1
|
Tricou T, Tannier E, de Vienne DM. Ghost lineages can invalidate or even reverse findings regarding gene flow. PLoS Biol 2022; 20:e3001776. [PMID: 36103518 PMCID: PMC9473628 DOI: 10.1371/journal.pbio.3001776] [Citation(s) in RCA: 9] [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: 01/31/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.
Collapse
Affiliation(s)
- Théo Tricou
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
| | - Eric Tannier
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
- INRIA Grenoble Rhône-Alpes, F-38334 Montbonnot, France
| | - Damien M. de Vienne
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
| |
Collapse
|
2
|
Mfueni Bikundi E, Coppieters Y. Prediction ability of vector species, environmental characteristics and socio-economic factors for malaria risk in Sub-Saharan African Countries. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:191-206. [PMID: 32279543 DOI: 10.1080/09603123.2020.1745763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
Malaria remains a major public health problem, causing 435,000 deaths in 2017. The objective of this study was to estimate the prediction ability of vector species associated with the prediction power of environmental and socio-economic factors for malaria risk. Logistic regression was used for malaria risk estimation. A Radial Basis Function model was applied for estimating the predictive ability of Anopheles species, environmental and socio-economic factors. The lowest fever prevalence was found where Anopheles melas was dominant. Anopheles coluzzi and Anopheles gambiae were the dominant species where prevalence of malaria was high. Altitude, country and vector species were the best predictive factors. Anopheles arabiensis, An. coluzzi and An. gambiae were most common in urban areas. This study will improve the prediction of malaria risk in targeted areas. We have observed how important it is to adapt health policies according to the dominant malaria vector in a region.
Collapse
Affiliation(s)
- Elvire Mfueni Bikundi
- Epidemiology, Biostatistics and Clinical Research Center, School of Public Health, Université Libre de Bruxelles (ULB), Campus Erasme, Brussels, Belgium
| | - Yves Coppieters
- Epidemiology, Biostatistics and Clinical Research Center, School of Public Health, Université Libre de Bruxelles (ULB), Campus Erasme, Brussels, Belgium
| |
Collapse
|
3
|
Hui TYJ, Brenas JH, Burt A. Contemporary N e estimation using temporally spaced data with linked loci. Mol Ecol Resour 2021; 21:2221-2230. [PMID: 33950582 PMCID: PMC8518636 DOI: 10.1111/1755-0998.13412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022]
Abstract
The contemporary effective population size Ne is important in many disciplines including population genetics, conservation science and pest management. One of the most popular methods of estimating this quantity uses temporal changes in allele frequency due to genetic drift. A significant assumption of the existing methods is the independence among loci while constructing confidence intervals (CI), which restricts the types of species or genetic data applicable to the methods. Although genetic linkage does not bias point Ne estimates, applying these methods to linked loci can yield unreliable CI that are far too narrow. We extend the current methods to enable the use of many linked loci to produce precise contemporary Ne estimates, while preserving the targeted CI width and coverage. This is achieved by deriving the covariance of changes in allele frequency at linked loci in the face of recombination and sampling errors, such that the extra sampling variance due to between‐locus correlation is properly handled. Extensive simulations are used to verify the new method. We apply the method to two temporally spaced genomic data sets of Anopheles mosquitoes collected from a cluster of villages in Burkina Faso between 2012 and 2014. With over 33,000 linked loci considered, the Ne estimate for Anopheles coluzzii is 9,242 (95% CI 5,702–24,282), and for Anopheles gambiae it is 4,826 (95% CI 3,602–7,353).
Collapse
Affiliation(s)
- Tin-Yu J Hui
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Jon Haël Brenas
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Saffron Walden, UK
| | - Austin Burt
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Wosula EN, Chen W, Fei Z, Legg JP. Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing. Genome Biol Evol 2018; 9:2958-2973. [PMID: 29096025 PMCID: PMC5714214 DOI: 10.1093/gbe/evx219] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2017] [Indexed: 12/27/2022] Open
Abstract
Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci sampled from cassava in eight countries in Africa were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker data and short sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. STRUCTURE analysis identified four ancestral B. tabaci populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. Evidence of gene flow was strongest for SNP-based groups occurring in central Africa. Comparison of the mtCOI and SNP identities of sampled insects provided a strong indication that hybrid populations are emerging in parts of Africa recently affected by the severe CMD pandemic. This study reveals that mtCOI is not an effective marker at distinguishing cassava-colonizing B. tabaci haplogroups, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of genetic compositions of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa.
Collapse
Affiliation(s)
- Everlyne N Wosula
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
| | - Wenbo Chen
- Boyce Thompson Institute, Ithaca, New York
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York.,USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, New York
| | - James P Legg
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
| |
Collapse
|
6
|
Orantes LC, Monroy C, Dorn PL, Stevens L, Rizzo DM, Morrissey L, Hanley JP, Rodas AG, Richards B, Wallin KF, Helms Cahan S. Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata. PLoS Negl Trop Dis 2018; 12:e0006730. [PMID: 30335763 PMCID: PMC6193617 DOI: 10.1371/journal.pntd.0006730] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/02/2018] [Indexed: 12/25/2022] Open
Abstract
Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.
