Phylogenomic incongruence in Castanopsis (Fagaceae) is primarily caused by gene flow rather than incomplete lineage sorting.

Reticulate evolution complicates phylogenetic reconstruction and obscures species delimitation. Investigating gene flow and its evolutionary consequences across the phylogenetic breadth of the genus provides critical insights into the mechanisms causing diversification within this lineage. By utilizing RAD-seq data from 39 Castanopsis species, we reconstructed phylogenetic relationships through both concatenation- and coalescent-based methods. To disentangle the contributions of gene flow and incomplete lineage sorting (ILS) to phylogenetic discordance, we employed an integrative approach combining topological analyses, polytomy tests, coalescent simulations, and phylogenetic network inference. Furthermore, we tracked the evolutionary trajectory of a key morphological trait across the genus. Despite pervasive gene tree incongruence, we recovered a well-supported species tree. Our analyses identified gene flow as the primary cause of phylogenomic discordance in Castanopsis, though the role of ILS could not be entirely ruled out. Ancient hybridization events along the phylogenetic backbone played a pivotal role in shaping the major clades of Castanopsis. The genus underwent an early rapid diversification during the Eocene, with speciation rates gradually declining thereafter. This study establishes a reliable phylogenetic framework for the examined Castanopsis species and demonstrates the utility of RAD-seq data in resolving complex evolutionary relationships. Our results provide novel insights into the diversification mechanisms of Castanopsis in China, emphasizing the profound impact of reticulate evolution on its evolutionary trajectory.