Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.

Most extant angiosperms belong to Mesangiospermae (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). Resolving the evolutionary relationships among these five lineages is essential for understanding the early diversification of angiosperms. However, the rapid early diversification of angiosperms within a short geological period complicates the untangling of phylogenetic relationships among these Mesangiospermae lineages. Here, we used 177 publicly available angiosperm genomes to reconstruct the phylogeny of Mesangiospermae using multiple orthology inference approaches, character coding schemes, and data filtering criteria. We further investigated the potential causes of phylogenetic discordance and inferred phylogenetic networks to explore reticulation events among the five Mesangiospermae lineages. Coalescent simulation analyses suggested that a combination of incomplete lineage sorting and hybridization could explain the extensive discordance among nuclear genes in the Mesangiospermae backbone. Cytonuclear discordance was also observed among the five Mesangiospermae lineages, likely resulting from ancient hybridization. Furthermore, systematic errors in species network inference cannot be excluded. Our findings indicate that deep phylogenetic discordances among the five Mesangiospermae lineages are shaped by multiple factors, particularly pervasive ancient hybridization.