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Anopheles funestus is the dominant malaria vector in most parts of East and Southern Africa. To better understand its population genetic structure in Tanzania, we sequenced the genomes of 334 individual An. funestus mosquitoes from 11 regions across the country. Signs of reduced migration between western and eastern cohorts across the semi-arid central region containing the Rift Valley suggest a partial barrier to gene flow between these populations. This was evidenced by population structure between the eastern and western cohorts, as well as asynchronous selective sweeps and copy number variant profiles at the Cyp9k1 gene and Cyp6p gene cluster. Eastern cohorts, despite having less diversity and greater inbreeding, also share genetic histories characterized by low genome-wide Fst values with those in the west. This suggests that the barrier to gene flow is porous and likely represents continuous spatial structure rather than a complete barrier to migration. The observed population disconnectedness should be considered for insecticide deployment, resistance management, and the rollout of novel genetic-based vector control approaches. These findings provide the most detailed study of Tanzanian An. funestus population structure and resistance genetics to date. Future research should examine the epidemiological relevance of this partial discontinuity in gene flow and whether these populations have different malaria transmission abilities.<\/jats:p>","DOI":"10.1093\/genetics\/iyaf117","type":"journal-article","created":{"date-parts":[[2025,7,7]],"date-time":"2025-07-07T04:42:56Z","timestamp":1751863376000},"source":"Crossref","is-referenced-by-count":7,"title":["Genomic evidence of spatially structured gene flow and divergent insecticide resistance backgrounds of the malaria vector <i>Anopheles funestus<\/i> in Tanzania"],"prefix":"10.1093","volume":"230","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8463-2122","authenticated-orcid":false,"given":"Joel O","family":"Odero","sequence":"first","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]},{"name":"School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow , Glasgow G12 8QQ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ismail H","family":"Nambunga","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamis","family":"Bwanary","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustav","family":"Mkandawile","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M","family":"Paliga","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salum A","family":"Mapua","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]},{"name":"Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University , Huxley Building, Keele, Staffordshire ST5 5BG ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophia H","family":"Mwinyi","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]},{"name":"School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow , Glasgow G12 8QQ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Halfan S","family":"Ngowo","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicodem J","family":"Govella","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel W","family":"Kaindoa","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. O. Box 53, Ifakara 67501 ,","place":["Tanzania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Tripet","sequence":"additional","affiliation":[{"name":"Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University , Huxley Building, Keele, Staffordshire ST5 5BG ,","place":["UK"]},{"name":"Department of Epidemiology and Public Health, Vector Biology Unit, Swiss Tropical and Public Health Institute , Kreuzstrasse 2 Allschwil 4123 ,","place":["Switzerland"]},{"name":"Department of Public Health, University of Basel , Petersplatz 1 Basel 4001 ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia","family":"Hernandez-Koutoucheva","sequence":"additional","affiliation":[{"name":"Genomic Surveillance Unit, Wellcome Sanger Institute , Wellcome Genome Campus, Hinxton CB10 1SA ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather M","family":"Ferguson","sequence":"additional","affiliation":[{"name":"School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow , Glasgow G12 8QQ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8757-1660","authenticated-orcid":false,"given":"Chris S","family":"Clarkson","sequence":"additional","affiliation":[{"name":"Genomic Surveillance Unit, Wellcome Sanger Institute , Wellcome Genome Campus, Hinxton CB10 1SA ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9018-4680","authenticated-orcid":false,"given":"Alistair","family":"Miles","sequence":"additional","affiliation":[{"name":"Genomic Surveillance Unit, Wellcome Sanger Institute , Wellcome Genome Campus, Hinxton CB10 1SA ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5820-1388","authenticated-orcid":false,"given":"David","family":"Weetman","sequence":"additional","affiliation":[{"name":"Department of Vector Biology, Liverpool School of Tropical Medicine , Liverpool L3 5QA ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Baldini","sequence":"additional","affiliation":[{"name":"Environmental Health and Ecological Sciences Department, Ifakara Health Institute , P. 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