Landscape Genomics of Tsetse Fly (Glossina palpalis) Populations in the Guinea Savanna Zone of Nigeria: Implications for Vector Control

Tsetse flies (Glossina spp.) are the biological vectors of African trypanosomiasis, a disease affecting both humans and livestock across sub-Saharan Africa. Understanding the genetic population structure of tsetse fly populations is critical for designing effective vector control strategies, including the use of sterile insect technique (SIT) and gene drive approaches. Glossina palpalis, the riverine species responsible for human transmission in Nigeria, has not been subject to landscape genomics analysis in the Guinea savanna ecological zone that traverses North Central and South West Nigeria. This dissertation applied landscape genomics to characterise G. palpalis population structure and identify landscape features driving gene flow across the Guinea savanna zone of Nigeria. Four hundred G. palpalis individuals were sampled from 20 riverine sites across Kwara, Kogi, Niger, and Oyo States. Whole genome low-coverage sequencing (5x depth) was performed on the Illumina NovaSeq. Population structure was assessed using PCAngsd, fineSTRUCTURE, and TreeMix. Landscape resistance modelling using Circuitscape was applied to identify landscape features correlated with genetic connectivity. River basin continuity was the primary driver of gene flow, while savanna-forest ecotone transitions represented significant barriers. Three genetically distinct management units were defined. A gene drive containment risk assessment, based on these population boundaries, is proposed for responsible SIT and gene drive deployment in Nigeria. Keywords: landscape genomics, Glossina palpalis, tsetse fly, Guinea savanna, gene drive