This study investigated the molecular, chemical and morphological variation in the Usnea pectinata aggregate using 42 specimens, 22 from Tanzania and 20 from São Tomé and Príncipe. A total of 31 sequences (13 ITS, 13 nuLSU and 5 RPB1) were generated. The results are presented in two phylogenies: first a three-markers ‘backbone’ phylogeny for the U. pectinata aggregate, where six distinct, strongly supported subclades indicate considerable genetic variation in the dataset; and second, an ITS phylogeny with 47 terminals along with a mapping of morphological and chemistry data. Several well-supported monophyletic clades were recovered in both phylogenies and these may well represent separate species in the complex referred to here as the U. pectinata aggregate. Three morphotypes characterized by axis pigmentation and four by branch shape were noted. Six chemotypes were observed.

A new species of Chaenotheca, C. biesboschii, has been found in the freshwater tidal area of the Biesbosch in the Netherlands, a national park well known for harbouring several rare and threatened mosses and lichens. A phylogenetic analysis of the ITS region revealed some strongly supported infrageneric clades in Chaenotheca which were given informal names, and some were assigned provisional names in anticipation of generic recognition. The analysis also showed that the new species differed in the sequenced region from other European Chaenotheca species. Chaenotheca biesboschii might be mistaken for C. gracillima but, in addition to a considerable difference in the ITS region, it also differs from this species in morphology. It is also similar to C. servitii but again differs in morphology. Chaenotheca biesboschii inhabits decorticated wood in the oldest stages of forest development of abandoned willow coppices. In 2016 and 2017 a fairly large population was found in an area comprising several square kilometres. In the Biesbosch area, extensive woodlands have developed only since the 1950s and therefore C. biesboschii might have been recently established in the area, possibly following climatic warming. The new species is characterized by having an immersed, glaucous green thallus; apothecia 0·9–1·4 mm high; capitulum on the lower side when young with a ring-like thickening covered by a yellow pruina; when mature with a rusty brown pruina on the capitulum and upper part of stalk; spherical spores, 3·5–5·5 µm diam., ornamented by irregular cracks, medium brown; photobiont Stichococcus. A key to the European species of Chaenotheca is provided.

The lichen species of the genus Thamnolia, with their striking wormlike thalli and frequent occurrence in arctic and tundra environments, have often been debated with regard to the use of chemistry in lichen taxonomy. Phylogenetic studies have arrived at different conclusions as to the recognition of species in the genus, but in a recent study based on the analyses of six nuclear markers (genes or noncoding regions) of a worldwide sample of Thamnolia, we showed the existence of three well-supported lineages with two different chemistries and geographical distributions. Here, we present two analyses based on ITS and three markers, respectively, which were extended from the study mentioned above to include type specimens and additional Thamnolia strains and taxa. In these analyses the same three clades were retrieved. A putative DEAD-box helicase is used here for the first time as an informative phylogenetic marker to provide taxonomic resolution at species level. The distribution of morphological and chemical characters across the phylogeny was analyzed and it was concluded that three morphologically cryptic, but genetically well supported, species occur: T. vermicularis s. str., T. subuliformis s. str. and T. tundrae sp. nov. Thamnolia vermicularis s. str. contains individuals with uniform secondary chemistry (producing thamnolic acid) and a rather limited distribution in the European Alps, Tatra Mts and the Western Carpathians, a distribution which might result from glacial survival in an adjacent refugium/refugia. Thamnolia subuliformis s. str. is widely distributed in all hemispheres and the samples contain two chemotypes (either with thamnolic or squamatic acids). Thamnolia tundrae is described as new; it produces baeomycesic and squamatic acids, and has a distribution limited to the arctic tundra of Eurasia extending to the Aleutian Islands in North America. It may have survived the latest glaciation in coastal refugia near its present distribution. Thus, secondary chemistry alone is not suitable for characterizing species in Thamnolia, secondary chemistry and geographical origin are informative, and the ITS region can be confidently used for species recognition. Nomenclatural notes are given on several other names that have been used in Thamnolia.

Two new species in the lichen genus Atla, A. alaskana and A. recondita, are described. The ITS rDNA region is used for their molecular characterization. Morphologically, Atla alaskana is characterized by its rather thick and well-developed whitish grey thallus, and the rather large perithecia having a thalline excipulum. The presence of a thalline excipulum renders it similar to Sporodictyon species; however, in A. alaskana a distinct zone around the ostiolum is without a thallus and covered only by a thick white pruina. Atla recondita has a thin olivaceous brown thallus and moderately sized, emerging perithecia. It is not possible to identify this species unequivocally as an Atla species only by morphology, and it might well be mistaken for a Polyblastia. A key to all six Atla species, including the two new species, is provided.

