Abstract
The members of Anopheles gambiae species complex are ubiquitous in Afro-tropics. They have been exposed continuously to insecticides, contributing to evolution of resistance within the complex. This study used whole genome sequence data from phase 3 of the An. gambiae 1000 Genomes Project to investigate the population structure and resistance mechanisms of a newly identified species, An. gambiae Bissau molecular form (Bissau) in The Gambia. Bissau exhibited subtle divergence from sister taxa An. coluzzii (Fixation index (F(ST)) of 0.013) and An. gambiae s.s. (F(ST) of 0.023), suggesting ongoing geneflow among them. It also displayed a low but evident level of sub-clustering correlating with geographical location, contrary to sister taxa whose populations were not spatially structured. Additionally, Bissau displayed a higher number of substitutions, though at very low frequencies, in target site regions (specifically Vgsc and Ace-1) of the genome compared to its sister taxa. The well-established Vgsc-L995F mutation, normally associated with dichloro-diphenyl-trichloroethane (DDT) and pyrethroid resistance, was detected in all taxa. Also present, but at a lower frequency (< 20%) was N1570Y allele, normally associated with increased level of pyrethroid resistance when it co-occurs with L995F. Additionally, variants T791M and A1746S were found to occur alongside L995F in Bissau population at an elevated linkage disequilibrium (LD r(2) = 0.7). These findings accentuate the critical role this novel species could play on the emergence and spread of insecticide resistance in The Gambia.