Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus <i>Ophrys</i> )

Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last five million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as ‘sexual swindling’. However, the rapid and substantial diversification of this genus, combined with its capacity for hybridisation and large genome size, poses significant challenges in addressing its systematics. We used phylotranscriptomics as a genome complexity reduction technique to infer the phylogenetic relationships among Ophrys main lineages. More than seven thousand gene trees enabled us to determine the relative contributions of gene flow and incomplete lineage sorting (ILS) in Ophrys evolution. First, we propose a new phylogenetic hypothesis for the genus with an unprecedented resolution that largely confirms the relationships between the main Ophrys lineages, but also provides new insights within each sub-genera. By combining phylogenetic network inference with introgression analyses based on gene tree topologies and branch lengths, we then show that the numerous phylogenetic incongruences among gene tree topologies result from a pervasive background of ILS, over which stand out several well-supported, ancient and potentially adaptive gene flow events between lineages. These major gene flow events provide a new perspective on the evolution of the Ophrys genus and its pollination, questioning previous hypotheses inferred without considering its reticulate evolution, and providing a better understanding of discrepancies observed among previous phylogenetic studies of the genus.