{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T18:14:30Z","timestamp":1776708870574,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pgen.1009253","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,2]],"date-time":"2021-02-02T00:00:00Z","timestamp":1612224000000}}],"reference-count":88,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2021,1,21]],"date-time":"2021-01-21T00:00:00Z","timestamp":1611187200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    Vector population control using insecticides is a key element of current strategies to prevent malaria transmission in Africa. The introduction of effective insecticides, such as the organophosphate pirimiphos-methyl, is essential to overcome the recurrent emergence of resistance driven by the highly diverse\n                    <jats:italic>Anopheles<\/jats:italic>\n                    genomes. Here, we use a population genomic approach to investigate the basis of pirimiphos-methyl resistance in the major malaria vectors\n                    <jats:italic>Anopheles gambiae<\/jats:italic>\n                    and\n                    <jats:italic>A<\/jats:italic>\n                    .\n                    <jats:italic>coluzzii<\/jats:italic>\n                    . A combination of copy number variation and a single non-synonymous substitution in the acetylcholinesterase gene,\n                    <jats:italic>Ace1<\/jats:italic>\n                    , provides the key resistance diagnostic in an\n                    <jats:italic>A<\/jats:italic>\n                    .\n                    <jats:italic>coluzzii<\/jats:italic>\n                    population from C\u00f4te d\u2019Ivoire that we used for sequence-based association mapping, with replication in other West African populations. The\n                    <jats:italic>Ace1<\/jats:italic>\n                    substitution and duplications occur on a unique resistance haplotype that evolved in\n                    <jats:italic>A<\/jats:italic>\n                    .\n                    <jats:italic>gambiae<\/jats:italic>\n                    and introgressed into\n                    <jats:italic>A<\/jats:italic>\n                    .\n                    <jats:italic>coluzzii<\/jats:italic>\n                    , and is now common in West Africa primarily due to selection imposed by other organophosphate or carbamate insecticides. Our findings highlight the predictive value of this complex resistance haplotype for phenotypic resistance and clarify its evolutionary history, providing tools to for molecular surveillance of the current and future effectiveness of pirimiphos-methyl based interventions.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1009253","type":"journal-article","created":{"date-parts":[[2021,1,21]],"date-time":"2021-01-21T13:25:27Z","timestamp":1611235527000},"page":"e1009253","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":58,"title":["Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1978-5824","authenticated-orcid":true,"given":"Xavier","family":"Grau-Bov\u00e9","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3892-1668","authenticated-orcid":true,"given":"Eric","family":"Lucas","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2230-6364","authenticated-orcid":true,"given":"Dimitra","family":"Pipini","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3407-4959","authenticated-orcid":true,"given":"Emily","family":"Rippon","sequence":"additional","affiliation":[]},{"given":"Arj\u00e8n E.","family":"van \u2018t Hof","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1564-4354","authenticated-orcid":true,"given":"Edi","family":"Constant","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4105-1010","authenticated-orcid":true,"given":"Samuel","family":"Dadzie","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4447-4027","authenticated-orcid":true,"given":"Alexander","family":"Egyir-Yawson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6864-2075","authenticated-orcid":true,"given":"John","family":"Essandoh","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1988-5403","authenticated-orcid":true,"given":"Joseph","family":"Chabi","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7381-6321","authenticated-orcid":true,"given":"Luc","family":"Djogb\u00e9nou","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5907-0773","authenticated-orcid":true,"given":"Nicholas J.","family":"Harding","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9018-4680","authenticated-orcid":true,"given":"Alistair","family":"Miles","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5023-0176","authenticated-orcid":true,"given":"Dominic","family":"Kwiatkowski","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5218-1497","authenticated-orcid":true,"given":"Martin