Morphology or molecules: How do we identify the major lineages of ciliates (Phylum Ciliophora)?

The ciliated protozoa (Phylum Ciliophora) have long been recognized as a monophyletic assemblage. In the mid-1960s the identification of major lineages was based on morphostatic and morphogenetic structures revealed by silver-staining. In the late 1970s, ultrastructural research focused attention on the fibrillar patterns of the kinetid, and provided a new set of characters for phylogenetic analyses. Nevertheless, the classifications of that period still relied heavily on oral features. The structural conservatism hypothesis directed attention to the primacy of the somatic kinetid and led to a radical revision of the major lineages in the mid-1980s and 1990s. With the advent of gene sequencing techniques, ribosomal RNA genes have been used to test these classifications based on somatic kinetid patterns. The two subphyla, the Postciliodesmatophora and the Intramacronucleata, and six classes (i.e. Karyorelictea, Heterotrichea, Litostomatea, Phyllopharyngea, Nassophorea, Colpodea) are well supported by both molecules and morphology. However, the remaining five classes (i.e. Spirotrichea, Armophorea, Plagiopylea, Prostomatea, Oligohymenophorea) are not. Directions to search for new characters will be suggested.