Collapse
Affiliation(s)
- Lucia C. Orantes
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, United States of America
| | - Carlota Monroy
- Laboratorio de Entomología Aplicada y Parasitología, Escuela de Biología, Universidad San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
| | - Patricia L. Dorn
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, Louisiana, United States of America
| | - Lori Stevens
- Department of Biology, University of Vermont, Burlington, Vermont, United States of America
| | - Donna M. Rizzo
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, Vermont, United States of America
| | - Leslie Morrissey
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, United States of America
| | - John P. Hanley
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, Vermont, United States of America
| | - Antonieta Guadalupe Rodas
- Laboratorio de Entomología Aplicada y Parasitología, Escuela de Biología, Universidad San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
| | - Bethany Richards
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, Louisiana, United States of America
| | - Kimberly F. Wallin
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, United States of America
- USDA Forest Service, Northern Research Station, Burlington, Vermont, United States of America
| | - Sara Helms Cahan
- Department of Biology, University of Vermont, Burlington, Vermont, United States of America
| |
Collapse
|
7
|
Wiltshire RM, Bergey CM, Kayondo JK, Birungi J, Mukwaya LG, Emrich SJ, Besansky NJ, Collins FH. Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda. Malar J 2018; 17:285. [PMID: 30081911 PMCID: PMC6080216 DOI: 10.1186/s12936-018-2432-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/30/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Malaria is the leading cause of global paediatric mortality in children below 5 years of age. The number of fatalities has reduced significantly due to an expansion of control interventions but the development of new technologies remains necessary in order to achieve elimination. Recent attention has been focused on the release of genetically modified (GM) mosquitoes into natural vector populations as a mechanism of interrupting parasite transmission but despite successful in vivo laboratory studies, a detailed population genetic assessment, which must first precede any proposed field trial, has yet to be undertaken systematically. Here, the genetic structure of Anopheles gambiae populations in north-western Lake Victoria is explored to assess their suitability as candidates for a pilot field study release of GM mosquitoes. METHODS 478 Anopheles gambiae mosquitoes were collected from six locations and a subset (N = 96) was selected for restriction site-associated DNA sequencing (RADseq). The resulting single nucleotide polymorphism (SNP) marker set was analysed for effective size (Ne), connectivity and population structure (PCA, FST). RESULTS 5175 high-quality genome-wide SNPs were identified. A principal components analysis (PCA) of the collinear genomic regions illustrated that individuals clustered in concordance with geographic origin with some overlap between sites. Genetic differentiation between populations was varied with inter-island comparisons having the highest values (median FST 0.0480-0.0846). Ne estimates were generally small (124.2-1920.3). CONCLUSIONS A reduced-representation SNP marker set for genome-wide An. gambiae genetic analysis in the north-western Lake Victoria basin is reported. Island populations demonstrated low to moderate genetic differentiation and greater structure suggesting some limitation to migration. Smaller estimates of Ne indicate that an introduced effector transgene will be more susceptible to genetic drift but to ensure that it is driven to fixation a robust gene drive mechanism will likely be needed. These findings, together with their favourable location and suitability for frequent monitoring, indicate that the Ssese Islands contain several candidate field locations, which merit further evaluation as potential GM mosquito pilot release sites.
Collapse
Affiliation(s)
- Rachel M Wiltshire
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Christina M Bergey
- Departments of Anthropology and Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jonathan K Kayondo
- Division of Entomology and Vector Biology, Uganda Virus Research Institute, Plot No. 51-59, Nakiwogo Road, Entebbe 49, Uganda
| | - Josephine Birungi
- Division of Entomology and Vector Biology, Uganda Virus Research Institute, Plot No. 51-59, Nakiwogo Road, Entebbe 49, Uganda
| | - Louis G Mukwaya
- Division of Entomology and Vector Biology, Uganda Virus Research Institute, Plot No. 51-59, Nakiwogo Road, Entebbe 49, Uganda
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nora J Besansky
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Frank H Collins
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| |
Collapse
|
8
|
Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories. PLoS One 2018; 13:e0190555. [PMID: 29364919 PMCID: PMC5783331 DOI: 10.1371/journal.pone.0190555] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 12/16/2017] [Indexed: 12/21/2022] Open
Abstract
Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO). Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.
Collapse
|
9
|
Abstract
Basic science holds enormous power for revealing the biological mechanisms of disease and, in turn, paving the way toward new, effective interventions. Recognizing this power, the 2011 Research Agenda for Malaria Eradication included key priorities in fundamental research that, if attained, could help accelerate progress toward disease elimination and eradication. The Malaria Eradication Research Agenda (malERA) Consultative Panel on Basic Science and Enabling Technologies reviewed the progress, continuing challenges, and major opportunities for future research. The recommendations come from a literature of published and unpublished materials and the deliberations of the malERA Refresh Consultative Panel. These areas span multiple aspects of the Plasmodium life cycle in both the human host and the Anopheles vector and include critical, unanswered questions about parasite transmission, human infection in the liver, asexual-stage biology, and malaria persistence. We believe an integrated approach encompassing human immunology, parasitology, and entomology, and harnessing new and emerging biomedical technologies offers the best path toward addressing these questions and, ultimately, lowering the worldwide burden of malaria.
