This is the first part of an ongoing taxonomic treatment of Bunodophoron (Sphaerophoraceae, Lecanorales) in the Neotropics, based on the molecular phylogenetic analysis of three markers together with studies of morphology and chemistry, and using the general mixed Yule coalescence (GMYC) method to delimit species boundaries. In the Neotropics, species in this genus grow on the ground or on shrubs in the páramos, and as epiphytes in the montane rainforests. We describe here a new species from the páramos of Colombia, Bunodophoron crespoae Soto, M. Prieto & Wedin sp. nov., and discuss its distinction from another large and common páramo species Bunodophoron flabellatum (Hue) Soto, M. Prieto & Wedin comb. nov. Both species are primarily terrestrial in the páramos, although B. flabellatum may occasionally also grow as an epiphyte. Bunodophoron crespoae is characterized by the white, c. 10–13 cm long, subterete to narrowly flattened, main branches. It differs from the otherwise similar B. flabellatum by being distinctly subterete, more abundantly branched, and by having smaller ascospores. Both are distinguished from the primarily epiphytic B. melanocarpum by the considerably larger thallus size, with the main branches of B. melanocarpum rarely exceeding 3·5 cm in length and 2 mm in width.

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.

Hypotrachyna is a speciose genus of primarily tropical and oceanic lichen-forming fungi. It includes species with distinct distribution patterns, such as pantropical, restricted and disjunct species. We used a dataset of mitochondrial SSU, nuclear ITS and LSU ribosomal DNA from 89 specimens to study the historical biogeography of the genus. We employed Bayesian and maximum likelihood approaches for phylogenetic analyses, a likelihood-based approach to ancestral area estimation, and a Bayesian approach to estimate divergence times of major lineages within the genus based on molecular evolutionary rates for ITS and a secondary calibration point at the Hypotrachyna clade – Parmeliopsis split. Our analyses suggest that the genus might have originated in the Neotropics during the Eocene and that the split of major lineages happened primarily during the Eocene and Oligocene. The major diversification within those clades is estimated to have occurred during the Miocene. Pantropical species distributions are explained by long-distance dispersal. A number of currently accepted species were found to be non-monophyletic, illustrating that the delimitation of species in the genus needs attention.

Species richness is not evenly distributed across the tree of life and a limited number of lineages comprise an extraordinarily large number of species. In lichen-forming fungi, only two genera are known to be ‘ultradiverse’ (>500 species), with the most diverse genus, Xanthoparmelia, consisting of c. 820 species. While Australia and South Africa are known as current centres of diversity for Xanthoparmelia, it is not well known when and where this massive diversity arose. To better understand the geographical and temporal context of diversification in this diverse genus, we sampled 191 Xanthoparmelia specimens representing c. 124 species/species-level lineages from populations worldwide. From these specimens, we generated a multi-locus sequence data set using Sanger and high-throughput sequencing to reconstruct evolutionary relationships in Xanthoparmelia, estimate divergence times and reconstruct biogeographical histories in a maximum likelihood and Bayesian framework. This study corroborated the phylogenetic placement of several morphologically or chemically diverse taxa within Xanthoparmelia, such as Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Omphalodiella, Paraparmelia, Placoparmelia and Xanthomaculina, in addition to improved phylogenetic resolution and reconstruction of previously unsampled lineages within Xanthoparmelia. Our data indicate that Xanthoparmelia most likely originated in Africa during the early Miocene, coinciding with global aridification and development of open habitats. Reconstructed biogeographical histories of Xanthoparmelia reveal diversification restricted to continents with infrequent intercontinental exchange by long-distance dispersal. While likely mechanisms by which Xanthoparmelia obtained strikingly high levels of species richness in Australia and South Africa remain uncertain, this study provides a framework for ongoing research into diverse lineages of lichen-forming fungi. Finally, our study highlights a novel approach for generating locus-specific molecular sequence data sets from high throughput metagenomic reads.

The family Peltulaceae is currently composed of the three genera Peltula, Phyllopeltula and Neoheppia. The last two genera, both with two species, are distinguished from Peltula only by a small number of morphological characters. The morphology of the genus Peltula varies from peltate-umbilicate thalli to squamulose-semifruticose or squamulose-compound types, as well as subfoliose-compound and crustose types. All types have an upper epinecral layer and possess medullary cavities of various sizes; a lower cortex is normally present but is usually not developed in the subfoliose and crustose types. The genera Neoheppia and Phyllopeltula differ from the common Peltula morphology by crustose-areolate and subfoliose-compound thalli, respectively. Both Neoheppia and Phyllopeltula are additionally characterized by the absence of medullary cavities and lower cortices. To investigate the phylogenetic validity of Phyllopeltula and Neoheppia, we sequenced six loci from representatives of these two genera together with 37 species from Peltula. Despite the relatively high amount of conflict among loci, the results clearly indicate that both Phyllopeltula and Neoheppia are not monophyletic, and are nested within the genus Peltula. Consequently, we subsumed species of these two genera within the genus Peltula.

Lasallia hispanica (Frey) Sancho & A. Crespo is one of three Lasallia species occurring in central-western Europe. It is an orophytic, photophilous Mediterranean endemic which is sympatric with the closely related, widely distributed, highly clonal sister taxon L. pustulata in the supra- and oro-Mediterranean belts. We sequenced the genome of L. hispanica from a multispore isolate. The total genome length is 41·2 Mb, including 8488 gene models. We present the annotation of a variety of genes that are involved in protein secretion, mating processes and secondary metabolism, and we report transposable elements. Additionally, we compared the genome of L. hispanica to the closely related, yet ecologically distant, L. pustulata and found high synteny in gene content and order. The newly assembled and annotated L. hispanica genome represents a useful resource for future investigations into niche differentiation, speciation and microevolution in L. hispanica and other members of the genus.

