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.

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 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.

Additions and corrections to the checklist published in 2008 are presented. Ten additional species are recognized: Allantoparmelia almquistii, Asahinea chrysantha, Hypogymnia bryophila, Hypotrachyna afrorevoluta, Melanelixia glabratula, Parmelia encryptata, Parmelina atricha, P. cryptotiliacea, Parmotrema cinereopruinata, and Punctelia rudecta. Myelochroa subaurulenta is deleted, and Xanthoparmelia perezdepazii is also noted as newly described from the Canary Islands. In addition, Cavernularia hultenii is now placed in Hypogymnia, the Canoparmelia crozalsiana group is included within Parmotrema, and Parmelinopsis is treated as a synonym of Hypotrachyna. The typification of the name Lichen quercinus is also corrected with the designation of the original figure as lectotype, and the new combination Hypotrachyna cryptochlora comb. nov. (syn. Parmelia cryptochlora) is made.

A new lichen species, Aspicilia digitata Sohrabi & Litterski, is described and illustrated. It differs from the Eurasian and American A. fruticulosa and A. hispida by having a more or less spherical thallus, a very intricate structure of finger-like, cylindrical branchlets and black spots on the tips of the branchlets. Aspicilia digitata is a terricolous vagrant species found at high altitudes in the Tian-Shan Mountains, Kyrgyzstan. It is not known in the fertile condition and presumably reproduces by fragmentation. Molecular comparisons with other related species are provided.

Members of the Cladonia gracilis group of lichen fungi are common terrestrial lichens where morphological features are more similar between members of the C. gracilis species complex and allied species outside the complex than they are between subspecies within the complex. The objectives of this study were to examine whether the Cladonia gracilis species complex is monophyletic, to determine whether morphological similarity is supported by genetic variation, and to examine the utility of the polyketide synthase (PKS) gene for phylogenetic studies among closely related species. Two loci, the ketosynthase region of the PKS gene and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, were sequenced and analysed by Maximum Parsimony, Bayesian and haplotype network analyses. Functional differences were also inferred through ITS2 RNA secondary structures and non-synonymous changes in translated PKS amino acid sequences. The monophyly of the C. gracilis complex is supported by 71% bootstrap in the ITS phylogeny, and 92% bootstrap with greater than 95% posterior probability in the PKS phylogeny. Morphological similarity is not always supported by genetic similarity. The PKS gene is less variable than the ITS but the PKS supports species hypotheses that are reflected in the ITS2 RNA model. We conclude that monophyly of the C. gracilis complex can be supported if C. cornuta, C. coniocraea and C. ochrochlora are included in the complex. In addition, C. maxima, C. phyllophora and C. subchordalis are supported as monophyletic species outside the C. gracilis complex. Cladonia maxima may form a separate species and variation among podetial morphology may be explained by convergent evolution.

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.

After a discussion of changing generic concepts in the parmelioid lichens, a checklist with the current species placements is presented. Twenty-five genera and 143 species are accepted for Europe, of which 17 genera and 112 species belong to the monophyletic parmelioid clade. The individual countries from which species are reported are provided, along with references to key publications. Synonyms used at species rank in Europe are cross-referenced, and the dates of publication of all names are provided. One new combination is made: Xanthoparmelia pulvinaris (syn. Parmelia pulvinaris, X. pseudohungarica).

Our close colleague for 30–40 years, the late Mason E. Hale Jr (1928–1990), was one of the most outstanding lichenologists of the 20th century. While he was terminally ill, he was anxious to complete his world monograph of Xanthoparmelia which he saw through to publication, and accepted 406 species (Hale 1990). Throughout the later periods of his career, his major aim was to document and describe the enormous extent of diversity in the graphidaceous and parmelioid lichens worldwide, and especially in the tropics where he travelled and collected extensively, describing numerous species new to science, 386 in parmelioid groups (Hale & DePriest 1999). In his later years he had, understandably, little time for the nuances of the Code, and, if the principle of adopting proposals for the protection of Names in Current Use (Greuter 1991) had been adopted this would have not caused problems. Sadly it was not, which means that some issues have to be reconsidered. One of these is the correct name for one of the commonest species of Xanthoparmelia, for which he used the name X. somloënsis in his monograph. During the last 15 years, many lichenologists have followed Hale in adopting X. somloënsis, but the nomenclaturally correct name for this species proves to be X. stenophylla.

A new species, Cladonia singhii Ahti & Dixit (type from the state of Arunachal Pradesh), is described. A further seven Cladonia species, C. corniculata, C. kanewskii, C. laii, C. luteoalba, C. mauritiana, C. mongolica and C. rei, are reported as new to the recent checklist of lichens of the Indian subcontinent. The presence of C. cartilaginea in India is confirmed.

A taxonomic revision of the lichen genus Gymnoderma Nyl. sensu Yoshimura & Sharp (Cladoniaceae) based on an integrative analysis of polyphasic characters supports the segregation of a new genus Cetradonia J.-C.Wei & Ahti in a new family Cetradoniaceae J.-C.Wei & Ahti. The monotypic genus and family are based on Cladonia linearis Evans. In addition, two species are recognized in genus Neophyllis F. Wilson and two species are retained in the genus Gymnoderma Nyl. of the Cladoniaceae.

Cladonia friabilis Ahti (type from Bahia, Brazil), C. pulviniformis Ahti (type from Bolivar, Venezuela), C. sufflata Ahti (type from Bolivar, Venezuela), and C. variegata Ahti (type from Bolivar, Venezuela) are described as new. Their major secondary metabolites are reported.