Using the response of epiphytic lichens in and around the city of Thessaloniki (Greece) to an air pollution source, the value of sampling lichens at breast height and the base of trees was compared. The data obtained were processed with detrended correspondence analysis and polythetic divisive two-way indicator species analysis, and IAP (index of atmospheric purity) values were estimated for each experimental site. The tree base IAP values were higher than those at breast height, reflecting the higher number of species present, the generally increased cover and frequency of occurrence. IAP values at the two sampling heights suggest a linear relationship and the same holds for the tree base IAP values and the first axis ordination scores. Sampling at the base resulted in better discrimination of sites, and may, therefore, offer more accurate monitoring of changes induced by air pollution.

Species identification in the tropical lichen genus Phyllopsora is generally challenging and is based on ascospore morphology, vegetative dispersal units, thallus structure and secondary chemistry. As several type specimens are in poor condition and difficult to interpret, it is often unclear how these old names fit with the currently used taxonomy. In the present study, we aim to identify species boundaries in Phyllopsora s. str. supported by an integrative approach using multiple sources of evidence. We investigated a substantial amount of herbarium as well as freshly collected material and generated mtSSU and ITS sequence data from most of the described species, including several types. Species delimitation analyses are applied on the gene trees using mPTP and we construct a species tree of both markers with *BEAST, facilitating discussion of species delimitation and sister-relationships. Comparing morphology, chemistry and molecular data, we found that the mPTP analyses split established species repeatedly. Based on our integrative results, we exclude nine species from the genus, resurrect one (P. melanoglauca Zahlbr.), reduce two into synonymy with other Phyllopsora species and describe five as new to science: Phyllopsora amazonica Kistenich & Timdal (which shares the secondary chemistry (atranorin and terpenoid pattern) with P. halei chemotype 1, but differs, e.g., in having smaller areolae that are attached to a thinner, white prothallus, and in having more persistently marginate and less convex apothecia), Phyllopsora concinna Kistenich & Timdal (which shares the secondary chemistry (atranorin and parvifoliellin) with P. parvifoliella and P. rappiana, but differs from both in forming larger isidia, having a white prothallus, apothecial margin paler than the disc, and longer and broader ascospores), Phyllopsora furfurella Kistenich & Timdal (which is here segregated from P. furfuracea based on having a white prothallus and in containing skyrin in the hypothecium (K+ red)), Phyllopsora isidosa Kistenich & Timdal (which differs from P. byssiseda in forming a more crustose thallus with more delicate isidia, and from P. isidiotyla in forming somewhat coarser, less branched isidia) and Phyllopsora neotinica Kistenich & Timdal (a neotropical species here segregated from the now exclusively paleotropical P. chodatinica, differing in containing an unknown xanthone (not chodatin)). Lectotypes are designated for Biatora pyrrhomelaena Tuck., Lecidea leucophyllina Nyl., L. pertexta Nyl., and P. brachyspora Müll. Arg. In total, we accept 54 species in the genus Phyllopsora.

Genetic variability and its relationship to substratum preferences within and among populations of the sorediate foliose lichen Hypogymnia physodes was investigated using sequence variation in the complete nrDNA internal transcribed spacer (ITS) region. A few samples of the putatively closely related, sorediate, H. tubulosa were also included. Samples were collected from each tree species in study sites in Estonia, Finland, and Sweden. In total, DNA sequences from 104 individuals of H. physodes and 16 of H. tubulosa were obtained. A group 1 intron situated at the end of the small subunit (SSU) of the nrDNA was detected in both species. Within-species variability was observed in both species: fifteen haplotypes were found for H. physodes and seven for H. tubulosa for the combined alignment of the intron and the ITS. Possible recombination within the total gene fragment was detected and hence the different regions (intron, ITS1, 5.8S, ITS2) were analysed separately. They show a different degree of variability both between each other and between the species. The number of haplotypes of H. physodes in the four regions are 5, 5, 1, and 5 and for H. tubulosa 5, 2, 1 and 2, respectively. A statistical parsimony estimation resulted in two unconnected networks; one containing all the samples of H. physodes and one containing all H. tubulosa samples. It was not possible to show different potentials of the different haplotypes for establishment on different substrata as the network of H. physodes indicates recombination within the ITS region which may be frequent enough to make this primarily clonally reproducing species to behave like a sexual species.

Caloplaca phlogina is shown here to have two kinds of soralia, yellow soralia with anthraquinones versus whitish or white-green soralia lacking pigments. Both kinds are present, growing side by side, in some localities in Scandinavia, but yellow soralia appear to be more common. In contrast, the populations from halophilous shrubs on the Black Sea coast have predominantly white soralia, and they were described as a separate species, C. scythica. A single collection from Chile also has white soralia. Molecular data and phenotype examinations convinced us that Scandinavian and Black Sea populations are conspecific. We consider the North European, phenotypically variable population as a source for the Black Sea population which is ecologically and phenotypically more uniform.

