Karl S, Walker ED. Genetic differentiation and bottleneck effects in the malaria vectors Anopheles farauti and Anopheles punctulatus after an LLIN-based vector control program in Papua New Guinea. Ecol Evol 2024; 14:e10917. [PMID: 38371856 PMCID: PMC10869881 DOI: 10.1002/ece3.10917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
Implementation of long-lasting insecticide-treated net (LLIN) programs to control human malaria transmission leads to substantial reductions in the abundance of Anopheles mosquitoes, but the impact on the population genetic structure of the malaria vectors is poorly known, nor has it been investigated in Papua New Guinea, where malaria is highly endemic and where several species of Anopheles have vector roles. Here, we applied Wright's F-statistic, analysis of molecular variance, Bayesian structure analysis, and discriminant analysis of principle components to microsatellite genotype data to analyze the population genetic structure of Anopheles farauti between and within the northern and southern lowland plains and of Anopheles punctulatus within the northern plain of Papua New Guinea after such a program. Bottleneck effects in the two malaria vectors were analyzed using Luikart and Cornuet's tests of heterozygosity. A large, panmictic population of An. punctulatus pre-LLIN program diverged into two subregional populations corresponding to Madang and East Sepik provinces post-LLIN distribution and experienced a genetic bottleneck during this process. By contrast, the An. farauti population existed as two regional populations isolated by mountain ranges pre-LLIN, a genetic structure that persisted after the distribution of LLINs with no further geographic differentiation nor evidence of a genetic bottleneck. These findings show the differential response of populations of different vector species to interventions, which has implications for program sustainability and gene flow.
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Affiliation(s)
- John B. Keven
- Department of Population Health and Disease Prevention, Program in Public HealthUniversity of California‐IrvineIrvineCaliforniaUSA
- Department of EntomologyMichigan State UniversityEast LansingMichiganUSA
- Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingMichiganUSA
- Vector‐borne Diseases UnitPapua New Guinea Institute of Medical ResearchMadangMadang ProvincePapua New Guinea
| | - Rebecca Vinit
- Vector‐borne Diseases UnitPapua New Guinea Institute of Medical ResearchMadangMadang ProvincePapua New Guinea
| | - Michelle Katusele
- Vector‐borne Diseases UnitPapua New Guinea Institute of Medical ResearchMadangMadang ProvincePapua New Guinea
| | - Lisa J. Reimer
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
| | - Peter A. Zimmerman
- Center for Global Health and Diseases, Pathology DepartmentCase Western Reserve UniversityClevelandOhioUSA
| | - Stephan Karl
- Vector‐borne Diseases UnitPapua New Guinea Institute of Medical ResearchMadangMadang ProvincePapua New Guinea
- Australian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQueenslandAustralia
| | - Edward D. Walker
- Department of EntomologyMichigan State UniversityEast LansingMichiganUSA
- Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingMichiganUSA
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de Melo ES, Wallau GL. Mosquito genomes are frequently invaded by transposable elements through horizontal transfer. PLoS Genet 2020; 16:e1008946. [PMID: 33253164 PMCID: PMC7728395 DOI: 10.1371/journal.pgen.1008946] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/10/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that parasitize basically all eukaryotic species genomes. Due to their complexity, an in-depth TE characterization is only available for a handful of model organisms. In the present study, we performed a de novo and homology-based characterization of TEs in the genomes of 24 mosquito species and investigated their mode of inheritance. More than 40% of the genome of Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus is composed of TEs, while it varied substantially among Anopheles species (0.13%-19.55%). Class I TEs are the most abundant among mosquitoes and at least 24 TE superfamilies were found. Interestingly, TEs have been extensively exchanged by horizontal transfer (172 TE families of 16 different superfamilies) among mosquitoes in the last 30 million years. Horizontally transferred TEs represents around 7% of the genome in Aedes species and a small fraction in Anopheles genomes. Most of these horizontally transferred TEs are from the three ubiquitous LTR superfamilies: Gypsy, Bel-Pao and Copia. Searching more than 32,000 genomes, we also uncovered transfers between mosquitoes and two different Phyla-Cnidaria and Nematoda-and two subphyla-Chelicerata and Crustacea, identifying a vector, the worm Wuchereria bancrofti, that enabled the horizontal spread of a Tc1-mariner element among various Anopheles species. These data also allowed us to reconstruct the horizontal transfer network of this TE involving more than 40 species. In summary, our results suggest that TEs are frequently exchanged by horizontal transfers among mosquitoes, influencing mosquito's genome size and variability.
