Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm

The angiosperm order Malpighiales includes ∼16,000 species and constitutes up to 40%of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics dur-ing the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from58 species,we identified 12 additional clades inMalpigh-iales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversi-ficationnoted in theBarbados cherries (Malpighiaceae), cocas (Eryth-roxylaceae), and passion flowers (Passifloraceae). We found that commonly used a priori approaches for partitioning concatenated data in maximum likelihood analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a poste