In recent years, the genus Bryoria (Parmeliaceae, Lecanoromycetes) has been the subject of considerable phylogenetic scrutiny. Here we used information on six gene regions, three nuclear protein-coding markers (Mcm7, GAPDH and Tsr1), two nuclear ribosomal markers (ITS and IGS) and a partial mitochondrial small subunit (mtSSU), to examine infrageneric relationships in the genus and to assess species delimitation in the Bryoria bicolor/B. tenuis group in section Divaricatae. For this purpose, phylogenetic analyses and several of the available algorithms for species delimitation (ASAP, GMYC single, GMYC multiple and bPTP) were employed. We also estimated divergence times for the genus using *BEAST. Our phylogenetic analyses based on the combined data set of six gene loci support the monophyly of sections Americanae, Divaricatae and Implexae, while section Bryoria is polyphyletic and groups in two clades. Species from Bryoria clade 1 are placed in an emended section Americanae. Our study reveals that section Divaricatae is young (c. 5 My) and is undergoing diversification, especially in South-East Asia and western North America. Separate phylogenetic analyses of section Divaricatae using ITS produced a topology congruent with the current species concepts. However, the remaining gene regions produced poorly resolved phylogenetic trees and the different species delimitation methods also generated highly inconsistent results, congruent with other studies that highlight the difficulty of species delimitation in groups with recent and rapid radiation. Based on our results, we describe the new species B. ahtiana sp. nov., characterized by its bicolorous, caespitose, widely divergent thallus, conspicuously thickening main stems, well-developed secondary branches, and rather sparse third-order branchlets. Another new lineage, referred to here as B. tenuis s. lat., is restricted to western North America and may represent a new species recently diverged from B. tenuis s. str., though further work is needed.

Peltigera globulata Miadl. & Magain, a new species in the P. ponojensis/monticola species complex of section Peltigera, is formally described. This clade was previously given the interim designation Peltigera sp. 17. It is found in sun-exposed and xeric habitats at high altitudes in Peru and Ecuador. Peltigera globulata can be easily recognized by its irregularly globulated margins covered mostly by thick, white pruina, somewhat resembling the sorediate thallus margins of P. soredians, another South American species from section Peltigera. The hypervariable region of ITS1 (ITS1-HR), which is in general highly variable among species of section Peltigera, does not have diagnostic value for species identification within the P. ponojensis/monticola complex. Nevertheless, no significant level of gene flow was detected among eight lineages representing a clade of putative species (including P. globulata) within this complex. ITS sequences from the holotype specimens of P. monticola Vitik. (collected in 1979) and P. soredians Vitik. (collected in 1981) and lectotype specimens of P. antarctica C. W. Dodge (collected in 1941) and P. aubertii C. W. Dodge (collected in 1952) were successfully obtained through Sanger and Illumina metagenomic sequencing. BLAST results of these sequences revealed that the type specimen of P. monticola falls within the P. monticola/ponojensis 7 clade, which represents P. monticola s. str., and confirmed that the type specimen of P. aubertii falls within a clade identified previously as P. aubertii based on morphology. The ITS sequence from the type specimen of P. soredians, which superficially resembles P. globulata, confirms its placement in the P. rufescens clade. Finally, we discovered that the name P. antarctica was erroneously applied to a lineage in the P. ponojensis/monticola clade. The ITS sequence from the type specimen of P. antarctica represents a lineage within the P. rufescens clade, which is sister to the P. ponojensis/monticola clade.

The genus Micarea was studied for the first time in the Taita Hills, Kenya. Based on new collections and existing data, we reconstructed a phylogeny using ITS, mtSSU and Mcm7 regions, and generated a total of 27 new sequences. Data were analyzed using maximum likelihood and maximum parsimony methods. Based mainly on new collections, we discovered four undescribed well-supported lineages, characterized by molecular and phenotypic features. These lineages are described here as Micarea pumila, M. stellaris, M. taitensis and M. versicolor. Micarea pumila is characterized by a minutely granular thallus, small cream-white or pale brownish apothecia, small ascospores and the production of prasinic acid. Micarea stellaris has a warted-areolate thallus, cream-white apothecia usually darker at the centre, a hymenium of light grey or brownish pigment that dissolves in K, and intense crystalline granules that appear as a belt-like continuum across the lower hymenium when studied in polarized light. Micarea taitensis is characterized by a warted-areolate thallus and cream-white or yellowish apothecia that sometimes produce the Sedifolia-grey pigment. Micarea versicolor is characterized by a warted-areolate, sometimes partly granular thallus and apothecia varying from cream-white to light grey to blackish in colour. This considerable variation in the coloration of its apothecia is caused by an occasional mixture of the Sedifolia-grey pigment in the epihymenium and another purplish brown pigment in the hymenium. Micarea stellaris, M. taitensis and M. versicolor produce methoxymicareic acid. The main distinguishing characters are presented in a species synopsis. Three of the new species are nested in the M. prasina group, and the fourth one (M. taitensis) resolves as a basal taxon to the M. prasina group. The new species inhabit montane cloud forests, which have fragmented dramatically throughout the Eastern Arc Mountains in recent decades.

