AbstractBackgroundThe last taxonomic account ofOlearecognises six subspecies withinOlea europaeaL., including the Mediterranean olive tree (subsp.europaea) and five other subspecies (laperrinei,guanchica,maroccana,cerasiformis, andcuspidata) distributed across the Old World, including Macaronesian islands. The evolutionary history of this monophyletic group (O. europaeacomplex) has revealed a reticulated scenario involving hybridization and polyploidization events, leading to the presence of a polyploid series associated with the subspecies. However, how the polyploids originated, and how the different subspecies contributed to the domestication of the cultivated olive are questions still debated. Tracing the recent evolution and genetic diversification of the species is key for the management and preservation of its genetic resources. To study the recent history of theO. europaeacomplex, we compared newly sequenced and available genomes for 27 individuals representing the six subspecies.ResultsOur results show discordance between current subspecies distributions and phylogenomic patterns, which support intricate biogeographic patterns. The subspeciesguanchica, restricted to the Canary Islands, is closely related to subsp.europaea, and shows a high genetic diversity. The subsp.laperrinei, restricted now to high mountains of the Sahara desert, and the Canarian subsp.guanchicacontributed to the formation of the allotetraploid subsp.cerasiformis(Madeira islands) and the allohexaploid subsp.maroccana(western Sahara region). Our phylogenomic data support the recognition of one more taxon (subsp.ferruginea) for the Asian populations, which is clearly segregated from the African subsp.cuspidata.ConclusionsIn sum, theO. europaeacomplex underwent several processes of hybridization, polyploidy, and geographical isolation resulting in seven independent lineages with certain morphological traits recognised into subspecies.