Molecular phylogeny of the tree-of-heaven family (Simaroubaceae) based on chloroplast and nuclear markers

Members of Simaroubaceae comprise a clade of 22 genera and ca. 100 species in the Sapindales. Previous phylogenetic analyses of the family were limited to a single gene and seven genera, and relationships among the genera remain poorly understood. Molecular data from three plastid genes (rbcL, atpB, and matK) and a nuclear gene (phyC), totaling ca. 6000 bp, are used to reconstruct the phylogeny of Simaroubaceae and clarify generic limits, employing maximum parsimony (MP) and Bayesian approaches. Individual analyses of genes are largely congruent, and both MP and Bayesian analyses of combined data produce well-supported phylogenies. Nothospondias, an African genus of uncertain affiliation, is found to be a member of the family. A clade composed of Picrasma, Holacantha, and Castela is sister to the rest of the family, and enigmatic Leitneria is sister to a clade of Brucea, Soulamea, and Amaroria. Abroad circumscription of Quassia is unwarranted given several well-supported clades corresponding to traditional generic limits. Comparisons among Bayesian analyses, partitioned variously by gene and codon position, reveal that the most complex method of partitioning best explains the data under a Bayes factor criterion. However, tree topology did not change among partitioning strategies, suggesting that the phylogenetic signal is robust and resistant to model misspecification.