Collapse
|
10
|
Kamdem C, Fouet C, White BJ. Chromosome arm-specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus. Mol Ecol 2017; 26:5552-5566. [PMID: 28833796 PMCID: PMC5927613 DOI: 10.1111/mec.14335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 02/02/2023]
Abstract
Chromosomal inversions facilitate local adaptation of beneficial mutations and modulate genetic polymorphism, but the extent of their effects within the genome is still insufficiently understood. The genome of Anopheles funestus, a malaria mosquito endemic to sub-Saharan Africa, contains an impressive number of paracentric polymorphic inversions, which are unevenly distributed among chromosomes and provide an excellent framework for investigating the genomic impacts of chromosomal rearrangements. Here, we present results of a fine-scale analysis of genetic variation within the genome of two weakly differentiated populations of Anopheles funestus inhabiting contrasting moisture conditions in Cameroon. Using population genomic analyses, we found that genetic divergence between the two populations is centred on regions of the genome corresponding to three inversions, which are characterized by high values of FST , absolute sequence divergence and fixed differences. Importantly, in contrast to the 2L chromosome arm, which is collinear, nucleotide diversity is significantly reduced along the entire length of three autosome arms bearing multiple overlapping chromosomal rearrangements. These findings support the idea that interactions between reduced recombination and natural selection within inversions contribute to sculpt nucleotide polymorphism across chromosomes in An. funestus.
Collapse
Affiliation(s)
- Colince Kamdem
- Department of Entomology, University of California, Riverside, CA 92521
| | - Caroline Fouet
- Department of Entomology, University of California, Riverside, CA 92521
| | - Bradley J. White
- Department of Entomology, University of California, Riverside, CA 92521
| |
Collapse
|
11
|
Fouet C, Kamdem C, Gamez S, White BJ. Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group. Evol Appl 2017; 10:897-906. [PMID: 29151881 PMCID: PMC5680430 DOI: 10.1111/eva.12492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 01/16/2023] Open
Abstract
Ongoing speciation in the most important African malaria vectors gives rise to cryptic populations, which differ remarkably in their behavior, ecology, and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is crucial for effective disease control because heterogeneity within vector species contributes to variability in malaria cases and allow fractions of populations to escape control efforts. To examine population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group-a large taxonomic group that diverged ~3 Myr ago. Using 4,343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high-FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA, and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.
Collapse
Affiliation(s)
- Caroline Fouet
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Colince Kamdem
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Stephanie Gamez
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Bradley J. White
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
- Center for Disease Vector ResearchInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
| |
Collapse
|
12
|
Riehle MM, Bukhari T, Gneme A, Guelbeogo WM, Coulibaly B, Fofana A, Pain A, Bischoff E, Renaud F, Beavogui AH, Traore SF, Sagnon N, Vernick KD. The Anopheles gambiae 2La chromosome inversion is associated with susceptibility to Plasmodium falciparum in Africa. eLife 2017. [PMID: 28643631 PMCID: PMC5482571 DOI: 10.7554/elife.25813] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome inversions suppress genetic recombination and establish co-adapted gene complexes, or supergenes. The 2La inversion is a widespread polymorphism in the Anopheles gambiae species complex, the major African mosquito vectors of human malaria. Here we show that alleles of the 2La inversion are associated with natural malaria infection levels in wild-captured vectors from West and East Africa. Mosquitoes carrying the more-susceptible allele (2L+a) are also behaviorally less likely to be found inside houses. Vector control tools that target indoor-resting mosquitoes, such as bednets and insecticides, are currently the cornerstone of malaria control in Africa. Populations with high levels of the 2L+a allele may form reservoirs of persistent outdoor malaria transmission requiring novel measures for surveillance and control. The 2La inversion is a major and previously unappreciated component of the natural malaria transmission system in Africa, influencing both malaria susceptibility and vector behavior.
Collapse
Affiliation(s)
- Michelle M Riehle
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, United States
| | - Tullu Bukhari
- Department of Zoology, Maseno University, Maseno, Kenya
| | - Awa Gneme
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Boubacar Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Abdrahamane Fofana
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Adrien Pain
- Department of Parasites and Insect Vectors, Unit of Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Hosts, Vectors and Pathogens, Paris, France.,Bioinformatics and Biostatistics Hub (C3BI), USR 3756 IP CNRS, Institut Pasteur, Paris, France
| | - Emmanuel Bischoff
- Department of Parasites and Insect Vectors, Unit of Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Hosts, Vectors and Pathogens, Paris, France
| | - Francois Renaud
- Laboratoire Maladies Infectieuses et Vecteurs: Ecologie Génétique, Evolution et Contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD), Montpellier, France.,UMR 224-5290, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Abdoul H Beavogui
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Sekou F Traore
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Kenneth D Vernick
- Department of Parasites and Insect Vectors, Unit of Genetics and Genomics of Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Hosts, Vectors and Pathogens, Paris, France
| |
Collapse
|
13
|
Kamdem C, Fouet C, Gamez S, White BJ. Pollutants and Insecticides Drive Local Adaptation in African Malaria Mosquitoes. Mol Biol Evol 2017; 34:1261-1275. [PMID: 28204524 PMCID: PMC5400387 DOI: 10.1093/molbev/msx087] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Anopheles gambiae complex contains a number of highly anthropophilic mosquito species that have acquired exceptional ability to thrive in complex human habitats. Thus, examining the evolutionary history of this Afrotropical mosquito may yield vital information on the selective processes that occurred during the adaptation to human-dominated environments. We performed reduced representation sequencing on 941 mosquitoes of the Anopheles gambiae complex collected across four ecogeographic zones in Cameroon. We find evidence for genetic and geographic subdivision within An. coluzzii and An. gambiae sensu stricto-the two most significant malaria vectors in the region. Importantly, in both species, rural and urban populations are genetically differentiated. Genome scans reveal pervasive signatures of selection centered on genes involved in xenobiotic resistance. Notably, a selective sweep containing detoxification enzymes is prominent in urban mosquitoes that exploit polluted breeding sites. Overall, our study suggests that recent anthropogenic environmental modifications and widespread use of insecticides are driving population differentiation and local adaptation in vectors with potentially significant consequences for malaria epidemiology.
