Organismal species exist as historical entities, and essentialistic thinking about ‘ defining ’ species and higher taxa should be avoided. Lichens are biological phenomena that are best understood as processes, and they behave very differently from the model organisms of most systematic theories. Classification and phylogenetic reconstructions are seen as different endeavours, having different aims and languages. A hierarchical classification is supported, and recognition of superspecific taxa is seen as a matter of convenience. Superspecific taxa may be recognized as groups having correlated features, whereas the common recognition of such taxa by a priori cardinal characters should be abandoned. Superspecific taxa having correlated features are distinctive and are likely to be monophyletic. Distinctive and phylogenetically coherent grades may need naming to avoid nomenclatural instability. In classifications, the hypothesized monophyletic status of taxa may be indicated by some convention. Phylogenetic reconstruction by cladistic parsimony analyses includes assumptions that need scrutinizing and modifying to improve the methodology. Analyses should be examined with respect to robustness for changes in the frequently applied equal weighting assumption. For some types of data an a priori weight assignment might be possible, or equal weighting may be justified.

Ostropales, in a wide sense, currently encompasses Ostropales s. str., with a few lichenized genera, and Graphidales, most of which are lichenized. Conotrema is the only lichenized genus undoubtedly placed in Ostropales s. str. We have sequenced the 18S rRNA gene from some key taxa to answer the questions as to whether one ortwo orders should be recognized and whether Conotrema should be kept in Ostropales if Graphidales is recognized. We have new sequences from Conotrema populorum (Stictidaceae, Ostropales), Cyanodermella viridula (Stictidaceae Ostropales), Graphis scripta (Graphidaceae Graphidales) and Diploschistes ocellatus var. almeriensis (Thelotremataceae Graphidales). In an analysis with 41 taxa, thelichenized D. ocellatus var. almeriensis and G. scripta are the sister group of the lichenized C. populorum and the non-lichenized C. viridula and Stictis radiata. Together they form a monophyletic cluster supported by a bootstrap value of 82%. Therefore, it is possible to use the ordinal name Ostropales in a wide sense to include the Graphidales. If Ostropales are conceived in a narrow sense, Conotrema should be kept in the Stictidaceae. Eight new PCR primer sequences are reported.

In order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.

Traditional classification concepts in lichenology are often, but not always, supported by molecular results. Molecular data should be compared and correlated with micro-morphological and ultrastructural information before systematic rearrangements are undertaken. Visualization of the distribution of morphological and other characters in specified groups is considered as a desirable result per se, but it is also important to discover whether correlating characters are dependent on each other or not; and if not, whether their distribution in a group might support existing classification concepts. A data set for lecanoralean and other lichenized and lichenicolous genera, comprising 90—mostly multi-state— characters was used to store morphological, chemical and ecological data, and to test character correlations. Several examples of such analyses are presented. The following pairs of characters show some degree of dependence: ascospore septation and number per ascus, ascospore wall type and pigmentation, ascospore and epihymenium pigmentation. Several authors postulated that ascus types are good phylogenetic markers. Ascus types have been widely used for classification concepts of the Lecanorales. Two-dimensional correlation queries of ascus types with the following morphologcal characters were made: substratum preference, thallus growth form and ascospore septation. These correlations supply characteristic profiles for the various ascus types, which have to be compared with forthcoming phylogenetic hypotheses based on molecular data.

The use of ascoma ontogeny in the systematics of lichenized ascomycetes is reviewed briefly. Two recently studied examples are discussed to illustrate the use of ontogenetic studies to discover phylogenetic relationships. As one example, the Agyriaceae was mainly circumscribed by the ascus type and included diverse genera. Xylographa is characterized by lirelliform apothecia. However, the ascoma development shares the ontogenetic pattern observed in Trapelia and its placement in the family was confirmed. In contrast, Anamylopsora exhibited a substantially different apothecial development and was separated as a family of its own. As a second example, the Candelariaceae is based on chemical characters. With the detection of pulvinic acid derivatives also in the genus Lecanora, the distinction of the Candelariaceae and Lecanoraceae became doubtful. Therefore, the ascoma ontogeny was employed to evaluate this classification and is illustrated here in detail for Candelaria fibrosa. The substantial similarity of the ascoma development found in both families suggests that both might be better united. Finally, a general discussion of the significance of ontogenetic characters in lichen taxonomy is included.

The integration of the taxonomy of lichenized and non-lichenized pyrenocarpous ascomycetes is still in progress. Within this group, at least 12 lichenization events, three re-lichenizations and at least 24 de-lichenization events, are supposed to have occurred during evolution. This is evident from the increasing amount of information regarding phylogeny and classification of pyrenocarpous fungi. The total number of lichenization events, including re- and de-lichenization, within all fungi is estimated to be at least 100. However, the vast majority of the pyrenocarpous lichens are concentrated in a few relatively large, presumably monophyletic, groups. In some cases, proposed integrations have proven to be untenable, for example Microtheliopsis and with the Herpotrichiellaceae, Flavobathelium with the Dimeriaceae and most notably the Normandina thallus with the basidiomycetes and its ascocarps with Sphaendina in the Mycosphaerellaceae. The same true for many cases where lichenized taxa were unwittingly included in otherwise non-lichenized groups, such as Didymosphaeria and Massarina, or even described new, presumably non-lichenized, genera like Holstiella, Starbaeckiella and Titanella.