{ "abstract": "Aedes aegypti is the primary vector of arboviruses such as dengue, yellow fever, Zika, and chikungunya. Here, we investigate the mitochondrial DNA (mtDNA) structure and insecticide resistance of Ae. aegypti populations across Kenya. Using 175 newly sequenced Kenyan COI mtDNA fragments, along with global reference sequences, we assess maternal ancestry and phylogeographic structure. Genetic structure across Kenya was not well explained by isolation-by-distance alone, with several populations deviating from this pattern. Nairobi and Mombasa, separated by >400 km, showed greater maternal genetic similarity than expected under isolation-by-distance, a pattern that may reflect gene flow along transportation corridors. Conversely, Ukunda, around 30 km from Mombasa, was comparatively divergent, and populations in Western Kenya were genetically distinct. We found no evidence of non-African ancestry in mtDNA from Rabai or Mombasa despite its previous detection in the nuclear genomes of these populations. Instead, a subset of samples from Marigat and Ukunda showed the closest maternal affinity to West African and non-African lineages. Insecticide assays revealed high susceptibility to bendiocarb, deltamethrin, and fenitrothion across populations, but substantial resistance to permethrin, particularly at coastal sites. Genotyping of the kdr 1534C allele showed the highest resistance allele frequencies in coastal populations, broadly consistent with the phenotypic patterns. This variation in resistance was not associated with mitochondrial ancestry, suggesting that local selection pressures rather than shared maternal ancestry may be shaping resistance. Together, these findings describe the maternal genetic structure of Ae. aegypti in Kenya and show that localised resistance evolution, in the absence of organised Ae. aegypti-targeted control, underscores the need to monitor resistance mechanisms. Author summary: Aedes aegypti mosquitoes transmit devastating viral diseases including dengue, yellow fever, Zika, and chikungunya to billions of people worldwide. Understanding the genetic makeup and insecticide resistance patterns of these mosquitoes in their ancestral African range is crucial for disease control. We studied Ae. aegypti populations across Kenya by analysing their mitochondrial DNA—genetic material inherited solely through the maternal line—and testing their susceptibility to commonly used insecticides. We discovered unexpected patterns of genetic relationships: mosquito populations in Nairobi and the coastal city of Mombasa, separated by over 400 kilometres, were genetically similar, likely due to mosquitoes travelling along major transport routes. Conversely, Ukunda, merely 30 kilometres from Mombasa, showed distinct genetic differences, possibly due to geographical barriers like water bodies. Intriguingly, whilst previous studies found evidence of non-African mosquitoes invading Kenya’s coast through nuclear DNA analysis, we found no such evidence in mitochondrial DNA, suggesting complex evolutionary processes at play. Our insecticide testing revealed concerning resistance to permethrin, particularly in coastal populations, despite the absence of organised mosquito control programmes targeting Ae. aegypti in Kenya. This resistance appears driven by local selection pressures rather than mosquito ancestry. These findings highlight the urgent need for resistance monitoring and inform strategies for controlling mosquito-borne diseases in East Africa, where dengue outbreaks increasingly threaten public health.", "abstract_shown": true, "affiliations": [ "International Centre of Insect Physiology and Ecology, Nairobi, Kenya", "Department of Genetics, University of Cambridge, Cambridge, United Kingdom", "Cambridge Biosecurity Hub, Cambridge, United Kingdom" ], "article_type": "Research Article", "arxiv": null, "author_total": 8, "authors": [ { "affs": [ 0 ], "name": "Brenda Musimbi" }, { "affs": [ 1 ], "name": "Sandy Hickson" }, { "affs": [ 2 ], "name": "Trizah K. Milugo" }, { "name": "Eleanor Robinson-Rice" }, { "name": "Josephine Osalla" }, { "name": "Gilbert Rotich" }, { "name": "Frank Jiggins" }, { "name": "David P. Tchouassi" } ], "bibtex": "https://research.draconitic.com/paper/8fxfd0dp9krxf.bib", "cited_by": 0, "doi": "10.1371/journal.pntd.0014670", "fulltext_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014670", "id": "8fxfd0dp9krxf", "issns": [ "1935-2735" ], "landing_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014670", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1311|Genetic diversity and population structure" ], [ "plos", "/Biology and life sciences/Agriculture/Agrochemicals/Insecticides" ], [ "plos", "/Biology and life sciences/Biochemistry/Bioenergetics/Energy-producing organelles/Mitochondria" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/Forms of DNA/Mitochondrial DNA" ], [ "plos", "/Biology and life sciences/Cell biology/Cellular structures and organelles/Energy-producing organelles/Mitochondria" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Population genetics" ], [ "plos", "/Biology and life sciences/Genetics/DNA/Forms of DNA/Mitochondrial DNA" ], [ "plos", "/Biology and life sciences/Genetics/Population genetics" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Animals/Invertebrates/Arthropoda/Insects/Mosquitoes" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Animals/Invertebrates/Arthropoda/Insects/Mosquitoes/Aedes aegypti" ], [ "plos", "/Biology and life sciences/Population biology/Population genetics" ], [ "plos", "/Biology and life sciences/Species interactions/Disease vectors/Insect vectors/Mosquitoes" ], [ "plos", "/Biology and life sciences/Species interactions/Disease vectors/Insect vectors/Mosquitoes/Aedes aegypti" ], [ "plos", "/Biology and life sciences/Zoology/Animals/Invertebrates/Arthropoda/Insects/Mosquitoes" ], [ "plos", "/Biology and life sciences/Zoology/Animals/Invertebrates/Arthropoda/Insects/Mosquitoes/Aedes aegypti" ], [ "plos", "/Biology and life sciences/Zoology/Entomology/Insects/Mosquitoes" ], [ "plos", "/Biology and life sciences/Zoology/Entomology/Insects/Mosquitoes/Aedes aegypti" ], [ "plos", "/Medicine and health sciences/Medical conditions/Infectious diseases/Disease vectors/Insect vectors/Mosquitoes" ], [ "plos", "/Medicine and health sciences/Medical conditions/Infectious diseases/Disease vectors/Insect vectors/Mosquitoes/Aedes aegypti" ], [ "plos", "/People and places/Geographical locations/Africa" ], [ "plos", "/People and places/Geographical locations/Africa/Kenya" ] ], "openalex": "W7211944474", "pdf_url": "https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0014670&type=printable", "pmcid": null, "pmid": null, "published": "2026-09-08", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/8fxfd0dp9krxf.ris", "sources": [ { "first_seen": "2026-10-30T12:17:56Z", "native_id": "10.1371/journal.pntd.0014670", "source": "plos", "url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014670" } ], "subjects": [ { "field": "biology", "origin": "plos:genetics", "subfield": "genetics-genomics" }, { "field": "biology", "origin": "plos:zoology", "subfield": "zoology-behaviour" }, { "field": "medicine", "origin": "plos:infectious diseases", "subfield": "infectious-disease" } ], "title": "Mitochondrial phylogeography and insecticide resistance of Aedes aegypti in Kenya", "title_text": "Mitochondrial phylogeography and insecticide resistance of Aedes aegypti in Kenya", "type": "peer-reviewed", "updated_at": "2026-10-30T12:17:56Z", "url": "https://research.draconitic.com/paper/8fxfd0dp9krxf", "venue": "PLOS Neglected Tropical Diseases", "versions": [] }