J.","family":"Donnelly","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5820-1388","authenticated-orcid":true,"given":"David","family":"Weetman","sequence":"additional","affiliation":[]},{"name":"The Anopheles gambiae 1000 Genomes Consortium","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2021,1,21]]},"reference":[{"key":"pgen.1009253.ref001","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1186\/s12936-016-1201-1","article-title":"Trends in US President\u2019s Malaria Initiative-funded indoor residual spray coverage and insecticide choice in sub-Saharan Africa (2008\u20132015): urgent need for affordable, long-lasting insecticides","volume":"15","author":"RM Oxborough","year":"2016","journal-title":"Malar J"},{"key":"pgen.1009253.ref002","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s13071-017-2608-4","article-title":"Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI\/USAID-supported IRS countries","volume":"11","author":"D Dengela","year":"2018","journal-title":"Parasit Vectors"},{"key":"pgen.1009253.ref003","unstructured":"World Health Organization. Report of the Sixteenth WHOPES Working Group Meeting. Gen\u00e8va; 2013."},{"key":"pgen.1009253.ref004","unstructured":"World Health Organization. Global report on insecticide resistance in malaria vectors: 2010\u20132016. Gen\u00e8va; 2018."},{"key":"pgen.1009253.ref005","doi-asserted-by":"crossref","first-page":"4982","DOI":"10.1038\/s41467-018-07357-w","article-title":"Systematic review of indoor residual spray efficacy and effectiveness against Plasmodium falciparum in Africa","volume":"9","author":"E Sherrard-Smith","year":"2018","journal-title":"Nat Commun"},{"key":"pgen.1009253.ref006","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1289\/ehp.1104340","article-title":"Global Trends in the Use of Insecticides to Control Vector-Borne Diseases","volume":"120","author":"H van den Berg","year":"2012","journal-title":"Environ Health Perspect"},{"key":"pgen.1009253.ref007","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.pt.2010.08.004","article-title":"Pyrethroid resistance in African anopheline mosquitoes: what are the implications for malaria control?","volume":"27","author":"Ranson H","year":"2011","journal-title":"Trends Parasitol"},{"key":"pgen.1009253.ref008","first-page":"17","article-title":"An observational analysis of the impact of indoor residual spraying with non-pyrethroid insecticides on the incidence of malaria in S\u00e9gou Region, Mali: 2012\u20132015","author":"J Wagman","year":"2018","journal-title":"Malar J"},{"key":"pgen.1009253.ref009","first-page":"1","article-title":"Impact of indoor residual spraying with pirimiphos-methyl (Actellic 300CS) on entomological indicators of transmission and malaria case burden in Migori County, western Kenya","volume":"10","author":"B Abong\u2019o","journal-title":"Sci Rep. 2020"},{"key":"pgen.1009253.ref010","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1186\/s12936-017-2087-2","article-title":"Multiple insecticide resistance in Anopheles gambiae from Tanzania: A major concern for malaria vector control","volume":"16","author":"WN Kisinza","year":"2017","journal-title":"Malar J"},{"key":"pgen.1009253.ref011","first-page":"13","article-title":"Resistance status of Anopheles gambiae (s.l.) to four commonly used insecticides for malaria vector control in South-East Nigeria","author":"O Chukwuekezie","year":"2020","journal-title":"Parasites and Vectors"},{"key":"pgen.1009253.ref012","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.cbi.2005.10.041","article-title":"Comparing the organophosphorus and carbamate insecticide resistance mutations in cholin- and carboxyl-esterases","volume":"157\u2013158","author":"JG Oakeshott","year":"2005","journal-title":"Chem Biol Interact"},{"key":"pgen.1009253.ref013","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/423136b","article-title":"Insecticide resistance in mosquito vectors","volume":"423","author":"M Weill","year":"2003","journal-title":"Nature"},{"key":"pgen.1009253.ref014","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1365-2583.2004.00452.x","article-title":"The unique mutation in ace-1 giving high insecticide resistance is easily detectable in mosquito vectors","volume":"13","author":"M Weill","year":"2004","journal-title":"Insect Mol Biol"},{"key":"pgen.1009253.ref015","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.pestbp.2015.01.004","article-title":"Genotype to phenotype, the molecular and physiological dimensions of resistance in