Modeling compositional heterogeneity resolves deep phylogeny of flowering plants.

Area of Science:

• Evolutionary Biology
• Plant Science
• Genomics

Background:

• Angiosperms are dominant terrestrial plants, but their rapid ancient radiations complicate phylogenetic resolution.
• Previous phylogenomic studies with large datasets improved understanding but left deeper relationships, particularly among Mesangiospermae, contentious.

Purpose of the Study:

• To resolve the contentious interrelationships among the five major lineages of Mesangiospermae using genome-scale data.
• To evaluate the effectiveness of different phylogenetic models in resolving ancient rapid radiations.

Main Methods:

• Phylogenomic analyses using genome-scale data from plastid, mitochondrial, and nuclear sources.
• Application and comparison of site-heterogeneous models (e.g., CAT-GTR+G4, LG+C20+F+G) against site-homogeneous or partition models.
• Bayesian cross-validation and approximate unbiased (AU) tests to assess model fit and tree robustness.

Main Results:

• Plastid and mitochondrial genomes alone provided insufficient phylogenetic signal for deep phylogeny.
• Site-heterogeneous models significantly outperformed simpler models in resolving relationships.
• Ceratophyllales were robustly resolved as sister to monocots, with this clade sister to magnoliids, Chloranthales, and eudicots.

Conclusions:

• The study successfully resolved the deeper phylogeny of angiosperms, clarifying the relationships among Mesangiospermae lineages.
• Modeling compositional heterogeneity is crucial for accurately resolving rapid radiations in plant evolution.
• This work provides a robust framework for understanding the evolutionary history of flowering plants.