Genome-wide sequence analysis of malaria vectors reveals genetically isolated Anopheles coluzzii populations along the slopes of Mount Cameroon

Malaria remains a major public health burden in sub-Saharan Africa, sustained by genetically diverse Anopheles vectors. Mount Cameroon’s altitudinal gradient harbours Anopheles gambiae complex subpopulations and unravelling the population structure of these vectors could provide crucial insights into parasite transmission dynamics and evolutionary adaptations that could inform strategies for disease control and elimination. This study explored whole genome sequence data of 276 An. gambiae complex mosquitoes collected between 2020 and 2021 in six communities across the altitudinal gradient of Mount Cameroon to determine the population structure of the complex. Anopheles gambiae complex were assigned into taxa based on known ancestral informative markers (AIMs) and a set of 100,000 neutral biallelic single nucleotide polymorphisms (SNPs) randomly selected for the analysis of population structure and differentiation using Principal Component Analysis (PCA) and Fixation Index ( F ST ) respectively, followed by Admixture, Identity by Descent (IBD) and population dynamics analysis. Ninety-three (93), 178 and 4 of the vectors were identified as An. coluzzii , An. gambiae s.s and An. melas respectively while one was unassigned. Population structure revealed two subpopulations of An. coluzzii [herein referred to as An. coluzzii A (83/93) and An. coluzzii B (10/93)], from the same locality (Missellele), indicating divergence despite probable sympatry, with the An. coluzzii B ancestrally closer to those from Burkina Faso. However, the An. coluzzii A sub-population was most differentiated from all other An. coluzzii populations, strongly driven by variants on the X and 2L chromosomes, suggesting possible local reproductive isolation and ecological adaptation. This genetic divergence and recent expansion of all species in all populations, call for further genomic surveillance to support locally tailored vector control and malaria elimination efforts.