Fig. 4 Heatmap of gene recovery efficiency. Each row represents 36
superrosid species and two outgroups, and each column represents one
target gene. Shading indicates the percentage of the target length
recovered. Asterisk indicates the two outgroup species.
The phylogeny we obtained for superrosids was identical in both the ML
and BI analyses, and we reconstructed a robust (ML bootstrap support
(BS)/BI posterior probability (PP); BS/PP = 100/1) phylogeny for
superrosids, with Vitales sister to Saxifragales plus the core rosids
(Fig. 5 ). Saxifragales was strongly supported (BS/PP = 100/1)
as a sister to the core rosids. Within the core rosids, the Geraniales +
Crossosomatales clade (BS/PP = 60/1), followed by a clade of
Zygophyllales + Myrtales (BS/PP =
100/1), were sisters to the remaining core rosids. The remaining core
rosids comprised two major subclades, which we are referring to here as
“fabids” and “malvids,” although these differ from the
circumscription given in APG IV; both clades as defined here received
maximal BS support. Here, the fabids comprised only four orders known as
the nitrogen-fixing clade, within which Fagales
(BS/PP = 100/1) and Rosales (BS/PP =
100/1) were subsequent sisters to Fabales + Cucurbitales. Among the
malvids defined here, Picramniales was sister to the remaining members.
COM clade orders (Celastrales, Oxalidales, and Malpighiales) did not
form a monophyletic group in our analyses. Celastrales and Malpighiales
grouped together (BS/PP = 100/1) as sisters to the remaining orders
(Huerteales, Oxalidales, Sapindales, Malvales, and Brassicales). For the
remaining five orders, Huerteales was then resolved as sister to the
other four orders with maximum support (BS/PP = 100/1); Oxalidales and
Sapindales were subsequently recovered as successive sisters to Malvales
+ Brassicales with strong support (BS/PP = 98/1).