arthropods","volume":"121","author":"R Feyereisen","year":"2015","journal-title":"Pestic Biochem Physiol"},{"key":"pgen.1009253.ref016","doi-asserted-by":"crossref","first-page":"15405","DOI":"10.1021\/ja0466154","article-title":"The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design","volume":"126","author":"HM Greenblatt","year":"2004","journal-title":"J Am Chem Soc"},{"key":"pgen.1009253.ref017","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.str.2017.11.021","article-title":"Structure of the G119S Mutant Acetylcholinesterase of the Malaria Vector Anopheles gambiae Reveals Basis of Insecticide Resistance","volume":"26","author":"J Cheung","year":"2018","journal-title":"Structure"},{"key":"pgen.1009253.ref018","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/S0197-0186(96)00118-0","article-title":"Analysis of molecular forms and pharmacological properties of acetylcholinesterase in several mosquito species","volume":"31","author":"D Bourguet","year":"1997","journal-title":"Neurochem Int"},{"key":"pgen.1009253.ref019","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1093\/molbev\/msm025","article-title":"Independent Duplications of the Acetylcholinesterase Gene Conferring Insecticide Resistance in the Mosquito Culex pipiens","volume":"24","author":"P Labb\u00e9","year":"2007","journal-title":"Mol Biol Evol"},{"key":"pgen.1009253.ref020","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1111\/j.1365-3156.2009.02243.x","article-title":"Distribution of insensitive acetylcholinesterase (ace-1R) in Anopheles gambiae s.l. populations from Burkina Faso (West Africa)","volume":"14","author":"KR Dabir\u00e9","year":"2009","journal-title":"Trop Med Int Heal"},{"key":"pgen.1009253.ref021","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1186\/1475-2875-9-167","article-title":"Distribution of ace-1R and resistance to carbamates and organophosphates in Anopheles gambiae s.s. populations from C\u00f4te d\u2019Ivoire","volume":"9","author":"LP Ahoua Alou","year":"2010","journal-title":"Malar J"},{"key":"pgen.1009253.ref022","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1186\/1475-2875-12-404","article-title":"Acetylcholinesterase (Ace-1) target site mutation 119S is strongly diagnostic of carbamate and organophosphate resistance in Anopheles gambiae s.s. and Anopheles coluzzii across southern Ghana","volume":"12","author":"J Essandoh","year":"2013","journal-title":"Malar J"},{"key":"pgen.1009253.ref023","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1475-2875-13-396","article-title":"Combining organophosphate-Treated wall linings and long-lasting insecticidal nets fails to provide additional control over long-lasting insecticidal nets alone against multiple insecticide-resistant Anopheles gambiae in C\u00f4te d\u2019Ivoire: An experimental hut","volume":"13","author":"C Ngufor","year":"2014","journal-title":"Malar J"},{"key":"pgen.1009253.ref024","doi-asserted-by":"crossref","first-page":"2656","DOI":"10.1111\/mec.13197","article-title":"Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae","volume":"24","author":"D Weetman","year":"2015","journal-title":"Mol Ecol"},{"key":"pgen.1009253.ref025","doi-asserted-by":"crossref","first-page":"790","DOI":"10.3390\/genes10100790","article-title":"The G119S Acetylcholinesterase (Ace-1) Target Site Mutation Confers Carbamate Resistance in the Major Malaria Vector Anopheles gambiae from Cameroon: A Challenge for the Coming IRS Implementation","volume":"10","author":"Nouage Elanga-Ndille","year":"2019","journal-title":"Genes (Basel)"},{"key":"pgen.1009253.ref026","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1186\/s12936-015-1000-0","article-title":"Distribution and frequency of G119S mutation in ace-1 gene within Anopheles sinensis populations from Guangxi, China","volume":"14","author":"X Feng","year":"2015","journal-title":"Malar J"},{"key":"pgen.1009253.ref027","doi-asserted-by":"crossref","first-page":"e2172","DOI":"10.1371\/journal.pone.0002172","article-title":"Evidence of Introgression of the ace-1R Mutation and of the ace-1 Duplication in West African Anopheles gambiae s. s.","volume":"3","author":"L Djogb\u00e9nou","year":"2008","journal-title":"PLoS One"},{"key":"pgen.1009253.ref028","doi-asserted-by":"crossref","first-page":"e1004236","DOI":"10.1371\/journal.pgen.1004236","article-title":"CYP6 P450 Enzymes and ACE-1 Duplication Produce Extreme and Multiple Insecticide Resistance in the Malaria Mosquito Anopheles gambiae.","volume":"10","author":"C V Edi","year":"2014","journal-title":"PLoS Genet"},{"key":"pgen.1009253.ref029","doi-asserted-by":"crossref","first-page":"14529","DOI":"10.1038\/srep14529","article-title":"An