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Affiliation(s)
- Elverson Soares de Melo
- Department of Entomology, Aggeu Magalhães Institute–Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Gabriel Luz Wallau
- Department of Entomology, Aggeu Magalhães Institute–Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
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Ruzzante L, Reijnders MJ, Waterhouse RM. Of Genes and Genomes: Mosquito Evolution and Diversity. Trends Parasitol 2019; 35:32-51. [DOI: 10.1016/j.pt.2018.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022]
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Wiegmann BM, Richards S. Genomes of Diptera. CURRENT OPINION IN INSECT SCIENCE 2018; 25:116-124. [PMID: 29602357 DOI: 10.1016/j.cois.2018.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.
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Affiliation(s)
- Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, United States.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77006, United States
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Lequime S, Lambrechts L. Discovery of flavivirus-derived endogenous viral elements in Anopheles mosquito genomes supports the existence of Anopheles-associated insect-specific flaviviruses. Virus Evol 2017; 3:vew035. [PMID: 28078104 PMCID: PMC5217911 DOI: 10.1093/ve/vew035] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Flavivirus genus encompasses several arboviruses of public health significance such as dengue, yellow fever, and Zika viruses. It also includes insect-specific flaviviruses (ISFs) that are only capable of infecting insect hosts. The vast majority of mosquito-infecting flaviviruses have been associated with mosquito species of the Aedes and Culex genera in the Culicinae subfamily, which also includes most arbovirus vectors. Mosquitoes of the Anophelinae subfamily are not considered significant arbovirus vectors; however, flaviviruses have occasionally been detected in field-caught Anopheles specimens. Whether such observations reflect occasional spillover or laboratory contamination or whether Anopheles mosquitoes are natural hosts of flaviviruses is unknown. Here, we provide in silico and in vivo evidence of transcriptionally active, flavivirus-derived endogenous viral elements (EVEs) in the genome of Anopheles minimus and Anopheles sinensis. Such non-retroviral endogenization of RNA viruses is consistent with a shared evolutionary history between flaviviruses and Anopheles mosquitoes. Phylogenetic analyses of the two newly described EVEs support the existence of a distinct clade of Anopheles-associated ISFs.
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Affiliation(s)
- Sebastian Lequime
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France; University Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
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St Laurent B, Supratman S, Asih PBS, Bretz D, Mueller J, Miller HC, Baharuddin A, Shinta, Surya A, Ngai M, Laihad F, Syafruddin D, Hawley WA, Collins FH, Lobo NF. Behaviour and molecular identification of Anopheles malaria vectors in Jayapura district, Papua province, Indonesia. Malar J 2016; 15:192. [PMID: 27060058 PMCID: PMC4826537 DOI: 10.1186/s12936-016-1234-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the Anopheles punctulatus group dominate Papua, Indonesia and Papua New Guinea (PNG), with a geographic range that extends south through Vanuatu. An. farauti and An. punctulatus are the presumed major vectors in this region. Although this group of species has been extensively studied in PNG and the southern archipelagoes within their range, their distribution, ecology and vector behaviours have not been well characterized in eastern Indonesia. METHODS Mosquitoes were collected in five villages in Jayapura province, Papua, Indonesia using human-landing collections, animal-baited tents and backpack aspirators. Mosquitoes were morphologically typed and then molecularly distinguished based on ribosomal ITS2 sequences and tested for Plasmodium falciparum and P. vivax infection using circumsporozoite ELISA and PCR. RESULTS The presence and vector status of An. farauti 4 in Papua, Indonesia is confirmed here for the first time. The data indicate that this species is entering houses at a rate that increases its potential to come into contact with humans and act as a major malaria vector. An. farauti 4 was also abundant outdoors and biting humans during early evening hours. Other species collected in this area include An. farauti 1, An. hinesorum, An. koliensis, An. punctulatus, and An. tessellatus. Proboscis morphology was highly variable within each species, lending support to the notion that this characteristic is not a reliable indicator to distinguish species within the An. punctulatus group. CONCLUSIONS The vector composition in Papua, Indonesia is consistent with certain northern areas of PNG, but the behaviours of anophelines sampled in this region, such as early and indoor human biting of An. farauti 4, may enable them to act as major vectors of malaria. Presumed major vectors An. farauti and An. punctulatus were not abundant among these samples. Morphological identification of anophelines in this sample was often inaccurate, highlighting the importance of using molecular analysis in conjunction with morphological investigations to update keys and training tools.