In this study we clarify the phylogeny and reassess the current taxonomy of the Micarea prasina group, focusing especially on the M. byssacea and M. micrococca complexes. The phylogeny was investigated using ITS, mtSSU and Mcm7 regions from 25 taxa belonging to the M. prasina group. A total of 107 new sequences were generated. Data were analyzed using maximum parsimony and maximum likelihood methods. The results reveal five undescribed well-supported lineages. Four of the lineages represent new species described as Micarea pseudomicrococca Launis & Myllys sp. nov., M. czarnotae Launis, van den Boom, Sérusiaux & Myllys sp. nov., M. microareolata Launis, Pykälä & Myllys sp. nov. and M. laeta Launis & Myllys sp. nov. In addition, a fifth lineage was revealed that requires further study. Micarea pseudomicrococca is characterized by an olive green granular thallus, small cream-white or brownish apothecia lacking the Sedifolia-grey pigment and two types of paraphyses up to 2 µm wide. Micarea czarnotae forms a granular, densely granular or continuous olive green thallus, convex to hemispherical apothecia often with the Sedifolia-grey pigment and no crystalline granules in the thallus. Micarea microareolata is characterized by a ± pale green areolate thallus (composed of goniocysts), cream-white apothecia lacking the Sedifolia-grey pigment and narrow spores. Micarea laeta has a vivid to olive green granular thallus, pale apothecia lacking the Sedifolia-grey pigment and wider spores compared to M. microareolata. Descriptions, images and a key are provided for the new species. Crystalline granules are introduced as a novel species-level character for Micarea.

Three new species of Verrucaria are described from calcareous and calciferous rocks in Finland based on morphology and ITS sequences. The species are all members of the Endocarpon group in the Verrucariaceae. Verrucaria oulankaensis sp. nov. is related to V. cernaensis but differing in its usually pruinose, small areolate thallus. It occurs in NE Finland on calcareous and calciferous rocks on river shores. Verrucaria ahtii sp. nov. and V. vitikainenii sp. nov. form a sister group in the ITS phylogeny. Verrucaria vitikainenii differs from V. ahtii in the darker and thinner thallus, absence of a prothallus and in the perithecia, which lack thalline cover. Verrucaria ahtii morphologically resembles V. apomelaena but differs in having a thinner involucrellum and a fimbriate prothallus. It has a southern distribution in Finland and prefers sun-exposed sites, particularly pebbles in lime quarries. The species is also reported from Lithuania and Russia. Verrucaria vitikainenii has an eastern distribution in Finland. The species is a strict calcicole, preferring half-shady habitats. Verrucaria apomelaena is excluded from the Finnish lichen flora.

Four new species of Verrucaria are described from calcareous rocks in Finland based on morphology and ITS sequences. Verrucaria lapponica sp. nov. differs from V. cincta by the smaller perithecia, thinner periphysoids and occasional occurrence of pale exciple walls. Verrucaria sublapponica sp. nov. is related to V. lapponica but differs by a shorter involucrellum and larger spores. Verrucaria saanaensis sp. nov. differs from V. nuoljae (H. Magn.) comb. ined. by having larger spores and a fimbriate prothallus. Verrucaria othmarbreussii sp. nov. is closely related to V. tenebrica, but differs by the paler and thinner, less areolate thallus. The four species belong to the Staurothele group based on the BLAST search and the ITS phylogeny. All four species are rare in Finland and all except V. othmarbreussii seem to have a narrow ecogeographical niche on calcareous mountains above the tree line. Lichens restricted to these habitats may be especially sensitive to climate warming.