ace-1 gene duplication resorbs the fitness cost associated with resistance in Anopheles gambiae, the main malaria mosquito","volume":"5","author":"BS Assogba","year":"2015","journal-title":"Sci Rep"},{"key":"pgen.1009253.ref030","doi-asserted-by":"crossref","first-page":"e2000618","DOI":"10.1371\/journal.pbio.2000618","article-title":"The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications. Barton N, editor","volume":"14","author":"BS Assogba","year":"2016","journal-title":"PLOS Biol"},{"key":"pgen.1009253.ref031","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1111\/eva.12619","article-title":"Adaptive deletion in resistance gene duplications in the malaria vector Anopheles gambiae","volume":"11","author":"BS Assogba","year":"2018","journal-title":"Evol Appl"},{"key":"pgen.1009253.ref032","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1101\/gr.262790.120","article-title":"The Anopheles gambiae 1000 Genomes Consortium. Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii","volume":"30","year":"2020","journal-title":"Genome Res"},{"key":"pgen.1009253.ref033","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1038\/nature24995","article-title":"Genetic diversity of the African malaria vector Anopheles gambiae","volume":"552","author":"A Miles","year":"2017","journal-title":"Nature"},{"key":"pgen.1009253.ref034","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1101\/gr.245795.118","article-title":"Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes","volume":"29","author":"ER Lucas","year":"2019","journal-title":"Genome Res"},{"key":"pgen.1009253.ref035","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.pestbp.2009.09.004","article-title":"Development of high-throughput real-time PCR assays for the identification of insensitive acetylcholinesterase (ace-1R) in Anopheles gambiae","volume":"96","author":"C Bass","year":"2010","journal-title":"Pestic Biochem Physiol"},{"key":"pgen.1009253.ref036","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1126\/science.1190371","article-title":"Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude","volume":"329","author":"X Yi","year":"2010","journal-title":"Science"},{"key":"pgen.1009253.ref037","first-page":"207","volume-title":"Nature","author":"AS Malaspinas","year":"2016"},{"key":"pgen.1009253.ref038","first-page":"7","article-title":"Association mapping from sequencing reads using k-mers","author":"A Rahman","year":"2018","journal-title":"Elife"},{"key":"pgen.1009253.ref039","doi-asserted-by":"crossref","first-page":"e1005004","DOI":"10.1371\/journal.pgen.1005004","article-title":"Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps.","volume":"11","author":"NR Garud","year":"2015","journal-title":"PLOS Genet"},{"key":"pgen.1009253.ref040","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/j.tree.2013.08.003","article-title":"Population genomics of rapid adaptation by soft selective sweeps","volume":"28","author":"PW Messer","year":"2013","journal-title":"Trends Ecol Evol"},{"key":"pgen.1009253.ref041","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1093\/molbev\/msr048","article-title":"Testing for Ancient Admixture between Closely Related Populations","volume":"28","author":"EY Durand","year":"2011","journal-title":"Mol Biol Evol"},{"key":"pgen.1009253.ref042","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1534\/genetics.112.145037","article-title":"Ancient Admixture in Human History","volume":"192","author":"N Patterson","year":"2012","journal-title":"Genetics"},{"key":"pgen.1009253.ref043","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1093\/jmedent\/44.3.463","article-title":"Different Amino-Acid Substitutions Confer Insecticide Resistance Through Acetylcholinesterase 1 Insensitivity in Culex vishnui and Culex tritaeniorhynchus (Diptera: Culicidae) from China","volume":"44","author":"H Alout","year":"2007","journal-title":"J Med Entomol"},{"key":"pgen.1009253.ref044","doi-asserted-by":"crossref","first-page":"e101484","DOI":"10.1371\/journal.pone.0101484","article-title":"Distribution and Frequency of kdr Mutations within Anopheles gambiae s.l. Populations and First Report of the Ace.1G119S Mutation in Anopheles arabiensis from Burkina Faso (West Africa)","volume":"9","author":"RK Dabir\u00e9","year":"2014","journal-title":"PLoS One"},{"key":"pgen.1009253.ref045","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/s12936-015-0599-1","article-title":"Novel mutations on the ace-1 gene of the malaria vector Anopheles albimanus provide evidence for balancing selection in an area of high insecticide resistance in Peru","volume":"14","author":"KA Liebman","year":"2015","journal-title":"Malar