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Flouri T, Jiao X, Huang J, Rannala B, Yang Z. Efficient Bayesian inference under the multispecies coalescent with migration. Proc Natl Acad Sci U S A 2023; 120:e2310708120. [PMID: 37871206 PMCID: PMC10622872 DOI: 10.1073/pnas.2310708120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/15/2023] [Indexed: 10/25/2023] Open
Abstract
Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp, which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
| | - Xiyun Jiao
- Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen518055, China
| | - Jun Huang
- Department of Intelligent Medical Engineering, School of Biomedical Engineering, Capital Medical University, Beijing100069, China
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
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2
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Gene drive in species complexes: defining target organisms. Trends Biotechnol 2023; 41:154-164. [PMID: 35868886 DOI: 10.1016/j.tibtech.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 01/24/2023]
Abstract
Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.
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Jeffries CL, Cansado-Utrilla C, Beavogui AH, Stica C, Lama EK, Kristan M, Irish SR, Walker T. Evidence for natural hybridization and novel Wolbachia strain superinfections in the Anopheles gambiae complex from Guinea. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202032. [PMID: 33868697 PMCID: PMC8025300 DOI: 10.1098/rsos.202032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/15/2021] [Indexed: 05/05/2023]
Abstract
Wolbachia, a widespread bacterium which can influence mosquito-borne pathogen transmission, has recently been detected within Anopheles (An.) species that are malaria vectors in Sub-Saharan Africa. Although studies have reported Wolbachia strains in the An. gambiae complex, apparent low density and prevalence rates require confirmation. In this study, wild Anopheles mosquitoes collected from two regions of Guinea were investigated. In contrast with previous studies, RNA was extracted from adult females (n = 516) to increase the chances for the detection of actively expressed Wolbachia genes, determine Wolbachia prevalence rates and estimate relative strain densities. Molecular confirmation of mosquito species and Wolbachia multilocus sequence typing (MLST) were carried out to analyse phylogenetic relationships of mosquito hosts and newly discovered Wolbachia strains. Strains were detected in An. melas (prevalence rate of 11.6%-16/138) and hybrids between An. melas and An. gambiae sensu stricto (prevalence rate of 40.0%-6/15) from Senguelen in the Maferinyah region. Furthermore, a novel high-density strain, termed wAnsX, was found in an unclassified Anopheles species. The discovery of novel Wolbachia strains (particularly in members, and hybrids, of the An. gambiae complex) provides further candidate strains that could be used for future Wolbachia-based malaria biocontrol strategies.
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Affiliation(s)
- Claire L. Jeffries
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Cintia Cansado-Utrilla
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Abdoul H. Beavogui
- Centre National de Formation et de Recherche en Santé Rurale de Mafèrinyah B.P. 2649, Conakry, Guinea
| | - Caleb Stica
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Eugene K. Lama
- Programme National de Lutte contre le Paludisme, Guinée, B.P. 6339 Conakry, Guinea
| | - Mojca Kristan
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Seth R. Irish
- The US President's Malaria Initiative and Entomology Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329-4027, USA
| | - Thomas Walker
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Wang G, Guo X, Song F, Zheng W, Tan W, Huang E, Wu J, Wang C, Yang Q, Li C, Zhao T. Is Genetic Continuity Between Anopheles sinensis (Diptera: Culicidae) and its Sibling Species Due to Gene Introgression or Incomplete Speciation? JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:1239-1252. [PMID: 31066895 DOI: 10.1093/jme/tjz049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Indexed: 06/09/2023]
Abstract
The Anopheles mosquito Hyrcanus Group is widely distributed geographically across both Palearctic and Oriental regions and comprises 26 valid species. Although the species Anopheles sinensis Wiedemann (1828) is the most common in China and has a low potential vector rank, it has nevertheless long been thought to be an important natural malaria vector within the middle and lower reaches of the Yangtze River. A number of previous research studies have found evidence to support the occurrence of natural hybridization between An. sinensis and Anopheles kleini Rueda, 2005 (a competent malaria vector). We, therefore, collected a sample series of An. sinensis and morphologically similar species across China and undertook ribosomal and mitochondrial DNA analyses in order to assess genetic differentiation (Fst) and gene flow (Nm) amongst different groups. This enabled us to evaluate divergence times between morphologically similar species using the cytochrome oxidase I (COI) gene. The results of this study reveal significant genetic similarities between An. sinensis, An. kleini, and Anopheles belenrae Rueda, 2005 and therefore imply that correct molecular identifications will require additional molecular markers. As results also reveal the presence of gene flow between these three species, their taxonomic status will require further work. Data suggest that An. kleini is the most basal of the three species, while An. sinensis and An. belenrae share the closest genetic relationship.
