Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales Zhenxiang Xia, Brad R. Ruhfela,b, Hanno Schaefera,c, André M. Amorimd, M. Sugumarane, Kenneth J. Wurdackf, Peter K. Endressg, Merran L. Matthewsg, Peter F. Stevensh, Sarah Mathewsi,1, and Charles C. Davisa,1 aDepartment of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138; bDepartment of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; cBiodiversitaet der Pflanzen, Technische Universitaet Muenchen, D-85354 Freising, Germany; dDepartamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, 45.662-900, Bahia, Brazil; eRimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia; fDepartment of Botany, Smithsonian Institution, Washington, DC 20013; gInstitute of Systematic Botany, University of Zurich, CH-8008 Zurich, Switzerland; hDepartment of Biology, University of Missouri, St. Louis, MO 63166; and iArnold Arboretum, Harvard University, Boston, MA 02131 Edited by Robert K. Jansen, University of Texas, Austin, TX, and accepted by the Editorial Board September 11, 2012 (received for review April 6, 2012) The angiosperm order Malpighiales includes ∼16,000 species and mental, and genomic investigations of flowering plants, but also constitutes up to 40% of the understory tree diversity in tropical rain for crop improvement. forests. Despite remarkable progress in angiosperm systematics dur- Despite substantial progress in resolving the angiosperm Tree ing the last 20 y, relationships within Malpighiales remain poorly of Life during the last 20 y (1, 8–12), phylogenetic relationships resolved, possibly owing to its rapid rise during the mid-Cretaceous. within Malpighiales remain poorly resolved. Molecular studies Using phylogenomic approaches, including analyses of 82 plastid (1, 4) using multiple gene regions from the plastid, mitochon- genes from 58 species, we identified 12 additional clades in Malpigh- drial, and nuclear genomes have confirmed the monophyly of iales and substantially increased resolution along the backbone. This Malpighiales and its component families with a high degree of greatly improved phylogeny revealed a dynamic history of shifts in confidence but have identified only a handful of well-supported net diversification rates across Malpighiales, with bursts of diversi- multifamily clades. The most recent analysis by Wurdack and EVOLUTION fication noted in the Barbados cherries (Malpighiaceae), cocas (Eryth- Davis (3) included 13 genes, totaling 15,604 characters, sampled roxylaceae), and passion flowers (Passifloraceae). We found that across all three genomes from 144 Malpighiales. Their results commonly used a priori approaches for partitioning concatenated indicated that all families are monophyletic, but interrelation- data in maximum likelihood analyses, by gene or by codon position, ships among the 16 major subclades remained unresolved. The fi performed poorly relative to the use of partitions identi ed a poste- difficulty in determining these deep relationships may result from riori using a Bayesian mixture model. We also found better branch the rapid rise of the order during the mid-Cretaceous (4). support in trees inferred from a taxon-rich, data-sparse matrix, We used phylogenomic approaches to resolve relationships which deeply sampled only the phylogenetically critical placehold- within Malpighiales to provide a framework for studying their ers, than in trees inferred from a taxon-sparse matrix with little tempo and mode of diversification. Our core data set included missing data. Although this matrix has more missing data, our a pos- 82 genes sampled from the plastomes of 58 species, 48 of which teriori partitioning strategy reduced the possibility of producing were newly sequenced for this study. We combined this core data multiple distinct but equally optimal topologies and increased phy- set with the previously described taxon-rich data set of Wurdack logenetic decisiveness, compared with the strategy of partitioning by gene. These approaches are likely to help improve phylogenetic and Davis (3). Our results greatly improve phylogenetic resolu- resolution in other poorly resolved major clades of angiosperms and tion within Malpighiales, highlight the value of a unique parti- to be more broadly useful in studies across the Tree of Life. tioning strategy for phylogenomic analyses, and reveal a dynamic history of shifts in net diversification rates across the order. alpighiales are one of the most surprising clades discov- Results and Discussion fl Mered in broad molecular phylogenetic studies of the ow- Taxon and Gene Sampling. Our core data set, the 82-gene matrix, – ∼ ering plants (1 3). The order contains 16,000 species