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).