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Affiliation(s)
- Gang Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
- Zhejiang International Travel Healthcare Center, Hangzhou, China
| | - Xiaoxia Guo
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Fenglin Song
- Liaoning International Travel Healthcare Center, Dalian, China
| | - Wei Zheng
- Zhejiang International Travel Healthcare Center, Hangzhou, China
| | - Weilong Tan
- Center for Disease Control and Prevention of Nanjing Command, Nanjing, China
| | - Enjiong Huang
- Fujian International Travel Healthcare Center, Fuzhou, China
| | - Jiahong Wu
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Chongcai Wang
- Hainan International Travel Healthcare Center, Haikou, China
| | - Qinggui Yang
- Jiangsu Academy of Science and Technology for Inspection and Quarantine, Nanjing, China
- Jiangsu International Travel Healthcare Center, Nanjing, China
| | - Chunxiao Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
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Bernardini F, Kriezis A, Galizi R, Nolan T, Crisanti A. Introgression of a synthetic sex ratio distortion system from Anopheles gambiae into Anopheles arabiensis. Sci Rep 2019; 9:5158. [PMID: 30914785 PMCID: PMC6435806 DOI: 10.1038/s41598-019-41646-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/14/2019] [Indexed: 12/04/2022] Open
Abstract
I-PpoI is a homing endonuclease that has a high cleavage activity and specificity for a conserved sequence within the ribosomal rDNA repeats, located in a single cluster on the Anopheles gambiae X chromosome. This property has been exploited to develop a synthetic sex ratio distortion system in this mosquito species. When I-PpoI is expressed from a transgene during spermatogenesis in mosquitoes, the paternal X chromosome is shredded and only Y chromosome-bearing sperm are viable, resulting in a male-biased sex ratio of >95% in the progeny. These distorter male mosquitoes can efficiently suppress caged wild-type populations, providing a powerful tool for vector control strategies. Given that malaria mosquito vectors belong to a species complex comprising at least two major vectors, we investigated whether the sex distorter I-PpoI, originally integrated in the A. gambiae genome, could be transferred via introgression to the sibling vector species Anopheles arabiensis. In compliance with Haldane’s rule, F1 hybrid male sterility is known to occur in all intercrosses among members of the Anopheles gambiae complex. A scheme based on genetic crosses and transgene selection was used to bypass F1 hybrid male sterility and introgress the sex distorter I-PpoI into the A. arabiensis genetic background. Our data suggest that this sex distortion technique can be successfully applied to target A. arabiensis mosquitoes.
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Affiliation(s)
- Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Antonios Kriezis
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
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Bernardini F, Galizi R, Wunderlich M, Taxiarchi C, Kranjc N, Kyrou K, Hammond A, Nolan T, Lawniczak MNK, Papathanos PA, Crisanti A, Windbichler N. Cross-Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex. Genetics 2017; 207:729-740. [PMID: 28860320 PMCID: PMC5629335 DOI: 10.1534/genetics.117.300221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/21/2017] [Indexed: 02/03/2023] Open
Abstract
Y chromosome function, structure and evolution is poorly understood in many species, including the Anopheles genus of mosquitoes-an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility. Here, we used an F1 × F0 crossing scheme to overcome a severe bottleneck of male hybrid incompatibilities that enabled us to experimentally purify a genetically labeled A. gambiae Y chromosome in an A. arabiensis background. Whole genome sequencing (WGS) confirmed that the A. gambiae Y retained its original sequence content in the A. arabiensis genomic background. In contrast to comparable experiments in Drosophila, we find that the presence of a heterospecific Y chromosome has no significant effect on the expression of A. arabiensis genes, and transcriptional differences can be explained almost exclusively as a direct consequence of transcripts arising from sequence elements present on the A. gambiae Y chromosome itself. We find that Y hybrids show no obvious fertility defects, and no substantial reduction in male competitiveness. Our results demonstrate that, despite their radically different structure, Y chromosomes of these two species of the gambiae complex that diverged an estimated 1.85 MYA function interchangeably, thus indicating that the Y chromosome does not harbor loci contributing to hybrid incompatibility. Therefore, Y chromosome gene flow between members of the gambiae complex is possible even at their current level of divergence. Importantly, this also suggests that malaria control interventions based on sex-distorting Y drive would be transferable, whether intentionally or contingent, between the major malaria vector species.
