Genetic Diversity and Population Structure of Anopheles funestus in Western Kenya Based on Mitochondrial DNA Marker COII

SIMPLE SUMMARY: An. funestus is a major vector of human malaria and is responsible for high transmissions in sub-Saharan Africa. In the malaria endemic region of western Kenya, it has adapted and colonized different ecological niches owing to its high resistance to pyrethroids and changing breeding environments. The genetic basis of its ecological adaptations to various settings, which could enrich our understanding of how the population is structured or segregated, is poorly understood. This study sought to evaluate the population structure and genetic diversity of Anopheles funestus in different landscapes in western Kenya. To achieve this, the cytochrome oxidase subunit II gene (COII) was PCR-amplified and sequenced. This study revealed an excess of low-frequency variations that are likely due to population expansion or possibly negative selection pressure. Our findings could serve as a guide for future genomic research to facilitate the design of control strategies. ABSTRACT: The mitochondrial marker, COII, was employed to assess the genetic structure and diversity of Anopheles funestus, a very important malaria vector in Africa that adapt and colonize different ecological niches in western Kenya. Mosquitoes were collected using mechanical aspirators in four areas (Bungoma, Port Victoria, Kombewa, and Migori) in western Kenya. Following morphological identification, PCR was used to confirm the species. The COII gene was amplified, sequenced, and analyzed to determine genetic diversity and population structure. A total of 126 (Port Victoria-38, Migori-38, Bungoma-22, and Kombewa-28) sequences of COII were used for population genetic analysis. Anopheles funestus had a high haplotype diversity (Hd = 0.97 to 0.98) but low nucleotide diversity (Π = 0.004 to 0.005). The neutrality test revealed negative Tajima’s D and Fs values indicating an excess of low-frequency variation. This could be attributed to either population expansion or negative selection pressure across all the populations. No genetic or structural differentiation (Fst = −0.01) and a high level of gene flow (Gamma St, Nm = 17.99 to 35.22) were observed among the populations. Population expansion suggests the high adaptability of this species to various ecological requirements, hence sustaining its vectorial capacity and malaria transmission.