Collapse
Affiliation(s)
- Colince Kamdem
- Department of Entomology, University of California, Riverside, CA
| | - Caroline Fouet
- Department of Entomology, University of California, Riverside, CA
| | - Stephanie Gamez
- Department of Entomology, University of California, Riverside, CA
| | - Bradley J. White
- Department of Entomology, University of California, Riverside, CA
- Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA
| |
Collapse
|
14
|
Campos M, Conn JE, Alonso DP, Vinetz JM, Emerson KJ, Ribolla PEM. Microgeographical structure in the major Neotropical malaria vector Anopheles darlingi using microsatellites and SNP markers. Parasit Vectors 2017; 10:76. [PMID: 28193289 PMCID: PMC5307779 DOI: 10.1186/s13071-017-2014-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent decades, throughout the Amazon Basin, landscape modification contributing to profound ecological change has proceeded at an unprecedented rate. Deforestation that accompanies human activities can significantly change aspects of anopheline biology, though this may be site-specific. Such local changes in anopheline biology could have a great impact on malaria transmission. The aim of this study was to investigate population genetics of the main malaria vector in Brazil, Anopheles darlingi, from a microgeographical perspective. METHODS Microsatellites and ddRADseq-derived single nucleotide polymorphisms (SNPs) were used to assess levels of population genetic structuring among mosquito populations from two ecologically distinctive agricultural settlements (~60 km apart) and a population from a distant (~700 km) urban setting in the western Amazon region of Brazil. RESULTS Significant microgeographical population differentiation was observed among Anopheles darlingi populations via both model- and non-model-based analysis only with the SNP dataset. Microsatellites detected moderate differentiation at the greatest distances, but were unable to differentiate populations from the two agricultural settlements. Both markers showed low polymorphism levels in the most human impacted sites. CONCLUSIONS At a microgeographical scale, signatures of genetic heterogeneity and population divergence were evident in Anopheles darlingi, possibly related to local environmental anthropic modification. This divergence was observed only when using high coverage SNP markers.
Collapse
Affiliation(s)
- Melina Campos
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), Sao Paulo State University (UNESP), Sao Paulo, Brazil
| | - Jan E Conn
- Department of Biomedical Sciences, School of Public Health, University at Albany (State University of New York), Albany, NY, USA.,New York State Department of Health, Wadsworth Center, Albany, NY, USA
| | - Diego Peres Alonso
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), Sao Paulo State University (UNESP), Sao Paulo, Brazil
| | - Joseph M Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California, La Jolla, San Diego, CA, USA.,Instituto de Medicina Tropical "Alexander von Humboldt," and Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kevin J Emerson
- Biology Department, St. Mary's College of Maryland, St. Mary's City, MD, USA
| | - Paulo Eduardo Martins Ribolla
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), Sao Paulo State University (UNESP), Sao Paulo, Brazil.
| |
Collapse
|
15
|
Love RR, Steele AM, Coulibaly MB, Traore SF, Emrich SJ, Fontaine MC, Besansky NJ. Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing. Mol Ecol 2016; 25:5889-5906. [PMID: 27759895 DOI: 10.1111/mec.13888] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 09/13/2016] [Accepted: 10/03/2016] [Indexed: 12/30/2022]
Abstract
The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination-reducing effect, are proposed instruments of ecotypic differentiation. Here, we study an ecologically diversifying lineage of Anopheles gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non-Bamako) An. gambiae and the sister species Anopheles coluzzii to investigate evolutionary relationships and genomewide patterns of nucleotide diversity and differentiation among lineages. Despite extensive shared polymorphism and limited differentiation from the other taxa, Bamako clusters apart from the other taxa, and forms a maximally supported clade in neighbour-joining trees based on whole-genome data (including inversions) or solely on collinear regions. Nevertheless, FST outlier analysis reveals that the majority of differentiated regions between Bamako and typical An. gambiae are located inside chromosomal inversions, consistent with their role in the ecological isolation of Bamako. Exceptionally differentiated genomic regions were enriched for genes implicated in nervous system development and signalling. Candidate genes associated with a selective sweep unique to Bamako contain substitutions not observed in sympatric samples of the other taxa, and several insecticide resistance gene alleles shared between Bamako and other taxa segregate at sharply different frequencies in these samples. Bamako represents a useful window into the initial stages of ecological and genomic differentiation from sympatric populations in this important group of malaria vectors.
Collapse
Affiliation(s)
- R Rebecca Love
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
| | - Aaron M Steele
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Mamadou B Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sékou F Traore
- Malaria Research and Training Centre, Faculty of Medicine Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Michael C Fontaine
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
| |
Collapse
|
16
|
Onyango MG, Aitken NC, Jack C, Chuah A, Oguya J, Djikeng A, Kemp S, Bellis GA, Nicholas A, Walker PJ, Duchemin JB. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia. BMC Genomics 2016; 17:769. [PMID: 27716062 PMCID: PMC5045647 DOI: 10.1186/s12864-016-3124-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. RESULTS This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. CONCLUSIONS The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance.
