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.