J"},{"key":"pgen.1009253.ref046","first-page":"2092","article-title":"Gene-dosage effects on fitness in recent adaptive duplications: ACE-1 in the mosquito culex pipiens","volume":"68","author":"P Labb\u00e9","year":"2014","journal-title":"Evolution (N Y)"},{"key":"pgen.1009253.ref047","first-page":"500","article-title":"Long-term trends in Anopheles gambiae insecticide resistance in C\u00f4te d\u2019Ivoire","volume":"7","author":"V Edi CA","year":"2014","journal-title":"Parasit Vectors"},{"key":"pgen.1009253.ref048","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1186\/s12936-015-1026-3","article-title":"Estimation of allele-specific Ace-1 duplication in insecticide-resistant Anopheles mosquitoes from West Africa","volume":"14","author":"LS Djogb\u00e9nou","year":"2015","journal-title":"Malar J"},{"key":"pgen.1009253.ref049","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1093\/trstmh\/trv017","article-title":"Evolution of insecticide resistance diagnostics in malaria vectors","volume":"109","author":"D Weetman","year":"2015","journal-title":"Trans R Soc Trop Med Hyg"},{"key":"pgen.1009253.ref050","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1186\/s12936-019-2888-6","article-title":"Susceptibility testing of Anopheles malaria vectors with the neonicotinoid insecticide clothianidin; Results from 16 African countries, in preparation for indoor residual spraying with new insecticide formulations","volume":"18","author":"RM Oxborough","year":"2019","journal-title":"Malar J"},{"key":"pgen.1009253.ref051","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1009253.ref052","first-page":"11.10.1","article-title":"From fastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline","volume":"11","author":"GA Van der Auwera","year":"2013","journal-title":"Curr Protoc Bioinforma"},{"key":"pgen.1009253.ref053","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1016\/j.ajhg.2013.09.002","article-title":"Haplotype estimation using sequencing reads","volume":"93","author":"O Delaneau","year":"2013","journal-title":"Am J Hum Genet"},{"key":"pgen.1009253.ref054","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"P Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"pgen.1009253.ref055","author":"The Anopheles gambiae 1000 Genomes Consortium","year":"2017"},{"key":"pgen.1009253.ref056","doi-asserted-by":"crossref","first-page":"D707","DOI":"10.1093\/nar\/gku1117","article-title":"VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases","volume":"43","author":"GI Giraldo-Calder\u00f3n","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009253.ref057","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1046\/j.1365-2915.2002.00393.x","article-title":"Simultaneous identification of species and molecular forms of the Anopheles gambiae complex by PCR-RFLP","volume":"16","author":"C Fanello","year":"2002","journal-title":"Med Vet Entomol"},{"key":"pgen.1009253.ref058","author":"World Health Organization","year":"2018","edition":"2"},{"key":"pgen.1009253.ref059","author":"by the Intramural Research Program IF, of the NIH","year":"2018"},{"key":"pgen.1009253.ref060","article-title":"pairwiseCI: Confidence Intervals for Two Sample Comparisons","author":"F Schaarschmidt","year":"2019"},{"key":"pgen.1009253.ref061","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/1475-2875-7-163","article-title":"Insertion polymorphisms of SINE200 retrotransposons within speciation islands of Anopheles gambiae molecular forms","volume":"7","author":"F Santolamazza","year":"2008","journal-title":"Malar J"},{"key":"pgen.1009253.ref062","doi-asserted-by":"crossref","first-page":"e0215669","DOI":"10.1371\/journal.pone.0215669","article-title":"Rapid high throughput SYBR green assay for identifying the malaria vectors Anopheles arabiensis, Anopheles coluzzii and Anopheles gambiae s.s. Giles","volume":"14","author":"J Chabi","year":"2019","journal-title":"PLoS One"},{"key":"pgen.1009253.ref063","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1534\/genetics.108.093153","article-title":"Linkage disequilibrium between loci with unknown phase","volume":"182","author":"AR Rogers","year":"2009","journal-title":"Genetics"},{"key":"pgen.1009253.ref064","author":"A Miles","year":"2017","journal-title":"scikit-allel"},{"key":"pgen.1009253.ref065","article-title":"SciPy: Open source scientific tools for Python","author":"E Jones","year":"2019"},{"key":"pgen.1009253.ref066","article-title":"Graphviz\u2014Graph Visualization Software","author":"J Ellson"},{"key":"pgen.1009253.ref067","article-title":"The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii","author":"CS Clarkson","year":"2018","journal-title":"BioRxiv"},{"key":"pgen.1009253.ref068","unstructured":"Clarkson C, Miles A. Hapclust. 