Major changes in circumscriptions of fabids and malvids
In most studies using organellar genes, core rosids consisted of two major groups: fabids and malvids. In our results, we recovered two major core rosid clades, but these differed in composition from those reported to date (Fig. 5, Fig. 6 ). The fabid clade consisted only of the nitrogen-fixing clade (Cucurbitales, Fagales, Fabales, and Rosales). Meanwhile, Picramniales, the CM clade, Huerteales, Oxalidales, Sapindales, Malvales, and Brassicales composed the “expanded” malvids. The remaining four core rosid orders (Geraniales, Crossosomatales, Zygophyllales, and Myrtales) were recovered in more early diverging positions and were not placed in either malvids or fabids, a relationship first reported by Qiu et al. (2010) . In our concatenation tree, Geraniales and Crossosomatales formed a strongly supported clade, Zygophyllales was sister to Myrtales with strong support, and these two clades were subsequently successive sisters to the fabids-malvids clade (Fig. 5 ). However, Geraniales and Crossosomatales did not form a clade in our coalescence analysis, although the support for relationships was weak in this part of the tree (Fig. 6 ). Zhao et al. (2016) recovered a similar rosid topology with fewer taxa based on 891 clusters of putative orthologous genes, except for the position of Zygophyllales; however, most studies did not recover early diverging positions for the four rosid orders. Missing data may be an important cause of inconsistent topologies because of their presence in previous nuclear phylogenomic studies (Kvist & Siddall, 2013; Roure et al., 2013 ). Further literature reviews concerning Picramniales and Huerteales are available in Discussion section S1.