Hybrid speciation and ghost ancestry shape the Anopheles gambiae species complex

Speciation within reticulate radiations can involve both lineage divergence and hybrid lineage formation, yet recurrent introgression obscures both histories. In the Anopheles gambiae complex, gene-family presence-absence data yielded a species tree favored over four sequence-derived alternatives by network-model comparison. D-BPP analyses recovered seven reticulation events, including multiple ghost-lineage contributions, and supported a ghost-mediated hybrid origin of A. merus . Simulations showed that sampled-parent hybrid origin generates temporal convergence between reticulation and lineage formation when analyzed under an ordinary introgression model; this signature supported hybrid speciation in A. gambiae . Loci with contrasting parental affinities contained olfactory and cuticular genes with potential roles in prezygotic isolation. Together, these results resolve species relationships and identify candidate genomic mechanisms through which hybridization may have contributed to reproductive isolation.