Two new species of Bryoria are described based on morphology, chemistry and molecular phylogeny (ITS and Mcm7). Both species belong in section Bryoria, which was resolved as a polyphyletic group in the ITS+Mcm7 phylogeny. Bryoria alaskana belongs to a clade restricted to South-East Asia and north-west North America, and is so far known from south-east Alaska and the Sino-Himalayan Mountains. This highly variable species is most reliably recognized by its pendent, esorediate thallus, its production of fumarprotocetraric acid, and the combination of isotomic branching, abundant, whitish, predominantly fusiform pseudocyphellae, and sparse, short perpendicular side branches. Black emorient patches are lacking. Bryoria irwinii is endemic to north-west North America and is closely related to B. araucana from South America, B. poeltii from South-East Asia, as well as B. nadvornikiana and B. trichodes, both widely distributed in the Northern Hemisphere. It is a subpendent, esorediate species recognized by its predominantly anisotomic branching, olivaceous hue, black emorient patches, conspicuous pale brownish, fusiform pseudocyphellae, and numerous perpendicular, more or less basally constricted, side branches.

Three new species of Atla are described from calcareous rocks in northern Finland based on morphology and ITS sequences. All new species have dark brown spores but have smaller perithecia and spores than previously known brown-spored species of Atla. Atla tibelliorum sp. nov. resembles Sporodictyon arcticum, but has a dark brown exciple and larger spores. Atla oulankaensis sp. nov. and A. vitikainenii sp. nov. differ from A. alpina in the smaller perithecia and spores. Atla vitikainenii has an involucrellum often slightly diverging from the exciple. Atla oulankaensis is similar to A. vitikainenii, differing in slightly narrower spores and in having some involucrella incurving under the exciple or even enveloping the exciple. An unidentified ITS sequence from Canada obtained from GenBank most probably belongs to A. oulankaensis and another unidentified sequence from the USA to A. tibelliorum. The new results strengthen the conclusion that the genera of Atla and Sporodictyon cannot be separated by morphology alone. A key to all known species of Atla and Sporodictyon is provided.

Bryoria pseudocapillaris and B. spiralifera are currently treated as members of Bryoria section Implexae although conspicuous, long and depressed pseudocyphellae characterizing both species resemble those found in the genus Sulcaria. Both genera belong in Parmeliaceae and form an alectorioid group together with Alectoria, Gowardia and Pseudephebe. Parsimony and Bayesian analyses of ITS, partial GAPDH and partial Mcm7 sequence data were used to examine the phylogenetic position of B. pseudocapillaris and B. spiralifera, and in light of these results evaluate the generic delimitation of Bryoria and Sulcaria. A total of 110 specimens of 53 species containing representatives from alectorioid and closely related genera were included in the analyses. The results clearly show first, that both B. pseudocapillaris and B. spiralifera belong in Sulcaria rather than in Bryoria, and second, that they should be considered conspecific. Bryoria pseudocapillaris is proposed as a synonym under B. spiralifera and the name Sulcaria spiralifera comb. nov. is introduced.

In this study we examined photobiont identity, diversity and selectivity in the genus Bryoria. We focused on B. fremontii and section Implexae in order to determine whether secondary chemistry is correlated with photobiont identity. DNA from two loci for photobionts and three loci for mycobionts was sequenced for both parsimony and Bayesian phylogenetic analyses. A comparison of photobiont and mycobiont phylogenies reveals that most Bryoria species associate exclusively with lineages of the Trebouxia simplex group; only B. smithii was associated with a different photobiont. We conclude that most Bryoria species included in our study are highly selective in their choice of algal partners and that the presence/concentration of different secondary compounds does not correlate with photobiont identity either in section Implexae or in B. fremontii.

Phylogenetic relationships of Stereocaulon with emphasis on the crustose taxa were studied based on nuclear ribosomal ITS1–5.8S–ITS2 and partial beta-tubulin sequences. The placement of four of the six crustose species currently included in the genus has previously been confirmed based on molecular data. It has, however, remained unresolved whether the crustose growth form is a plesiomorphic or apomorphic feature within Stereocaulon, due to contradictory placements of the crustose species in earlier studies. The aim of this study was to clarify the position of the crustose species by including additional data, especially of S. nivale and S. plicatile, which have not been included in previous analyses. The inclusion of S. plicatile in the genus is of particular interest as it is the only species in the genus with submurifrom to muriform ascospores. Altogether 37 specimens representing 31 species of the ingroup, including all the crustose Stereocaulon species, were incorporated in the analyses. Conventional, as well as direct optimization parsimony, maximum likelihood and Bayesian analyses were performed. The results show that the crustose species do not form a monophyletic entity and that the crustose growth form is a plesiomorphic feature within Stereocaulon. The crustose S. nivale and S. plicatile are nested within the genus and their inclusion in Stereocaulon is thereby confirmed. The nested position of S. plicatile indicates that the submuriform to muriform spore type has been gained independently within the genus. Here, S. plicatile is also reported for the first time from Scandinavia.