Collapse
Affiliation(s)
- Maria G Onyango
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia.,School of Medicine, Deakin University, 75 Pidgons Road, Waurn Ponds, 3216, VIC, Australia
| | - Nicola C Aitken
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Cameron Jack
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Aaron Chuah
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - James Oguya
- International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya
| | - Appolinaire Djikeng
- International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya.,Biosciences eastern and central Africa-ILRI Hub (BecA-ILRI Hub), ILRI, PO Box 30709, 00100, Nairobi, Kenya
| | - Steve Kemp
- International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya
| | - Glenn A Bellis
- Northern Australia Quarantine Strategy, 1 Pederson Road, Marrara, 0812, NT, Australia.,Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, 0909, NT, Australia
| | - Adrian Nicholas
- NSW Department of Primary Industries, Biosecurity, 4 Marsden Park Road, Calala, 2340, NSW, Australia
| | - Peter J Walker
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia
| | - Jean-Bernard Duchemin
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia.
| |
Collapse
|
17
|
Main BJ, Lee Y, Ferguson HM, Kreppel KS, Kihonda A, Govella NJ, Collier TC, Cornel AJ, Eskin E, Kang EY, Nieman CC, Weakley AM, Lanzaro GC. The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis. PLoS Genet 2016; 12:e1006303. [PMID: 27631375 PMCID: PMC5025075 DOI: 10.1371/journal.pgen.1006303] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
Abstract
Malaria transmission is dependent on the propensity of Anopheles mosquitoes to bite humans (anthropophily) instead of other dead end hosts. Recent increases in the usage of Long Lasting Insecticide Treated Nets (LLINs) in Africa have been associated with reductions in highly anthropophilic and endophilic vectors such as Anopheles gambiae s.s., leaving species with a broader host range, such as Anopheles arabiensis, as the most prominent remaining source of transmission in many settings. An. arabiensis appears to be more of a generalist in terms of its host choice and resting behavior, which may be due to phenotypic plasticity and/or segregating allelic variation. To investigate the genetic basis of host choice and resting behavior in An. arabiensis we sequenced the genomes of 23 human-fed and 25 cattle-fed mosquitoes collected both in-doors and out-doors in the Kilombero Valley, Tanzania. We identified a total of 4,820,851 SNPs, which were used to conduct the first genome-wide estimates of "SNP heritability" for host choice and resting behavior in this species. A genetic component was detected for host choice (human vs cow fed; permuted P = 0.002), but there was no evidence of a genetic component for resting behavior (indoors versus outside; permuted P = 0.465). A principal component analysis (PCA) segregated individuals based on genomic variation into three groups which were characterized by differences at the 2Rb and/or 3Ra paracentromeric chromosome inversions. There was a non-random distribution of cattle-fed mosquitoes between the PCA clusters, suggesting that alleles linked to the 2Rb and/or 3Ra inversions may influence host choice. Using a novel inversion genotyping assay, we detected a significant enrichment of the standard arrangement (non-inverted) of 3Ra among cattle-fed mosquitoes (N = 129) versus all non-cattle-fed individuals (N = 234; χ2, p = 0.007). Thus, tracking the frequency of the 3Ra in An. arabiensis populations may be of use to infer selection on host choice behavior within these vector populations; possibly in response to vector control. Controlled host-choice assays are needed to discern whether the observed genetic component has a direct relationship with innate host preference. A better understanding of the genetic basis for host feeding behavior in An. arabiensis may also open avenues for novel vector control strategies based on driving genes for zoophily into wild mosquito populations.
Collapse
Affiliation(s)
- Bradley J Main
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
- * E-mail:
| | - Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Heather M. Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Katharina S. Kreppel
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Environmental Health and Ecological Sciences Group, Ifakara Health Institute, Ifakara, United Republic of Tanzania
| | - Anicet Kihonda
- Environmental Health and Ecological Sciences Group, Ifakara Health Institute, Ifakara, United Republic of Tanzania
| | - Nicodem J. Govella
- Environmental Health and Ecological Sciences Group, Ifakara Health Institute, Ifakara, United Republic of Tanzania
| | - Travis C. Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Anthony J. Cornel
- Department of Entomology and Nematology, University of California, Davis, Davis, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eun Yong Kang
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Catelyn C. Nieman
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Allison M. Weakley
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| | - Gregory C. Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology/University of California, Davis, Davis, California, United States of America
| |
Collapse
|
18
|
Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol 2016; 25:2337-60. [PMID: 26836441 PMCID: PMC4915564 DOI: 10.1111/mec.13557] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022]
Abstract
Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns - which may contribute to reproductive barriers - are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
Collapse
Affiliation(s)
- Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
19
|
O'Loughlin SM, Magesa SM, Mbogo C, Mosha F, Midega J, Burt A. Genomic signatures of population decline in the malaria mosquito Anopheles gambiae. Malar J 2016; 15:182. [PMID: 27013475 PMCID: PMC4806450 DOI: 10.1186/s12936-016-1214-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/05/2016] [Indexed: 01/15/2023] Open
Abstract
Background Population genomic features such as nucleotide diversity and linkage disequilibrium are expected to be strongly shaped by changes in population size, and might therefore be useful for monitoring the success of a control campaign. In the Kilifi district of Kenya, there has been a marked decline in the abundance of the malaria vector Anopheles gambiae subsequent to the rollout of insecticide-treated bed nets. Methods To investigate whether this decline left a detectable population genomic signature, simulations were performed to compare the effect of population crashes on nucleotide diversity, Tajima’s D, and linkage disequilibrium (as measured by the population recombination parameter ρ). Linkage disequilibrium and ρ were estimated for An. gambiae from Kilifi, and compared them to values for Anopheles arabiensis and Anopheles merus at the same location, and for An. gambiae in a location 200 km from Kilifi. Results In the first simulations ρ changed more rapidly after a population crash than the other statistics, and therefore is a more sensitive indicator of recent population decline. In the empirical data, linkage disequilibrium extends 100–1000 times further, and ρ is 100–1000 times smaller, for the Kilifi population of An. gambiae than for any of the other populations. There were also significant runs of homozygosity in many of the individual An. gambiae mosquitoes from Kilifi. Conclusions These results support the hypothesis that the recent decline in An. gambiae was driven by the rollout of bed nets. Measuring population genomic parameters in a small sample of individuals before, during and after vector or pest control may be a valuable method of tracking the effectiveness of interventions. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1214-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samantha M O'Loughlin
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK.
