Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting

Although the phylogenetic backbone of Moraceae, an ecologically important angiosperm family in tropical rainforests, has been significantly improved, phylogenetic discordance among nuclear genes and between nuclear and plastid genomes remains common at various phylogenetic depths. However, the patterns and causes of this discordance across the entire family have not been systematically investigated. Here, we reconstructed a comprehensive phylogeny of 319 species of Moraceae using sequences from nuclear and plastid gene datasets to investigate family-wide phylogenetic conflict, identify the evolutionary drivers of conflict, and inform taxonomic revision. Phylogenetic analyses showed general congruence at the section level and above in nuclear datasets, but notable conflicts occurred at several nodes (e.g., Chlorophoreae, Bagassa, and Sloetiopsis). Discordance between nuclear and plastid trees was widespread, especially within the tribes Antiarideae, Artocarpeae, Dorstenieae, and Ficeae. Coalescent simulations and phylogenetic network analyses suggest that the observed discordance arises from a combination of incomplete lineage sorting and ancient hybridization. Based on integrated phylogenetic and morphological evidence, we propose several taxonomic revisions for the family. Overall, this work elucidates the evolutionary history of Moraceae, emphasizing the role of hybridization in its diversification, and provides a robust phylogenetic framework for future research on its classification, biogeography, and diversification.