Detecting Introgression in Anopheles Mosquito Genomes using a Reconciliation-Based Approach

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 modeling in a phylogenetic network context. Introgression leaves a phylogenetic signal similar to horizontal gene transfer, and it has been suggested that its detection can also be approached through the gene tree / species tree reconciliation framework, which accounts jointly for other evolutionary mechanisms such as gene duplication and gene loss. However so far the use of a reconciliation-based approach to detect introgression has not been investigated in large datasets. In this work, we apply this principle to a large dataset of Anopheles mosquito genomes. Our reconciliation-based approach recovers the extensive introgression that occurs in the gambiae complex, although with some variations compared to previous reports. Our analysis also suggests a possible ancient introgression event involving the ancestor of An. christyi.