| | - Stephen M Magesa
- NIMR Amani Research Centre, P.O. Box 81, Muheza, Tanzania.,Global Health Division, RTI International, Dar es Salaam, Tanzania
| | - Charles Mbogo
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, P.O. Box 428, Kilifi, Kenya.,Malaria Public Health Department, Centre for Geographic Medicine, KEMRI-Wellcome Trust Research Programme, Kenyatta National Hospital Grounds, P.O. Box 43640-00100, Nairobi, Kenya
| | - Franklin Mosha
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Janet Midega
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, P.O. Box 428, Kilifi, Kenya.,Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.,Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, SL5 7PY, UK
| |
Collapse
|
20
|
Crawford JE, Riehle MM, Guelbeogo WM, Gneme A, Sagnon N, Vernick KD, Nielsen R, Lazzaro BP. Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex. Genome Biol Evol 2015; 7:3116-31. [PMID: 26615027 PMCID: PMC4994751 DOI: 10.1093/gbe/evv203] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Speciation as a process remains a central focus of evolutionary biology, but our
understanding of the genomic architecture and prevalence of speciation in the face of gene
flow remains incomplete. The Anopheles gambiae species complex of malaria
mosquitoes is a radiation of ecologically diverse taxa. This complex is well-suited for
testing for evidence of a speciation continuum and genomic barriers to introgression
because its members exhibit partially overlapping geographic distributions as well as
varying levels of divergence and reproductive isolation. We sequenced 20 genomes from wild
A. gambiae s.s., Anopheles coluzzii, Anopheles
arabiensis, and compared these with 12 genomes from the “GOUNDRY” subgroup of
A. gambiae s.l. Amidst a backdrop of strong
reproductive isolation, we find strong evidence for a speciation continuum with
introgression of autosomal chromosomal regions among species and subgroups. The X
chromosome, however, is strongly differentiated among all taxa, pointing to a
disproportionately large effect of X chromosome genes in driving speciation among
anophelines. Strikingly, we find that autosomal introgression has occurred from
contemporary hybridization between A. gambiae and A.
arabiensis despite strong divergence (∼5× higher than autosomal divergence) and
isolation on the X chromosome. In addition to the X, we find strong evidence that lowly
recombining autosomal regions, especially pericentromeric regions, serve as barriers to
introgression secondarily to the X. We show that speciation with gene flow results in
genomic mosaicism of divergence and introgression. Such a reticulate gene pool connecting
vector taxa across the speciation continuum has important implications for malaria control
efforts.
Collapse
Affiliation(s)
- Jacob E Crawford
- Department of Entomology, Cornell University Department of Integrative Biology, University of California, Berkeley
| | | | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Awa Gneme
- 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
| | - Kenneth D Vernick
- Unit of Insect Vector Genetics and Genomics, Institut Pasteur, Paris, France
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley
| | | |
Collapse
|
21
|
Talas F, McDonald BA. Genome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombination. BMC Genomics 2015; 16:996. [PMID: 26602546 PMCID: PMC4659151 DOI: 10.1186/s12864-015-2166-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 10/29/2015] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Fusarium graminearum (Fg) is a ubiquitous pathogen of wheat, barley and maize causing Fusarium head blight. Large annual yield losses and contamination of foodstuffs with harmful mycotoxins make Fg one of the most-studied plant pathogens. Analyses of natural field populations can lead to a better understanding of the evolutionary processes affecting this pathogen. Restriction site associated DNA sequencing (RADseq) was used to conduct population genomics analyses including 213 pathogen isolates from 13 German field populations of Fg. RESULTS High genetic diversity was found within Fg field populations and low differentiation (FST = 0.003) was found among populations. Linkage disequilibrium (LD) decayed rapidly over a distance of 1000 bp. The low multilocus LD indicates that significant sexual recombination occurs in all populations. Several recombination hotspots were detected on each chromosome, but different chromosomes showed different levels of recombination. There was some evidence for selection hotspots. CONCLUSIONS The population genomic structure of Fg is consistent with a high degree of sexual recombination that is not equally distributed across the chromosomes. The high gene flow found among these field populations should enable this pathogen to adapt rapidly to changes in its environment, including deployment of resistant cultivars, applications of fungicides and a warming climate.
Collapse
Affiliation(s)
- Firas Talas
- ETH Zurich, Institute of Integrative Biology, Zurich (IBZ), Plant Pathology, 8092, Zurich, Switzerland.
| | - Bruce A McDonald
- ETH Zurich, Institute of Integrative Biology, Zurich (IBZ), Plant Pathology, 8092, Zurich, Switzerland.
