Figure 2.

Analysis of genetic diversity in CYP6P9a key pyrethroid resistance gene in An. funestus populations across seven different African countries. (A) Sliding-window analysis of nucleotide polymorphism (Pi) in Southern Africa (158 accessions), Eastern (46 accession) and Central Africa (18 accessions). Pi was calculated for segments of 400 bp at 100 bp intervals. The black bar shows CYP6P9a gene’s exon. (B) Maximum likelihood tree of the CYP6P9a gene sampled from throughout Africa, showing clear geographical divergence between southern Africa (MZ, MAL, ZB and TZ; 99% bootstrap support), East Africa (UG; 98% bootstrap support) and Central Africa (DRC and CAM; 49% bootstrap support). (C) Haplotype network for non-synonymous nucleotide variants in CYP6P9a. Mosquito populations from MOZ, MAL, ZB and TZ form a defined clade from UG, DRC and CAM populations, and are dominated by a single Major haplotype. UG forms a distinct haplotype related to CAM and DRC populations that also form two distinct but related haplotypes. Haplotypes are labelled by colour and shape where the area of each circle is proportional to the frequency of the haplotype it represents. Lines connecting haplotypes and each node represent a single mutation. (D) Phylogenetic tree generated by the Neighbor-Joining method based on pairwise F_st distance obtained from 1139-bp CYP6P9a gene, including 111 A. funestus sequences from seven African countries according to each sample’s country of origin.