Phylogenomic conflict and reticulate evolution during radiative diversification of the genus <i>Rheum</i>

BACKGROUND AND AIMS: The evolutionary mechanisms that underpin the remarkable morphological diversity observed in rapidly radiating plant lineages within mountainous ecosystems continue to captivate the attention of evolutionary biology. The genus Rheum (rhubarb), is an alpine genus renowned for its striking variation in growth forms and specialized bracts in the Qinghai-Tibet Plateau and adjacent regions, thus presenting an exceptional system to address this inquiry. METHODS: We employed a phylogenomic approach, integrating nuclear gene and plastid gene information derived from transcriptome data encompassing 64 samples across 31 species, to reconstruct the evolutionary trajectory of the genus Rheum. Phylogenetic reconstruction, network analyses, and ancestral state reconstruction of key morphological traits were performed to elucidate evolutionary history and identify processes such as incomplete lineage sorting (ILS) and hybridization. KEY RESULTS: Our analyses reveal cytonuclear discordance within Rheum, likely resulting from both incomplete lineage sorting (ILS) and considerable historical hybridization, the latter being supported by phylogenetic network analyses. Furthermore, ancestral state reconstruction of key morphological traits uncovers multiple independent origins of dwarfism, and specialized "greenhouse" bracts, pointing to pervasive convergent evolution. The recurrent emergence of these morphological traits may be driven by similar environmental stresses, highlighting the role of ecological adaptation in facilitating phenotypic diversification. CONCLUSIONS: The key morphological traits of Rheum exhibit repeated independent origins and are associated with complex evolutionary processes within the context of rapid radiation, including incomplete lineage sorting and historical hybridization. Furthermore, ecological adaptation may have contributed to their phenotypic convergence.