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Affiliation(s)
- Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Mariana Wunderlich
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Chrysanthi Taxiarchi
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Mara N K Lawniczak
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, United Kingdom
| | - Philippos Aris Papathanos
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132, Italy
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
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7
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Walker ED, Thibault AR, Thelen AP, Bullard BA, Huang J, Odiere MR, Bayoh NM, Wilkins EE, Vulule JM. Identification of field caught Anopheles gambiae s.s. and Anopheles arabiensis by TaqMan single nucleotide polymorphism genotyping. Malar J 2007; 6:23. [PMID: 17326831 PMCID: PMC1808465 DOI: 10.1186/1475-2875-6-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 02/27/2007] [Indexed: 11/12/2022] Open
Abstract
Background Identification of Anopheles gambiae s.s. and Anopheles arabiensis from field-collected Anopheles gambiae s.l. is often necessary in basic and applied research, and in operational control programmes. The currently accepted method involves use of standard polymerase chain reaction amplification of ribosomal DNA (rDNA) from the 3' 28S to 5' intergenic spacer region of the genome, and visual confirmation of amplicons of predicted size on agarose gels, after electrophoresis. This report describes development and evaluation of an automated, quantitative PCR method based upon TaqMan™ single nucleotide polymorphism (SNP) genotyping. Methods Standard PCR, and TaqMan SNP genotyping with newly designed primers and fluorophore-labeled probes hybridizing to sequences of complementary rDNA specific for either An. gambiae s.s. or An. arabiensis, were conducted in three experiments involving field-collected An. gambiae s.l. from western Kenya, and defined laboratory strains. DNA extraction was from a single leg, sonicated for five minutes in buffer in wells of 96-well PCR plates. Results TaqMan SNP genotyping showed a reaction success rate, sensitivity, and species specificity comparable to that of standard PCR. In an extensive field study, only 29 of 3,041 (0.95%) were determined to be hybrids by TaqMan (i.e., having rDNA sequences from both species), however, all but one were An. arabiensis by standard PCR, suggesting an acceptably low (ca. 1%) error rate for TaqMan genotyping in mistakenly identifying species hybrids. Conclusion TaqMan SNP genotyping proved to be a sensitive and rapid method for identification of An. gambiae s.l. and An. arabiensis, with a high success rate, specific results, and congruence with the standard PCR method.
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Affiliation(s)
- Edward D Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Alisha R Thibault
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Annette P Thelen
- Department of Biochemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Blair A Bullard
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Juan Huang
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Maurice R Odiere
- Centre for Vector Biology and Control Research, Kenya Medical Research Institute, P.O. Box 1578, Kisumu, Kenya
| | - Nabie M Bayoh
- Centre for Vector Biology and Control Research, Kenya Medical Research Institute, P.O. Box 1578, Kisumu, Kenya
| | - Elizabeth E Wilkins
- Atlanta Research & Education Foundation, Malaria Research and Reference Reagent Resource Center, Centers for Disease Control and Prevention, 4770 Buford Hwy., Mailstop F-42, Atlanta GA 30341, USA
| | - John M Vulule
- Centre for Vector Biology and Control Research, Kenya Medical Research Institute, P.O. Box 1578, Kisumu, Kenya
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