The Cladonia cervicornis group comprises lichen-forming fungi characterized by having scyphi with central proliferations. It includes c. 20 species globally. The taxonomy of this group is poorly resolved, with many species not thoroughly disentangled. The focus of this study is the European species in the C. cervicornis group. In order to estimate the phylogenetic relationships of these species, six loci were used: ITS rDNA, IGS rDNA, RPB1, RPB2, ef1α and cox1. Species delimitation methods (ASAP, PTP and GMYC) were used to infer the species boundaries based on four loci, ITS rDNA, IGS rDNA, cox1 and RPB2. A morphological analysis based on multivariate methods was performed to assess the importance of phenotypic differences among the lineages. The phylogenetic reconstructions placed the species of this group in the subclade Cladonia. Five lineages were recovered, corresponding to C. cervicornis, C. macrophyllodes, C. pulvinata, C. verticillata and a new lineage that we describe here, C. teuvoana. Our analyses revealed that Cladonia cineracea, C. stricta and C. trassii are polyphyletic.

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.

The lichen species Cladonia angustiloba is characterized by a well-developed primary thallus and narrow squamules which show deep incisions, and the presence of usnic and fumarprotocetraric acids. Morphologically it is similar to C. foliacea and C. convoluta, from which it can be distiguished by the squamule size and morphology. Since similar characters were used to distinguish C. foliacea from C. convoluta which do not represent different lineages, it is necessary to examine the taxonomic status of C. angustiloba by means of DNA sequences. In this study, the species delimitation within the C. foliacea complex was studied by sequencing three loci, ITS rDNA, cox1 and RPB2. The data were analyzed by means of phylogenetic and species delimitation methods (GMYC, PTP, ABGD and BPP). Our results show that none of the three species is monophyletic. Most of the species delimitation methods did not support the current species as evolutionary lineages. Only some of the BPP analyses supported C. angustiloba as a species distinct from C. foliacea and C. convoluta. However, the hypothesis that considers the C. foliacea complex as constituted by a unique species obtained the best Bayes Factor value. Therefore, C. angustiloba and C. convoluta are synonymized with C. foliacea. A new, thoroughly checked synonymy with typifications of the whole C. foliacea complex is presented. An updated survey of the world distribution data is compiled.

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.

In our ongoing study of the genus Cladonia, we have encountered several specimens that have proved to represent undescribed species. Four of them are described here as new. Cladonia camerunensis (Cameroon) resembles C. didyma (Fée) Vain., but the former has a coarsely granular surface and a melanotic podetial base; C. compressa (Bolivia) is distinguished by a dominant primary thallus and deeply divided and phyllopodiate podetia; C. longisquama (Seychelles) has well-developed squamules and contains barbatic acid; C. vescula (Bolivia, Peru) differs from C. peziziformis (With.) J. Laundon by an ecorticate podetial surface and the production of homosekikaic acid. The names C. aspera Ahti & Kashiw. and C. crinita (Delise ex Pers.) Ahti are shown to be illegitimate later homonyms and are replaced by the names C. asperula and C. perfoliata, respectively. The neglected name C. botryoides (Tuck.) Vain. is shown to be a synonym of C. squamosa. Another overlooked name, C. crinita Bertol., is shown to be the earliest name for C. evansii, but we propose to retain the latter through conservation. The typification of C. beaumontii Tuck. is amended. Cladonia conspicua is reinstated on the basis of new data. New range extensions in Canada and the United States are given for the poorly documented species C. oricola.

Cladonia is one of the largest lichen-forming ascomycete genera. It was formerly divided into ten sections, three of which, Crustaceae (Cladina), Tenues, and Impexae, are called the reindeer lichens. While previous studies have elucidated the relationships between species and sections, they often examined only one or a few specimens of each species in the analysis. This study examined the monophyly of selected members of sections Crustaceae, Tenues, and Impexae and their relationships in the genus Cladonia using the internal transcribed spacer region of the nuclear ribosomal DNA (ITS rDNA) and the mitochondrial small subunit gene of the mitochondrial ribosomal DNA (mtSSU). The phylogenetic tree contained four clades, two representing species in section Impexae, one representing species that belong to sections Crustaceae and Tenues, and one clade with C. arbuscula and related species. Five of 22 species, C. pycnoclada, C. stellaris, C. evansii, C. ciliata and C. subtenuis, showed monophyly in the phylogenetic tree; some of these 5 species have been shown previously to be monophyletic. The thallus branching pattern was interpreted as an important heritable character using the mtSSU network. Three duplets of paraphyletic species were further examined using ITS rDNA haplotype networks and AMOVA analysis. The results for the species duplets showed some mixing of haplotypes but the AMOVA analysis provided support for species separation within the duplets. While the evidence supports distinct species, further study is needed to conclusively show separate species in these duplets.