and 42 included 58 taxa (48 are newly sequenced; SI Appendix, Table families (2, 3) that exhibit remarkable morphological and eco- S2) and 82 plastid genes common to most angiosperms (72,828 logical diversity. A few examples include cactus-like succulents characters; 17% of the cells in the matrix were gaps or missing (Euphorbiaceae), epiphytes (Clusiaceae), holoparasites (Raf- data; each taxon was represented by an average of 86% of the 82 flesiaceae), submerged aquatics (Podostemaceae), and wind- genes; SI Appendix, Tables S2 and S3). The taxa were carefully pollinated trees (temperate Salicaceae). The order is ecologically selected to capture the basal nodes within deeply diverged important: species in Malpighiales constitute up to 40% of the families, such as Centroplacaceae and Euphorbiaceae (4); understory tree diversity in tropical rain forests worldwide (4). They also include many economically important species, such as Barbados nut (Jatropha curcas L., Euphorbiaceae), cassava Author contributions: Z.X., B.R.R., H.S., K.J.W., S.M., and C.C.D. designed research; Z.X., B.R.R., (Manihot esculenta Crantz, Euphorbiaceae), castor bean (Ricinus A.M.A., M.S., M.L.M., and C.C.D. performed research; Z.X., B.R.R., H.S., P.K.E., P.F.S., S.M., and communis L., Euphorbiaceae), coca (Erythroxylum coca Lam., C.C.D. analyzed data; and Z.X., B.R.R., H.S., K.J.W., P.K.E., S.M., and C.C.D. wrote the paper. Erythroxylaceae), flax (Linum usitatissimum L., Linaceae), the The authors declare no conflict of interest. poplars (Populus spp., Salicaceae), and the rubber tree (Hevea This article is a PNAS Direct Submission. R.K.J. is a guest editor invited by the brasiliensis Müll. Arg., Euphorbiaceae). Partially for this rea- Editorial Board. Data deposition: The sequence reported in this paper has been deposited in the GenBank son, genomic resources for Malpighiales are growing at a rapid database (accession no. JX661767–JX665032). pace and include whole-genome sequencing projects com- 1To whom correspondence may be addressed. E-mail: [email protected] or smathews@ pleted or near completion for Barbados nut (5), cassava, castor oeb.harvard.edu. fl bean (6), ax, and poplar (7). Thus, a resolved phylogeny of Mal- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. pighiales is critical not only for evolutionary, ecological, develop- 1073/pnas.1205818109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1205818109 PNAS Early Edition | 1of6 Downloaded by guest on September 23, 2021 they represent 39 of the 42 families of Malpighiales (excluding sensu Wurdack and Davis (3) (clade 7). Surprisingly, the Lophopyxidaceae, Malesherbiaceae, and Rafflesiaceae; SI Ap- euphorbioid clade (64 BP, 0.61 PP) reunites most of the former pendix, SI Materials and Methods) and relevant outgroups. To Euphorbiaceae (including Euphorbiaceae, Peraceae, Phyllan- obtain the most comprehensive phylogenetic tree for the order, thaceae, and Picrodendraceae but excluding Putranjivaceae) we used the 82-gene matrix as a scaffold to which we added the (13, 14) with the well-supported (96 BP, 1.0 PP) linoid clade existing taxon-rich but character-sparse 13-gene matrix (186 taxa; (clade 6; Ixonanthaceae + Linaceae) we identified. Within the 15,574 characters; 15% missing data) (3) to create our combined- euphorbioids, the linoids are well-supported (clade 5; 84 BP, 1.0 incomplete matrix (Table 1). This matrix included 191 taxa and 91 PP) as sister to the phyllanthoids (Phyllanthaceae + Picroden- genes (82 plastid genes, six mitochondrial genes, and three nu- draceae; 100 BP, 1.0 PP). The second major subclade identified clear genes; 81,259 characters; 64% missing data). We also cre- here, clade 7 (62 BP, 0.79 PP), includes Humiriaceae and the ated a combined-complete matrix by reducing the taxon sampling parietal clade (100 BP, 1.0 PP). Within the parietal clade, Gou- in the combined-incomplete matrix to match the taxon sampling of piaceae is sister to Violaceae (clade 9; 75 BP, 0.62 PP). Also the 82-gene matrix. This greatly reduced the percentage of within the parietal clade, (Malesherbiaceae (Passifloraceae + missing data cells in our alignment from 64% to 12%. The Turneraceae)) is sister to the salicoids [clade 8; (Lacistemataceae combined-complete matrix included 58 taxa and 91 genes (81,117 (Samydaceae (Salicaceae + Scyphostegiaceae))); 96 BP, 1.0 PP]. characters). Finally, we reanalyzed the 13-gene matrix alone to Clade 2 (83 BP, 1.0 PP) includes three subclades in a tri- determine the phylogenetic impact of adding the 82-gene matrix. chotomy. Its first major subclade, clade 10 (70 BP, 0.81 PP), Each of the four matrices was analyzed using four different data includes