Abstract: Introgression is an important evolutionary mechanism in insects and animals evolution. Current methods for detecting introgression rely on the analysis of phylogenetic incongruence, using either statistical tests based on expected phylogenetic patterns in small phylogenies or probabilistic modelling in a phylogenetic network context, in which case prior hypothesis on possible introgression events are needed. However, introgression leaves a phylogenetic signal similar to horizontal gene transfer, which suggests that introgression detection can also be approached through the gene tree / species tree reconciliation framework. This allows to account jointly for other evolutionary mechanisms such as gene duplication and gene loss. In this work, we apply this principle to a large dataset of Anopheles mosquito genomes and recover the extensive introgression that occurs in the gambiae complex, although with some variations compared to previous reports, and observe a strong support for an ancient introgression event involving An. christyi.

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