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As with most disciplines in biology, molecular genetics has revolutionized our understanding of lichenized fungi. Nowhere has this been more true than in systematics, especially in the delimitation of species. In many cases, molecular research has verified long-standing hypotheses, but in others, results appear to conflict with existing morphological species concepts. This work reports on recent progress regarding two main issues: (i) cryptic species, i.e., two or more independent lineages exhibiting similar morphology; and (ii) species pairs, two species with similar morphology but exhibiting different reproductive modes. Both concepts have in common a lack of correlation between phylogenetic and morphological data, at least for characters normally used in lichen systematics. We review the available literature on cryptic species and species pairs, focusing especially on the family Parmeliaceae (Lecanoromycetes, Ascomycota). Molecular data have repeatedly demonstrated the existence of cryptic species in lichenized fungi, although taxonomists have often been slow to recognize the resulting taxa. However, careful observation of fine-scale morphological, ecological and/or geographical features tends to provide support for the recognition of these species. In the case of species pairs, by contrast, few if any of the pairs studied to date have been confirmed to consist of independent lineages. Differences in reproductive mode alone appear not to be a sufficient reason to recognise new species.

Cryptic species and species pairs in lichens: A discussion on the relationship between molecular phylogenies and morphological characters