The lichenicolous fungi Endococcus cladiae Zhurb. & Pino-Bodas, Lichenopeltella soiliae Zhurb. & Pino-Bodas and Lichenosticta hoegnabbae Zhurb. & Pino-Bodas are described as new to science from New Zealand growing on podetia of Cladia species. In addition to their host selection, Endococcus cladiae is distinguished by its ascospore size, (9·9–)11·5–14·1(–15·7) × (2·7–)3·1–3·9(–4·6) μm, Lichenopeltella soiliae by ascomata without ostiolar setae and production of 4-spored asci and 1-septate ascospore, occasionally with three pairs of setulae, and Lichenosticta hoegnabbae by comparatively long, bacilliform to fusiform conidia, (7·8–)9·1–10·9(–12·6) × (1·9–)2·1–2·3(–2·7) μm. Niesslia cladoniicola is reported for the first time from Australasia on C. aggregata in New Zealand. A key to the lichenicolous fungi growing on Cladia is provided.

The Cladonia furcata complex treated here comprises C. farinacea, C. furcata, C. multiformis, C. scabriuscula, C. stereoclada, and C. subrangiformis. The well-known taxonomic complexity of this group is caused by wide phenotypic variation and high morphological similarity among the species, for which reason we investigated the distribution in the phylogeny of the phenotypic characters traditionally used to distinguish the species in this complex. A phylogenetic analysis of the C. furcata complex is presented here, based on three loci (ITS rDNA, IGS rDNA and RPB2), representing specimens from a broad geographical range (Europe, North America and New Zealand). The phylogenetic reconstructions were performed using Maximum Likelihood and Bayesian analyses. In addition, 14 features traditionally used for species delimitation within this complex were mapped onto the Bayesian phylogeny. All the species currently accepted, with the exception of C. stereoclada, turned out to be polyphyletic. Most of the phenotypic characters studied are highly homoplasious with the exception of the podetium type. The solid podetia represent a diagnostic character of C. stereoclada.

The species from Cladonia section Unciales are characterized by the absence of squamules and soredia on the corticate podetia and the presence of usnic acid. Different subspecies, varieties and forms have been distinguished in the type species C. uncialis. In this study, a molecular phylogeny of Cladonia uncialis and members of the traditionally recognized section Unciales, along with additional potentially allied species, was constructed. DNA sequences from three gene loci, namely ITS rDNA, IGS rDNA and ß-tubulin, were analyzed using Maximum Parsimony, Maximum Likelihood, and Bayesian methods. Eleven species were analyzed for the first time using DNA sequence data. Cladonia uncialis subsp. uncialis and subsp. biuncialis were recognized as distinct taxa. The recognition of C. pseudostellata as a species was not supported by the analyses, but it represents a hypothamnolic acid chemotype, which is reported here as new to Europe (Scotland). The presence of subsp. biuncialis in North America (Newfoundland) was substantiated. The subsp. uncialis usually lacks squamatic acid, but in the eastern United States a morph referred to as subsp. uncialis does normally contain that acid. However, this morph did not attain taxonomic recognition based on phylogenetic analyses. All the other taxa formerly included in sect. Unciales turned out to belong to other groups of Cladonia, mainly Amaurocraeae, Borya, Divaricatae, and Perviae. The formerly recognized genus Cladina (reindeer lichens) is non-monophyletic, consisting of three groups within Cladonia, making the concept Cladina even nomenclaturally useless. Alternative topology tests rejected the monophyly of C. pseudostellata, section Unciales and Cladina.

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.

Phenotypic characters, either morphological or chemical, have shown to be insufficient to delimit species boundaries in the genus Cladonia. The present study addresses the circumscription of species within the Cladonia cariosa group, examining a number of specimens of the currently accepted taxa Cladonia cariosa, C. symphycarpa, C. acuminata, C. subcariosa and C. latiloba. We employed maximum likelihood and Bayesian methods of phylogenetic reconstructions based on DNA sequences of ITS, rpb2 and ef1α regions. Our results show that the C. cariosa group consists of at least four phylogenetic lineages. It is also shown that each of these lineages is chemically variable, which restricts the taxonomic value of the chemical differences within the group. However, anatomical differences, such as squamule surface and cortex structure, were found to correlate with the distinct lineages found in the phylogenetic analysis. This result confirms the taxonomic value of the cortical surface under SEM, as was found in other lichen groups.