Phylogenomics of the flowering plant order Malpighiales

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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 phylogenetics during the last 20 years, relationships within Malpighiales have remained poorly resolved, possibly due to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 new clades in Malpighiales and substantially increased resolution along the backbone (Chapter 1). This greatly improved phylogeny revealed a dynamic history of shifts in net species' diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We also found that commonly used a priori approaches for partitioning data in similar large-scale analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model.