Systematic extinctions can leave major morphological gaps between living crown-group clades. Such morphological gaps would be perceived, from a neontological point of view, as major evolutionary transitions. In order to fill these morphological gaps and to map the evolutionary steps toward major evolutionary transitions, we need to integrate extinct stem-group taxa in phylogenetic studies. However, the recognition of stem group has not been widely adopted in the study of early animal fossils, despite that all fossils are stem groups at one level or another. Part of the difficulty is that stem groups may not have all features that collectively diagnose the respective crown group, and they can have unique (autapomorphic) features, making them tantalizingly similar to and frustratingly different from the crown group (e.g., stem-group eukaryotes can be prokaryotic and stem-group animals can be protistan). The need to embrace stem groups and to implement the PhyloCode, in order to achieve phylogenetic clarity and to offer key paleontological insights into the origin and early animal evolution, is illustrated in debates on several controversial Ediacaran and Cambrian fossils.