Population Genomics of Anopheles gambiae Complex in Relation to Insecticide Resistance Allele Frequencies Across Six States in the South-South Geopolitical Zone

Insecticide resistance in Anopheles gambiae complex populations poses a major threat to the effectiveness of insecticide-based malaria vector control tools including insecticide-treated nets (ITNs) and indoor residual spraying (IRS). Population genomics approaches enable the simultaneous characterization of resistance allele frequencies and population genetic structure across broad geographic ranges. This study investigated population genomics and insecticide resistance allele distribution in An. gambiae complex mosquitoes across six South-South states (Rivers, Bayelsa, Cross River, Akwa Ibom, Delta, and Edo) using reduced-representation genotyping-by-sequencing (GBS) approaches. Adult female mosquitoes were collected by indoor resting catches, and species identification was performed by PCR-RFLP. GBS libraries were prepared using a PstI/MspI dual-enzyme protocol and sequenced on Illumina HiSeq. SNPs were called using GATK, and resistance-associated loci (kdr mutations L1014F and L1014S, ace-1 G119S) were genotyped at the population level. An. gambiae sensu stricto dominated (68%), with An. coluzzii comprising 29%. L1014F kdr allele frequency exceeded 0.70 in five of six states, while ace-1 G119S was observed at lower frequencies (0.18-0.34). Significant FST-based population differentiation was detected between coastal and inland populations, suggesting partial geographic barriers to gene flow. These population genomic findings have direct implications for resistance management strategies in South-South Nigeria's malaria vector control programs. Keywords: Anopheles gambiae, insecticide resistance, population genomics, kdr mutation, South-South Nigeria.