Based on morphological, anatomical, chemical, ecological and molecular evidence, Blarneya is synonymized here with Tylophoron. The molecular phylogeny derived from sequences obtained from sporodochia of Blarneya places this genus, described to accommodate an anamorphic lichen with white cushion-shaped sporodochia, within Tylophoron. This conclusion is further supported by the discovery of Tylophoron-type ascomata emerging directly from thalli with Blarneya-type sporodochia and producing identical hyaline conidia. In one specimen pycnidia were also observed. This represents a surprising variety of morphologically different conidiomata. A different anamorphic type was previously reported from Tylophoron, and this is confirmed here by molecular analysis for T. moderatum: besides thalli with ascomata this species has anamorphic thalli with an irregularly delimited brown sporodochial felt and brown conidia. Ascomata are not known from these entirely anamorphic thalli, whereas they do occur infrequently in Tylophoron species with Blarneya-type sporodochia. A key to all currently accepted species of Tylophoron is provided. In addition to the corticolous Tylophoron hibernicum, confined to humid forests, two saxicolous species with Blarneya-type sporodochia are described here as new: T. galapagoense, known only from Galapagos, differs from T. hibernicum by a thicker, more compact, beige rather than white, more strongly C+ red thallus, growing below sheltered rock overhangs in dry forests; T. stalactiticum has a C− thallus with stipitate, white, C+ red sporodochia; the species is known only from a single locality in Tenerife, on a large slope with volcanic boulders.

The new species Megaspora rimisorediata Valadbeigi & A. Nordin is described from Iran, where it mainly grows on tree bark but also on calciferous rocks and mosses. It is characterized by a pale ochraceous to bluish grey, cracked and sorediate thallus, very rarely producing ascomata. It appears to be rather commonly distributed in Iran. Its close affinity with Megaspora verrucosa is illustrated in a graph resulting from a phylogenetic network analysis of nuclear rDNA ITS1-5.8S-ITS2 sequences from specimens representing the different genera of Megasporaceae.

Aspicilia fluviatilis and A. granulosa, two arctic and/or (sub)alpine species with elongate ± diverging and ± branching marginal areoles, are described as new and compared with similar species occurring in Fennoscandia. A parsimony analysis based on ITS indicates a close relationship with the mainly coastal A. epiglypta. Aspicilia epiglypta, A. disserpens and A. sublapponica are lectotypified and A. disserpens is reduced to synonymy with A. perradiata. Aspicilia alboradiata and A. circularis are excluded from the Fennoscandian lichen biota. A key to Fennoscandian Aspicilia species with radiating thalli and/or elongate ± diverging and ± branching marginal areoles is also presented.

The new genus Atla forms a well-supported clade in a molecular phylogeny based on the ITS1-5.8S-ITS2 and LSU regions of the nuclear ribosomal DNA. The genus has a crustose thallus, a hamathecium at maturity without hyphal elements except for pseudoparaphyses remaining at the ostiolum, and large, muriform spores. Atla wheldonii was previously referred to Polyblastia. Three new species, A. alpina (the type of the new genus), A. palicei and A. praetermissa, are included in the genus and described here as new to science. They were found on calcareous rocks and soil in Northern Scandinavia; A. alpina also occurs in Central Europe, and A. wheldonii likewise in Central Europe, the Pyrenées and in the British Isles. An identification key to the species and a revision of the genus are also provided.

We describe Calicium sequoiae as a new species of lichenized Ascomycota from north-western California, USA. The species is distinguished morphologically from other known members of Calicium by its stalks that react I+ blue, mature ascospores that are ornamented with spiral ridges, and apothecia that produce prominent white pruina. It is also the only Calicium known to produce thamnolic acid as a major secondary substance. Sequences from the ITS-region showed C. sequoiae to be unique among calicioid Physciaceae, and phylogenetic analysis positioned it close to C. adspersum, C. chlorosporum, C. lenticulare, Cyphelium notarisii, and C. tigillare. Thus far, Calicium sequoiae has been collected only from old-growth redwood (Sequoia sempervirens) forests, where it occurred on thick, fibrous bark of large redwood trees. A key to the 12 species of Calicium known from the Pacific Northwest is provided.