| |
Collapse
|
22
|
Artemov GN, Sharakhova MV, Naumenko AN, Karagodin DA, Baricheva EM, Stegniy VN, Sharakhov IV. A standard photomap of ovarian nurse cell chromosomes in the European malaria vector Anopheles atroparvus. MEDICAL AND VETERINARY ENTOMOLOGY 2015; 29:230-237. [PMID: 25776224 PMCID: PMC4515173 DOI: 10.1111/mve.12113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/20/2014] [Accepted: 06/04/2014] [Indexed: 06/04/2023]
Abstract
Anopheles atroparvus (Diptera: Culicidae) is one of the main malaria vectors of the Maculipennis group in Europe. Cytogenetic analysis based on salivary gland chromosomes has been used in taxonomic and population genetic studies of mosquitoes from this group. However, a high-resolution cytogenetic map that could be used in physical genome mapping in An. atroparvus is still lacking. In the present study, a high-quality photomap of the polytene chromosomes from ovarian nurse cells of An. atroparvus was developed. Using fluorescent in situ hybridization, 10 genes from the five largest genomic supercontigs on the polytene chromosome were localized and 28% of the genome was anchored to the cytogenetic map. The study established chromosome arm homology between An. atroparvus and the major African malaria vector Anopheles gambiae, suggesting a whole-arm translocation between autosomes of these two species. The standard photomap constructed for ovarian nurse cell chromosomes of An. atroparvus will be useful for routine physical mapping. This map will assist in the development of a fine-scale chromosome-based genome assembly for this species and will also facilitate comparative and evolutionary genomics studies in the genus Anopheles.
Collapse
Affiliation(s)
- Gleb N. Artemov
- Tomsk State University, Institute of Biology and Biophysics, Tomsk, Russia
| | - Maria V. Sharakhova
- Tomsk State University, Institute of Biology and Biophysics, Tomsk, Russia
- Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA
| | - Anastasia N. Naumenko
- Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA
| | | | | | | | - Igor V. Sharakhov
- Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA
| |
Collapse
|
23
|
Behura SK. Insect phylogenomics. INSECT MOLECULAR BIOLOGY 2015; 24:403-11. [PMID: 25963452 PMCID: PMC4503476 DOI: 10.1111/imb.12174] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 03/10/2015] [Accepted: 04/04/2015] [Indexed: 05/08/2023]
Abstract
Phylogenomics, the integration of phylogenetics with genome data, has emerged as a powerful approach to study the evolution and systematics of species. Recently, several studies employing phylogenomic tools have provided better insights into insect evolution. Next-generation sequencing methods are now increasingly used by entomologists to generate genomic and transcript sequences of various insect species and strains. These data provide opportunities for comparative genomics and large-scale multigene phylogenies of diverse lineages of insects. Phy-logenomic investigations help us to better understand systematic and evolutionary relationships of insect species that play important roles as herbivores, predators, detritivores, pollinators and disease vectors. It is important that we critically assess the prospects and limitations of phylogenomic methods. In this review, I describe the current status, outline the major challenges and remark on potential future applications of phylogenomic tools in studying insect systematics and evolution.
Collapse
Affiliation(s)
- S K Behura
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| |
Collapse
|
24
|
Song SV, Downes S, Parker T, Oakeshott JG, Robin C. High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep. Heredity (Edinb) 2015; 115:460-70. [PMID: 26174024 DOI: 10.1038/hdy.2015.53] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/01/2015] [Accepted: 05/06/2015] [Indexed: 11/09/2022] Open
Abstract
Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of 'selective sweeps'. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci in three Australian H. armigera populations. We find that estimates of π are in the higher range among other insects and linkage disequilibrium decays over short distances. One of the surveyed loci, a cytochrome P450, shows an unusual haplotype configuration with a divergent allele at high frequency that led us to investigate the possibility of an adaptive introgression around this locus.
Collapse
Affiliation(s)
- S V Song
- Department of Genetics, University of Melbourne and Bio21 Institute, Melbourne, Victoria, Australia
| | - S Downes
- Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Narrabri, New South Wales, Australia
| | - T Parker
- Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Narrabri, New South Wales, Australia
| | - J G Oakeshott
- Land and Water Flagship, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - C Robin
- Department of Genetics, University of Melbourne and Bio21 Institute, Melbourne, Victoria, Australia
| |
Collapse
|
25
|
Emerson KJ, Conn JE, Bergo ES, Randel MA, Sallum MAM. Brazilian Anopheles darlingi Root (Diptera: Culicidae) Clusters by Major Biogeographical Region. PLoS One 2015; 10:e0130773. [PMID: 26172559 PMCID: PMC4501553 DOI: 10.1371/journal.pone.0130773] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/23/2015] [Indexed: 11/18/2022] Open
Abstract
The major drivers of the extensive biodiversity of the Neotropics are proposed to be geological and tectonic events together with Pliocene and Pleistocene environmental and climatic change. Geographical barriers represented by the rivers Amazonas/Solimões, the Andes and the coastal mountain ranges in eastern Brazil have been hypothesized to lead to diversification within the primary malaria vector, Anopheles (Nyssorhynchus) darlingi Root, which primarily inhabits rainforest. To test this biogeographical hypothesis, we analyzed 786 single nucleotide polymorphisms (SNPs) in 12 populations of An. darlingi from across the complex Brazilian landscape. Both model-based (STRUCTURE) and non-model-based (Principal Components and Discriminant Analysis) analysis of population structure detected three major genetic clusters that correspond with newly described Neotropical biogeographical regions: 1) Atlantic Forest province (= southeast population); 2) Parana Forest province (= West Atlantic forest population, with one Chacoan population - SP); and 3) Brazilian dominion population (= Amazonian population with one Chacoan population - TO). Significant levels of pairwise genetic divergences were found among the three clusters, allele sharing among clusters was negligible, and geographical distance did not contribute to differentiation. We infer that the Atlantic forest coastal mountain range limited dispersal between the Atlantic Forest province and the Parana Forest province populations, and that the large, diagonal open vegetation region of the Chacoan dominion dramatically reduced dispersal between the Parana and Brazilian dominion populations. We hypothesize that the three genetic clusters may represent three putative species.