2018. Available: https:\/\/github.com\/malariagen\/agam-vgsc-report"},{"key":"pgen.1009253.ref069","doi-asserted-by":"crossref","first-page":"1258524","DOI":"10.1126\/science.1258524","article-title":"Extensive introgression in a malaria vector species complex revealed by phylogenomics","volume":"347","author":"MC Fontaine","year":"2015","journal-title":"Science"},{"key":"pgen.1009253.ref070","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"L-TT Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"pgen.1009253.ref071","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"S Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"pgen.1009253.ref072","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the Ultrafast Bootstrap Approximation","volume":"35","author":"DT Hoang","year":"2018","journal-title":"Mol Biol Evol"},{"key":"pgen.1009253.ref073","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1093\/molbev\/mst024","article-title":"Ultrafast approximation for phylogenetic bootstrap","volume":"30","author":"BQ Minh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"pgen.1009253.ref074","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1111\/j.2041-210X.2011.00169.x","article-title":"phytools: an R package for phylogenetic comparative biology (and other things)","volume":"3","author":"LJ Revell","year":"2012","journal-title":"Methods Ecol Evol"},{"key":"pgen.1009253.ref075","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Schwartz R, editor","volume":"35","author":"E Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"pgen.1009253.ref076","unstructured":"Cavalli-Sforza L. Human Diversity. Proceedings of the 12th International Congress of Genetics. 1969. pp. 405\u2013416."},{"key":"pgen.1009253.ref077","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1093\/genetics\/132.2.583","article-title":"Estimation of levels of gene flow from DNA sequence data","volume":"132","author":"RR Hudson","year":"1992","journal-title":"Genetics"},{"key":"pgen.1009253.ref078","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1101\/gr.154831.113","article-title":"Estimating and interpreting FST: The impact of rare variants","volume":"23","author":"G Bhatia","year":"2013","journal-title":"Genome Res"},{"key":"pgen.1009253.ref079","unstructured":"Klaus B, Strimmer. K. fdrtool: Estimation of (Local) False Discovery Rates and Higher Criticism. 2015."},{"key":"pgen.1009253.ref080","doi-asserted-by":"crossref","first-page":"e190","DOI":"10.1371\/journal.pgen.0020190","article-title":"Population Structure and Eigenanalysis","volume":"2","author":"N Patterson","year":"2006","journal-title":"PLoS Genet"},{"key":"pgen.1009253.ref081","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"G Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"key":"pgen.1009253.ref082","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria; 2017. Available: https:\/\/www.r-project.org\/"},{"key":"pgen.1009253.ref083","doi-asserted-by":"crossref","first-page":"D807","DOI":"10.1093\/nar\/gky1053","article-title":"OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs","volume":"47","author":"V Kriventseva E","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009253.ref084","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"B Buchfink","year":"2014","journal-title":"Nat Methods"},{"key":"pgen.1009253.ref085","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"pgen.1009253.ref086","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"S Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1009253.ref087","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"SQ Le","year":"2008","journal-title":"Mol Biol Evol"},{"key":"pgen.1009253.ref088","unstructured":"Geneious. Geneious. 2019. Available: www.geneious.com"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1009253","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,2]],"date-time":"2021-02-02T00:00:00Z","timestamp":1612224000000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009253","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,2]],"date-time":"2021-02-02T15:59:23Z","timestamp":1612281563000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009253"}},"subtitle":[],"editor":[{"given":"Richard H.","family":"ffrench-Constant","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,1,21]]},"references-count":88,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,1,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1009253","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.05.18.102343","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,1,21]]}}}