Speciation Caught in the Act: Derived Ciliary Patterns Budded Off From the <i>Oxytricha granulifera</i>‐Like Lineages (Alveolata, Ciliophora)

ABSTRACT Oxytricha is a well‐known ciliate genus having a long, but convoluted taxonomic history, which aside from its non‐monophyly and subsequent dismembering into other genera, has a major issue: the type species O. granulifera is consistently paraphyletic. To understand their paraphyly in the context of our perception of species and genera according to the integrated taxonomy concept, we evaluated the phylogenetic status of different O. granulifera ‐like populations using nuclear and mitochondrial genes. We demonstrate that in the clade formed by O. granulifera and its closely related species, which we designate as the ‘OAN‐clade’, O. granulifera populations have diverged into distinct sub‐clades; and these sub‐clades also encompass O. atypica , Architricha indica and Neogastrostyla species including the herein described N. chongmingensis nov. spec. Genetic variations discerned through the secondary structure of ITS2 molecules, pairwise genetic distances of the COI gene, and a range of phylogenetic trees indicate that speciation events have widely occurred within the OAN‐clade, with Architricha , Neogastrostyla and O. atypica evolving from certain O. granulifera ‐like lineages by developmental changes and other lineages retaining ancestral characteristics of O. granulifera . Moreover, our results reveal a recognisable pattern of environmental transition between freshwater and soil in the OAN‐clade, which provides a clue for further splitting the O. granulifera ‐ like populations. Additionally, our findings suggest that cortical granules, as is the case of cyathiform mucocysts containing glycosylated proteins present in the OAN‐clade, could serve as a criterion for delimiting the genus Oxytricha and the family Oxytrichidae, thus excluding other Oxytricha species with other kinds of cortical granules or lacking them.