Whole‐genome data shed light on speciation and within‐species differentiation of the <scp> <i>Papilio machaon</i> </scp> complex around the Mediterranean Basin

Abstract Within swallowtail butterflies, the type species Papilio machaon Linnaeus has fostered many studies leading to a complex taxonomy. With &gt;40 subspecies formally recognized in the Palaearctic and recently simplified to 14 subspecies, there is still a need to address the taxonomic delineation within this complex. A previous phylogenomic analysis including Holarctic subspecies has revealed that Palaearctic P. machaon formed several monophyletic groups, leading to treat P. saharae Oberthür as a subspecies and the Nearctic P. machaon as a separate species ( P. bairdii Edwards). Here, we aim at testing the taxonomic boundaries and relationships in the Western Palaearctic using whole‐genome data of taxa from the Mediterranean region, which include first draft genomes of P. hospiton Géné (41× coverage depth) and P. saharae (51× coverage depth). We refined the species boundary of P. machaon and confirmed the species status of P. saharae . We assessed subspecies limits of Mediterranean P. machaon and P. saharae through Bayesian multispecies coalescent inferences and population genomic analyses, indicating that a taxonomic simplification is needed, with the exclusion of P. machaon from North Africa ( P. saharae mauretanica Verity, comb. nov .) and the synonymy of subspecies ( P. saharae neosaharae Tarrier, syn. nov .). We revealed heterogeneous levels of heterozygosity between island and continental lineages that warrant further taxonomic actions. We also found evidence of low gene flow between Corsican P. machaon and P. hospiton , endemic to Corsica (and Sardinia). We discuss how the speciation and phylogeographic patterns are in line with past climatic and geological changes of the Mediterranean Basin.