tristanpwdennis/kdr_funestus_report_2023

Analysis code supporting the genomic surveillance of malaria mosquitoes in Tanzania. ## Discovery of knock-down resistance in the major African malaria vector _Anopheles funestus_. This project was a big IR phenotype and genomic surveillance study in Tanzania. An. funestus were collected from across Tanzania, phenotyped for IR, and genome sequenced to identify selection at IR loci, and IR allele frequencies, as well as population structure and history. The IR phenotype surveillance data is published in Joel's paper here. These data showed that mosquitoes were resistant to DDT - strange, given DDT is an obsolete, banned, pesticide. Genome sequencing data collected and analysed as part of this project showed evidence of weak selection at the _Vgsc_ locus, in samples from a single region in Tanzania. Further examination of the _Vgsc_ locus revealed that _knock-down resistance_, in the form of the L976F (995S/F in _An. gambiae_ and 1014F/S in _M. domestica_), had appeared in _An. funestus_ where, hitherto, IR had only emerged in the form of metabolic resistance through detoxification enzymes and others. _Kdr_ in _An. funestus_ appeared often in concert with another linked mutation, P1842S, and appeared as part of a weak selective sweep in Morogoro region. We found that _Kdr_ appeared to confer resistance to DDT, and not to other, more widely used vector control pesticides. A range of plausible hypotheses for DDT emergence in _An. funestus_ present themselves, but one we found the most plausible was extensive DDT pollution across Tanzania, as well as unofficial use by farmers. This repository contains the code used to analyse the data generated in this analysis. The R-markdown contains: 1. Map of sequenced samples. 2. The statistical models associating DDT resistance phenotypes with _Kdr_. 3. Plots of the previously published bioassay data. 4. Allele frequency by location and timepoint, showing the frequency of _Vsgc_ mutations, and a possible decline in frequency over time in Morogoro region. 5. LD heatmap plots showing that 976F and 1842S occur as l …