The distributions of anopheline larval habitats were aggregated in valley bottoms in Kenya in both the rainy and dry seasons, although the degree of aggregation was higher in the dry season than in the rainy season. Larvae of the Anopheles gambiae complex larvae were found more frequently in habitats in farmlands and pastures. However, An. funestus larvae were found more frequently in natural swamps and pastures. Canopy cover was the only variable significantly associated with the occurrence of the An. gambiae complex and An. funestus. The average canopy cover was significantly less in the habitats with the An. gambiae complex and An. funestus larvae than those without the anopheline larvae. Thus, land cover types and topographic features showed important effects on the distribution of anopheline larval habitats. These results suggest that clearing riparian forests would improve growing conditions of the An. gambiae complex and An. funestus larvae in Kenyan highlands.

Malaria causes more than 300 million clinical cases and 665,000 deaths each year, and the majority of the mortality and morbidity occurs in sub-Saharan Africa. Due to the lack of effective vaccines and wide-spread resistance to antimalarial drugs, mosquito control is the primary method of malaria prevention and control. Currently, malaria vector control relies on the use of insecticides, primarily pyrethroids. The extensive use of insecticides has imposed strong selection pressures for resistance in the mosquito populations. Consequently, resistance to pyrethroids in Anopheles gambiae, the main malaria vector in sub-Saharan Africa, has become a major obstacle for malaria control. A key element of resistance management is the identification of resistance mechanisms and subsequent development of reliable resistance monitoring tools. Field-derived An. gambiae from Western Kenya were phenotyped as deltamethrin-resistant or -susceptible by the standard WHO tube test, and their expression profile compared by RNA-seq. Based on the current annotation of the An. gambiae genome, a total of 1,093 transcripts were detected as significantly differentially accumulated between deltamethrin-resistant and -susceptible mosquitoes. These transcripts are distributed over the entire genome, with a large number mapping in QTLs previously linked to pyrethorid resistance, and correspond to heat-shock proteins, metabolic and transport functions, signal transduction activities, cytoskeleton and others. The detected differences in transcript accumulation levels between resistant and susceptible mosquitoes reflect transcripts directly or indirectly correlated with pyrethroid resistance. RNA-seq data also were used to perform a de-novo Cufflinks assembly of the An. gambiae genome.