Speciation and evolution in the Anopheles gambiae complex in the face of widespread introgressive hybridization

This thesis explores the genetic variation and evolution of mosquito populations within the Anopheles gambiae complex (AGC), a closely related group of mosquito species serving as major vectors for the malaria parasite Plasmodium falciparum . Understanding AGC's genetic diversity is crucial for comprehending its evolutionary history and disease transmission potential. The research primarily focuses on cataloging genetic diversity in 1,142 mosquitoes collected across sub-Saharan Africa, paying special attention to introgression patterns in both nuclear and mitochondrial genomes.
Within the nuclear genome, genetic studies identify connectivity patterns among mosquito populations, areas of genetic diversity with potential insecticide resistance, and suitable gene drive targets for innovative vector control strategies. The study also delves into mitochondrial genetic variation within AGC species and its correlation with nuclear genes, shedding light on evolutionary relationships and potential adaptations. Additionally, tools for specimen identification are developed, essential for precise genetic research and effective control measures. A proof-of-concept application for mosquito specimen identification using mitochondrial genomes and publicly available sequence data is presented.
The thesis consists of six chapters, covering various aspects of the research. It begins with an overview of speciation research and AGC biology and progresses to population genetics analysis of nuclear DNA, mitochondrial DNA studies, the development of new methodologies for species tree inference considering gene flow, and the application of mitochondrial DNA for mosquito specimen identification in Southeast Asia. The final chapter summarizes key findings and discusses the integration of theoretical biology and genomics studies.