The new name Aspicilia berntii is proposed to accommodate Lecanora mastoidea Lynge in Aspicilia and a lectotype is designated. Additional characters are added to the species description and a comparison is made with similar species. The species is reported as new to Scandinavia with localities in northern Norway. An assessement of the phylogenetic relationships, based on a split network analysis of ITS sequences, places A. berntii close to A. verrucigera in the A. cinerea group.

The morphological features and chemical compounds found in the first European collection of Calicium victorianum are compared with type material from Australia of C. piperatum F. Wilson. The phylogenetic relationships of the species are discussed by comparing its nuclear rDNA ITS1-5.8S-ITS2 with that of other species of Calicium.

Tetramelas phaeophysciae, a new obligately lichenicolous species occurring in Scandinavia, Iceland and Greenland, is described, and the closely related Buellia pulverulenta, together with B. triphragmioides, are transferred to Tetramelas. Phylogenetic reconstructions based on sequence data from nITS1-5.8S-ITS2 rDNA, using Bayesian inference and parsimony analyses, support the segregation of the new species from B. pulverulenta as well as the segregation of Tetramelas and Diplotomma from Buellia s. str.

The phylogenetic relationships of Tholurna dissimilis were investigated in relation to a phylogeny of twenty-three species in Caliciaceae and eighteen species from Physciaceae. ITS and LSU regions of the nuclear ribosomal DNA were used for the reconstruction of phylogenies by maximum parsimony methods. Calicium adaequatum was shown to be the closest relative of and possibly congeneric with Tholurna. Calicium is thus not monophyletic unless Tholurna is included. Calicium in the molecular phylogeny contains several distinct clades, which to some extent can be characterized morphologically. Cyphelium in a traditional sense is probably not monophyletic. Cyphelium s. str. has immersed apothecia, large smooth spores and a very thin excipulum throughout. C. inquinans and C. karelicum, which form a distinct and highly supported clade, may be accommodated in Acolium, possibly along with other Cyphelium and Calicium species. The phylogenies presented here do not support the recognition of neither Physciaceae nor Caliciaceae in a narrow sense, but they also do not exclude this. Numerous spliceosomal and unclassified insertions were found in the LSU sequences. They to some extent offered phylogenetic information both with respect to location and by their sequence similarities.

The lichens Usnea florida and U. subfloridana have since long been recognised as distinct species. They show many similarities in morphology, but have different reproductive strategies. Usnea florida is always provided with many apothecia and produces no specialised asexual propagules. Usnea subfloridana has soralia, isidiomorphs and occasionally apothecia. Phylogenetic analyses based on continuous sequences of the ITS and LSU regions of the nuclear ribosomal DNA and the gene coding for β-tubulin, show that specimens of the two species form one monophyletic group of intermixed specimens, and not two groups corresponding to morphology, which would have been expected if two species were at hand. The ‘species pair’ concept in lichenology is discussed. Other Usnea species included in the study are: U. articulata, U. barbata, U. ceratina, U. filipendula, U. hirta, U. rigida and U. wasmuthii.

Cybebe was described as a monotypic genus in the Coniocybaceae distinguished from Chaenotheca by its unusual ascus ontogeny and its unpigmented spore wall. In a molecular phylogeny based on maximum parsimony analyses of their ITS1-5.8S-ITS2 rDXA sequences, specimens of Cybebe gracilenta formed a strongly supported group with Chaenotheca gracillima. Thisgroup in turn is also well supported as a part of Chaenotheca indicating that the features characteristic of Cybebe are indeed autapomorphic and that Cybebe gracilenta should be included in Chaenotheca.

The aim of the present paper is to investigate if Mycocalicium subtile as presently circumscribed is a morphologically highly variable species, or in fact represents two or more cryptic species, and further to investigate the status of M. minutellum. The morphological variation of 19 specimens of Mycocalicium subtile from five continents was investigated and the ITS1-5.8S-ITS2 region of their rDNA sequenced. Sequences from closely related taxa, 4 specimens of M. albonigrum, 2 of Mycocalicium sp., and Chaenothecopsis nana were also included. For comparison the corresponding sequence of M. victoriae and C. pusilla were also determined. We used the sequence of Monascus purpureus as the outgroup for the analysis. The sequences were used for phylogenetic inference using parsimony and distance methods. All the specimens assigned to M. subtile with the exception of two, form a well-supported monophyletic group. Those two specimens represent a morphologically cryptic, but genetically distinctive taxon. The infraspecific clades of M. subtile in the molecular phylogeny did not correspond to geographical origin. Only a weak correlation with geographical origin was found in the morphological analysis. The molecular analysis supports the suggestion that Mycocalicium minutellum is a taxonomic synonym of M. subtile.

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.