Some definitions of the term ‘lichen’ have often emphasized the role of the mycobiont as exhabitant in the symbiosis. Mastodia tessellata and Turgidosculum ulvae, both forming lichen-like associations with foliose algae, have traditionally defied that definition. In this study, we delve into the poorly known association of T. ulvae with Blidingia minima. Using four molecular markers (nrLSU, nrSSU, RPB1, mtSSU) we show that T. ulvae is a member of the family Verrucariaceae, closely related to the marine species Verrucaria ditmarsica. The presence of bitunicate asci and single-cell ascospores is confirmed. Our analysis of a fragment of the rbcL marker demonstrates that the photosynthetic partner belongs to B. minima, although relationships within this taxon remain unclear. Transmission electron microscopy allowed us to illustrate how T. ulvae interacts with Blidingia cells, and how haustoria in that species differ from those previously investigated in other marine lichen-forming fungi.

Intrathalline phycobiont diversity was investigated in a rosette-forming lichen, Parmotrema pseudotinctorum, using a combination of Sanger sequencing, 454-pyrosequencing, conventional light and confocal microscopy, and transmission electron microscopy. A total of 39 thalli sampled in five Canary Island populations were investigated. Three novel lineages of lichen phycobionts were detected, all being inferred within the Trebouxia clade G. The most abundant phycobiont lineage, occurring in all lichen populations investigated, is described here as Trebouxia crespoana sp. nov. This species produces spherical to pyriform cells possessing a crenulate chloroplast with lobes elongated at their ends, and one corticola-type pyrenoid with very thin, unbranched tubules of curved profile. Trebouxia crespoana is clearly distinguished from all other Trebouxia species by a characteristic cap-like cell wall thickening produced on one side of vegetative cells, and the larger size of vegetative cells that reach 21(–26) µm in diameter.

Currently, change in lichen community structure depends on a combination of several pollutants instead of just one. Consequently, alpha lichen diversity no longer represents an effective response variable for assessing trends in atmospheric pollutants over time. Here we investigated the value of the relationship between alpha diversity and different aspects of gamma diversity (similarity, replacement and differences in richness of species) together with that of beta diversity (calculated as the sum of replacement and difference in richness of species), for assessing complex variations in epiphytic lichen communities in response to a changing pollution scenario. We considered an area subjected to extreme variation in atmospheric pollution in recent decades and explored temporal and spatial aspects of lichen community succession over short-, intermediate- and long-term reference periods. We found that variation in lichen communities for long- and intermediate-term reference periods was strongly dependent on the alpha diversity of single trees at the beginning of the observation period. The occurrence of nitrophytic species, which responded to the decrease in SO2 concentrations, contribute to this trend. The effect of land use was observed only over long observation periods, with trees in urban areas showing less variation than those located in rural areas. In particular, the analysis of similarity, species replacement and differences in richness of tree pairs demonstrated that trends and patterns within lichen communities are neither always nor to the same extent associated with alpha diversity. Our results show that a thorough study of gamma diversity, including beta diversity and similarity, is required to detect changes in air quality in long-term biomonitoring surveys.

This paper, based on data from the latest checklist of Italy, analyzes the distribution patterns of rare and common lichen species within biogeographically homogeneous versus heterogeneous areas of Italy, and the relationships with some main drivers of rarity and commonness. The following data were used: 1) commonness-rarity values of 2565 species in nine ecoregions; 2) frequency of 353 nationally rare and 387 nationally common species in 21 administrative regions. The following functional and ecological traits were considered: growth form, photobiont(s), type of reproduction, substrata, bioclimatic range, ecological indicator values for aridity and eutrophication, and poleophoby. Within each ecoregion, rare species by far outweigh common species but about one third of these are common in other ecoregions. At the level of regional floras, rarity is significantly associated with epiphytic substrata, non-trebouxioid photobionts and high air humidity, while commonness is associated with saxicolous substrata, trebouxioid photobionts and eutrophication. Rarity seems to mainly depend on two factors, bioclimate (many rare species are outside the limit of their bioclimatic optima) and reduced availability of suitable habitats (e.g. old-growth forests), while commonness is mainly related to disturbance (eutrophication, creation of drier habitats). Most of the nationally rare lichens belong to an oceanic-suboceanic element with tropical affinities or to a small set of continental species with their optima in the dry steppe biome, which suggests that many rare species can persist in microrefugia, that is sites with microclimates that support small populations of species beyond the boundaries of the climatic limits of their main distributions.

Lichens are one of the common dominant biota in biological soil crusts (biocrusts), a community that is one of the largest in extent in the world. Here we present a summary of the main features of the lifestyle of soil crust lichens, emphasizing their habitat, ecophysiology and versatility. The soil crust is exposed to full light, often to high temperatures and has an additional water source, the soil beneath the lichens. However, despite the open nature of the habitat the lichens are active under shady and cooler conditions and avoid climate extremes of high temperature and light. In temperate and alpine habitats they can also be active for long periods, several months in some cases. They show a mixture of physiological constancy (e.g. similar activity periods and net photosynthetic rates) but also adaptations to the habitat (e.g. the response of net photosynthesis to thallus water content can differ for the same lichen species in Europe and the USA and some species show extensive rhizomorph development). Despite recent increased research, aspects of soil crust ecology, for example under snow, remain little understood.