This is a good case study of a problem that is common enough that anyone in this field encounters it sooner or later, and that occurs in many groups of organisms. Specifically, the situation in which extant members of a group form three clades resulting from divergence early in the evolutionary history of the group, and the crown of each clade is subtended by a relatively long branch going back to the early divergence events (Fig.

With the advent of next-generation sequencing technologies, whole-plastome data can be obtained as a byproduct of low-coverage sequencing of the plant genomic DNA. This provides an opportunity to study plastid evolution across groups, as well as testing phylogenetic relationships among taxa. Within the order Malpighiales (∼16,000 spp.), the Podostemaceae (∼300 spp.) stand out for their unique habit, living attached to rocks in fast-flowing aquatic habitats, and displaying highly modified morphologies that confound our understanding of their classification, biology, and evolution.