We found that Cypripedium diverged first, followed by Selenipedium, and finally the three conduplicate genera, although the sister relationship between Selenipedium and the conduplicate genera is not very strongly supported (Fig. 2). That is, the plicate-leaved genera could be more primitive, while the conduplicate-leaved genera are more advanced. We also found that the two New World genera Mexipedium and Phragmipedium are most closely related and form a clade sister to the Old World Paphiopedilum (Fig. 2; Supplementary Figs. S1, S2, S3, S4). Moreover, the close relationship between the two neotropical conduplicate genera is corroborated by the shared loss of the ndhF gene. Based on the combined chloroplast and nuclear gene phylogeny (Fig. 2), in slipper orchids, the coriaceous conduplicate leaf has a single origin, but ovary number is not phylogenetically informative.