Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

Angiosperms experienced one of the most remarkable radiations of land plants and are now the dominant autotrophs in terrestrial ecosystems. Recent phylogenomic studies based on large-scale data from plastid, mitochondrial, or nuclear transcriptomes/genomes and increased taxon sampling have provided unprecedent resolution into the phylogeny of flowering plants. However, owing to ancient rapid radiations, the interrelationships among the five lineages of Mesangiospermae, the vast majority of angiosperms, remain contentious. Here we show that, although plastid and mitochondrial genomes lack sufficient phylogenetic signal for resolving deeper phylogeny, the relationships among five mesangiosperm lineages can be confidently resolved under better-fitting models using genome-scale data. According to our Bayesian cross-validation and model test in a maximum likelihood framework, site-heterogeneous models (e.g., CAT-GTR + G4, LG + C20 + F + G) outperform site-homogeneous or partition models often used in previous studies. Under site-heterogeneous models, the approximately unbiased test favored our preferred tree recovered from various datasets: Ceratophyllales (coontails) are robustly recovered as sister to monocots, and they together are sister to the clade comprising magnoliids, Chloranthales, and eudicots. Our phylogenomic analyses resolve the last enigma of the deeper phylogeny of angiosperms and emphasize the efficacy of modeling compositional heterogeneity in resolving rapid radiations of plants.