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Affiliation(s)
- Brandy St Laurent
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.
| | - Sukowati Supratman
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | | | - David Bretz
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - John Mueller
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Shinta
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Asik Surya
- Department of Parasitology, Faculty of Medicine, Hasanuddin University, Makasaar, 90245, Indonesia
| | - Michelle Ngai
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Ferdinand Laihad
- National Malaria Control Programme, Ministry of Health, Jakarta, Indonesia
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Parasitology, Faculty of Medicine, Hasanuddin University, Makasaar, 90245, Indonesia
| | | | - Frank H Collins
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Neil F Lobo
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
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Small ST, Reimer LJ, Tisch DJ, King CL, Christensen BM, Siba PM, Kazura JW, Serre D, Zimmerman PA. Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes. Mol Ecol 2016; 25:1465-77. [PMID: 26850696 PMCID: PMC4808423 DOI: 10.1111/mec.13574] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 01/19/2016] [Accepted: 01/26/2016] [Indexed: 02/01/2023]
Abstract
Wuchereria bancrofti is a parasitic nematode and the primary cause of lymphatic filariasis--a disease specific to humans. W. bancrofti currently infects over 90 million people throughout the tropics and has been acknowledged by the world health organization as a vulnerable parasite. Current research has focused primarily on the clinical manifestations of disease and little is known about the evolutionary history of W. bancrofti. To improve upon knowledge of the evolutionary history of W. bancrofti, we whole genome sequenced 13 W. bancrofti larvae. We circumvent many of the difficulties of multiple infections by sampling larvae directly from mosquitoes that were experimentally inoculated with infected blood. To begin, we used whole genome data to reconstruct the historical population size. Our results support a history of fluctuating population sizes that can be correlated with human migration and fluctuating mosquito abundances. Next, we reconstructed the putative pedigree of W. bancrofti worms within an infection using the kinship coefficient. We deduced that there are full-sib and half-sib relationships residing within the same larval cohort. Through combined analysis of the mitochondrial and nuclear genomes we concluded that this is likely a results of polyandrous mating, the first time reported for W. bancrofti. Lastly, we scanned the genomes for signatures of natural selection. Annotation of putative selected regions identified proteins that may have aided in a parasitic life style or may have evolved to protect against current drug treatments. We discuss our results in the greater context of understanding the biology of an animal with a unique life history and ecology.
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Logue K, Keven JB, Cannon MV, Reimer L, Siba P, Walker ED, Zimmerman PA, Serre D. Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing. PLoS Negl Trop Dis 2016; 10:e0004512. [PMID: 26963245 PMCID: PMC4786206 DOI: 10.1371/journal.pntd.0004512] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/13/2016] [Indexed: 11/18/2022] Open
Abstract
Understanding mosquito host choice is important for assessing vector competence or identifying disease reservoirs. Unfortunately, the availability of an unbiased method for comprehensively evaluating the composition of insect blood meals is very limited, as most current molecular assays only test for the presence of a few pre-selected species. These approaches also have limited ability to identify the presence of multiple mammalian hosts in a single blood meal. Here, we describe a novel high-throughput sequencing method that enables analysis of 96 mosquitoes simultaneously and provides a comprehensive and quantitative perspective on the composition of each blood meal. We validated in silico that universal primers targeting the mammalian mitochondrial 16S ribosomal RNA genes (16S rRNA) should amplify more than 95% of the mammalian 16S rRNA sequences present in the NCBI nucleotide database. We applied this method to 442 female Anopheles punctulatus s. l. mosquitoes collected in Papua New Guinea (PNG). While human (52.9%), dog (15.8%) and pig (29.2%) were the most common hosts identified in our study, we also detected DNA from mice, one marsupial species and two bat species. Our analyses also revealed that 16.3% of the mosquitoes fed on more than one host. Analysis of the human mitochondrial hypervariable region I in 102 human blood meals showed that 5 (4.9%) of the mosquitoes unambiguously fed on more than one person. Overall, analysis of PNG mosquitoes illustrates the potential of this approach to identify unsuspected hosts and characterize mixed blood meals, and shows how this approach can be adapted to evaluate inter-individual variations among human blood meals. Furthermore, this approach can be applied to any disease-transmitting arthropod and can be easily customized to investigate non-mammalian host sources.
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Affiliation(s)
- Kyle Logue
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John Bosco Keven
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Matthew V. Cannon
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Lisa Reimer
- Liverpool School of Tropical Medicine and Hygiene, Liverpool, United Kingdom
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Edward D. Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Peter A. Zimmerman
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (PAZ); (DS)
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail: (PAZ); (DS)
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