Collapse
Affiliation(s)
- Kevin J. Emerson
- Biology Department, St. Mary’s College of Maryland, St. Mary’s City, Maryland, United States of America
| | - Jan E. Conn
- The Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences—School of Public Health, SUNY Albany, Albany, New York, United States of America
| | - Eduardo S. Bergo
- Superintendência de Controle de Endemias, Secretaria de Estado da Saúde de São Paulo, Araraquara, São Paulo, Brazil
| | - Melissa A. Randel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
26
|
Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 2015; 347:1258524. [PMID: 25431491 PMCID: PMC4380269 DOI: 10.1126/science.1258524] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here, we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between these malaria vectors means that only a small fraction of the genome, mainly on the X chromosome, has not crossed species boundaries. Our results suggest that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between nonsister species.
Collapse
Affiliation(s)
- Michael C Fontaine
- 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
| | - James B Pease
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Aaron Steele
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Robert M Waterhouse
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Daniel E Neafsey
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Xiaofang Jiang
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Andrew B Hall
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - Evdoxia Kakani
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - Sara N Mitchell
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Yi-Chieh Wu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
| | - Hilary A Smith
- 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
| | - 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
| | - Mara K Lawniczak
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Michel A Slotman
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA. Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA. School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.
| | - 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.
| |
Collapse
|
27
|
Abstract
Natural selection is expected to drive adaptive evolution in genes involved in host–pathogen interactions. In this study, we use molecular population genetic analyses to understand how natural selection operates on the immune system of Anopheles coluzzii (formerly A. gambiae “M form”). We analyzed patterns of intraspecific and interspecific genetic variation in 20 immune-related genes and 17 nonimmune genes from a wild population of A. coluzzii and asked if patterns of genetic variation in the immune genes are consistent with pathogen-driven selection shaping the evolution of defense. We found evidence of a balanced polymorphism in CTLMA2, which encodes a C-type lectin involved in regulation of the melanization response. The two CTLMA2 haplotypes, which are distinguished by fixed amino acid differences near the predicted peptide cleavage site, are also segregating in the sister species A. gambiae (“S form”) and A. arabiensis. Comparison of the two haplotypes between species indicates that they were not shared among the species through introgression, but rather that they arose before the species divergence and have been adaptively maintained as a balanced polymorphism in all three species. We additionally found that STAT-B, a retroduplicate of STAT-A, shows strong evidence of adaptive evolution that is consistent with neofunctionalization after duplication. In contrast to the striking patterns of adaptive evolution observed in these Anopheles-specific immune genes, we found no evidence of adaptive evolution in the Toll and Imd innate immune pathways that are orthologously conserved throughout insects. Genes encoding the Imd pathway exhibit high rates of amino acid divergence between Anopheles species but also display elevated amino acid diversity that is consistent with relaxed purifying selection. These results indicate that adaptive coevolution between A. coluzzii and its pathogens is more likely to involve novel or lineage-specific molecular mechanisms than the canonical humoral immune pathways.
Collapse
|
28
|
Weetman D, Steen K, Rippon EJ, Mawejje HD, Donnelly MJ, Wilding CS. Contemporary gene flow between wild An. gambiae s.s. and An. arabiensis. Parasit Vectors 2014; 7:345. [PMID: 25060488 PMCID: PMC4124135 DOI: 10.1186/1756-3305-7-345] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/21/2014] [Indexed: 11/10/2022] Open
Abstract
Background In areas where the morphologically indistinguishable malaria mosquitoes Anopheles gambiae Giles and An. arabiensis Patton are sympatric, hybrids are detected occasionally via species-diagnostic molecular assays. An. gambiae and An. arabiensis exhibit both pre- and post-reproductive mating barriers, with swarms largely species-specific and male F1 (first-generation) hybrids sterile. Consequently advanced-stage hybrids (back-crosses to parental species), which would represent a route for potentially-adaptive introgression, are expected to be very rare in natural populations. Yet the use of one or two physically linked single-locus diagnostic assays renders them indistinguishable from F1 hybrids and levels of interspecific gene flow are unknown. Methods We used data from over 350 polymorphic autosomal SNPs to investigate post F1 gene flow via patterns of genomic admixture between An. gambiae and An. arabiensis from eastern Uganda. Simulations were used to investigate the statistical power to detect hybrids with different levels of crossing and to identify the hybrid category significantly admixed genotypes could represent. Results A range of admixture proportions were detected for 11 field-collected hybrids identified via single-locus species-diagnostic PCRs. Comparison of admixture data with simulations indicated that at least seven of these hybrids were advanced generation crosses, with backcrosses to each species identified. In addition, of 36 individuals typing as An. gambiae or An. arabiensis that exhibited outlying admixture proportions, ten were identified as significantly mixed backcrosses, and at least four of these were second or third generation crosses. Conclusions Our results show that hybrids detected using standard diagnostics will often be hybrid generations beyond F1, and that in our study area around 5% (95% confidence intervals 3%-9%) of apparently ‘pure’ species samples may also be backcrosses. This is likely an underestimate because of rapidly-declining detection power beyond the first two backcross generations. Post-F1 gene flow occurs at a far from inconsequential rate between An. gambiae and An. arabiensis, and, especially for traits under strong selection, could readily lead to adaptive introgression of genetic variants relevant for vector control. Electronic supplementary material The online version of this article (doi:10.1186/1756-3305-7-345) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | - Craig S Wilding
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
| |
Collapse
|