Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens.

The phylogenetic relationships of many lichen-forming perithecioid ascomycetes are unknown. We generated nuLSU and mtSSU rDNA sequences of members of seven families of pyrenocarpous lichens and used a Bayesian framework to infer a phylogenetic estimate. Members of the perithecioid Protothelenellaceae, Thelenellaceae and Thrombiaceae surprisingly cluster within the mainly discocarpous Lecanoromycetes, while Strigulaceae, Verrucariaceae and Pyrenulaceae are related to the ascolocular Chaetothyriomycetes. Micromorphological studies of the ascomata showed that the two main groups of pyrenocarpous lichen-forming fungi differ in their ascus types. The Strigulaceae, Verrucariaceae and Pyrenulaceae have apically and laterally thick-walled asci, whereas the Thelenellaceae, Protothelenellaceae and Thrombiaceae have only apically thickened asci. The latter two show ring-shaped amyloid apical structures. Based on morphological and molecular evidence we propose to reduce Thrombiaceae to synonymy with Protothelenellaceae.