Phylogenomic discordance is mainly driven 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 the five lineages of Mesangiospermae is important for understanding the early diversification process 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. Importantly, we investigated the potential causes of phylogenetic discordance and inferred phylogenetic networks to explore reticulating events among the five lineages of Mesangiospermae. Coalescent simulation analyses suggested that a combination of incomplete lineage sorting and hybridization could explain the high levels of discordance among nuclear genes in the backbone of Mesangiospermae. Cytonuclear discordance was observed among the five Mesangiospermae lineages, potentially resulting from hybridization. Furthermore, systematic errors in species networks cannot be overlooked. Our study revealed that deep phylogenetic discordances among the five Mesangiospermae lineages were affected by multiple factors, particularly pervasive ancient hybridization.