Molecular studies have revealed the presence of yet another species in the Bryoria bicolor complex in China, which confirms that the mountains of SE Asia to be an evolutionary centre for Bryoria sect. Divaricatae. The new species B. rigida is formally described. It is characterized by a stiff and coarse thallus, which contains fumarprotocetraric acid and often protocetraric acid as the main substances. A key to the divaricate species of Bryoria in the Himalayan region is provided.

The phylogenetic relationships of the genus Bryoria were examined using ITS, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and mitochondrial SSU rDNA sequence data in addition to 20 chemical and morphological characters. This first comprehensive molecular study to assess Bryoria phylogeny includes representatives from all the traditionally recognized four sections. Combined cladistic analyses of 88 Bryoria specimens representing at least 25 species resulted in highly resolved phylogenies. Based on the results, a new infrageneric classification for the genus is proposed. Five sections are recognized, largely corresponding to the existing classification, with the addition of section Americanae. The study shows that while most species with an erect growth-form are clearly monophyletic, current species status of many pendent taxa can be questioned.

Fourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str., Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided.

Bryoria fremontii and B. tortuosa are the only species in the lichenized ascomycete genus Bryoria known to contain the pulvinic acid derivative vulpinic acid. In B. fremontii this yellow pigment is restricted to the soralia and apothecia, while in B. tortuosa it can occur throughout the thallus. The actual amount of vulpinic acid produced by B. tortuosa is rather variable, however, with intermediate specimens bearing both white and yellow pseudocyphellae. We studied the relationship between the two species with parsimony analysis using four DNA regions: 1) the internal transcribed spacers of the nuclear rDNA including the 5.8S region (ITS), 2) partial sequences from the intergenic spacer of the nuclear rDNA (IGS), 3) partial sequences from the small subunit of the mitochondrial rDNA (mtSSU), and 4) partial sequences from the protein-coding glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH). Our phylogenetic analysis revealed that B. fremontii and B. tortuosa must be regarded as conspecific, but allowing for some genetic differentiation between European and North American populations. Bryoria tortuosa is therefore synonymized with B. fremontii.

Primers for amplification and sequencing of partial glyceraldehyde-3-phosphate dehydrogenase (gpd) gene were designed for lichenized fungi. The 5’ gpd primer is most probably fungal specific, since a BLAST search in GenBank found identical sequences only from ascomycetous taxa, whereas the 3’ gpd primer was more universal. Utility of the gpd primers and previously designed beta-tubulin primers was tested in nine lichen taxa. Both the gpd and beta-tubulin primer pairs amplified in most of the taxa examined: the gpd primers generated a c. 1100 nucleotide fragment, whereas the PCR product obtained from the beta-tubulin primers was c. 900 nucleotides long. The gpd amplification products of Cladonia arbuscula and C. rangiferina were sequenced and both were found to contain three introns, the length of which varied between 49 to 83 nucleotides. To examine the applicability of gpd sequences in resolving relationships within Ascomycota, trees were calculated from 22 fungal gpd sequences obtained from GenBank together with the two Cladonia sequences using parsimony jackknifing. The gpd tree was compared with the SSU rDNA tree of the respective species (or genera). A similar analysis of the beta-tubulin gene was not performed, because only a few beta-tublin sequences from the same taxa were available in GenBank. The gpd tree was well resolved but in conflict with the SSU rDNA tree. In contrast to the SSU rDNA tree, the gpd tree did not support the monophyly of the Ascomycota. Analysis of the combined data set produced a tree very similar to that of the SSU rDNA data. However, the relationship of Lecanorales to the other orders remained unresolved. Even though gpd and beta-tubulin are highly conserved proteins, the third codon positions and introns are variable and both genes have the potential for inferring phylogenetic relationships at the lower taxonomic levels in the lichenized fungi. The two genes may be useful even below species level, depending on the species investigated.