Lichens of the Ramalina siliquosa complex dominate seashore cliffs in Europe and South-East Asia, but their taxonomy has been vigorously debated for over a century. On many cliffs, they exhibit a bewildering zonation of chemotypes that resembles the classic zonation of organisms that occupy the littoral zone below. Do the chemotypes represent separate species, or infraspecific variation? To better understand the systematics of this group, sequences from four genetic loci (ITS, IGS, RPB1 and RPB2) were obtained for 59 samples from Denmark, France, Iceland, Norway, UK, Japan and Korea, including all major chemotypes. Maximum likelihood analysis of these sequences, together with sequences from 36 other Ramalina species, reveals that the complex comprises two distinct phylogenetic lineages, each including multiple chemotypes. These two putative species-level lineages correspond to the currently accepted taxa R. cuspidata and R. siliquosa. There is no evidence that these two taxa are phylogenetic sister species. Consequently, the explanation of this chemotype complex as an example of ‘sibling speciation’ is rejected. Specimens traditionally called ‘R. siliquosa’ from South-East Asia form a third clade, identified here as R. semicuspidata, with an additional, divaricatic acid chemotype. Other results include a robustly supported clade of Ramalina species that produce medullary depsides and depsidones; this clade includes another well-supported clade of south-eastern United States coastal plain and tropical Ramalina species. By contrast, large, strap-shaped Ramalina species that lack medullary depsides and depsidones occur in separate lineages. In addition, close relationships between the following groups of species are indicated: R. farinacea with R. subfarinacea; R. fraxinea with R. leptocarpha, R. menziesii and R. subleptocarpha; R. sinensis with R. unifolia. Furthermore, a new, variolaric acid-only chemotype is reported for R. farinacea, and a new, acid-deficient chemotype is reported for a more broadly circumscribed R. culbersoniorum.

The lichen Lecanora somervellii Paulson, first described from the northern slopes of Mt Everest in Tibet, has been collected at four other localities in the High Himalayas, at altitudes between 3750 and 5540 m. As the type material appears to be missing, a neotype is designated here. The species has an unusual lemon yellow colour due to the pigment calycin; this compound is in addition to usnic acid, which is widespread in Lecanora. Lecanora somervellii is otherwise very similar in essential characters to the complex including Lecanora concolor Ram. and L. orbicularis (Schaerer) Vainio, high alpine species well-known, for example, from the Alps. It is supposed, that L. somervellii is derived from this aggregate by the production of calycin (in addition to usnic acid), which acts as an additional protective pigment at these very high altitudes.

The epiphytic lichen Porina pseudohibernica is described as new. It is characterized by a richly isidiate thallus, 7–8(–9)-septate ascospores and the presence of periphyses. It resembles P. hibernica s. str., differing in the size and septation of ascospores, and in the dimensions of the terete, branched isidia. The new species was found fertile at a single site in the Carnic Alps (SE Alps, Italy), but it is also known in a sterile condition from scattered localities in the humid (sub-)montane belt of Slovenia, the Czech Republic and Ukraine, occurring on smooth bark of Fagus and Carpinus. Porina hibernica is restricted to the coastal lowlands of Atlantic Europe, and it prefers rather dry, base-rich bark of Quercus and Ulmus. The characters previously used to segregate the isidiate European Porina into the genus Zamenhofia are also discussed.

The photosynthetic capacity changes that have previously been documented in lichens are reviewed together with the mechanisms of photosynthetic capacity change in free-living algae recently proposed by Prezelin and co-workers. Examination of seasonal capacity changes in Peltigera praetextata, P. rufescens, Cladonia rangiferina, C. stellaris, and Caloplaca trachyphylla using photosynthetic-illumination curves, provisionally establishes that synthesis of additional photosynthetic units, seasonal interruption of energy transduction, as well as enzymatic rate changes in the Calvin cycle, are all involved in these capacity changes.

A simple scale using tropical lichen species has been used by secondary school students to assess air pollution zones in Hong Kong. The distribution of lichens was found to be related to the sites of power stations, a desalting plant, and heavily industrialised areas. As in temperate climates, both complexity of growth form and numbers of species increase with distance from the sources of air pollution.

Two new species, Xanthoria karrooensis S. Kondratyuk & Kärnefelt and Xanthoria alexanderbaai S. Kondratyuk & Kärnefelt, both apparently endemic to South Africa, are described and illustrated. Other xanthorioid species known from southern Africa are listed in a Table and a preliminary key is provided for the African species. The new species are compared with a number of presumably related species, and a Table is provided comparing the character states for the new species and related species.

Melaspilea circumserpens Nyl., hitherto known only from the type specimen, collected in Tasmania in 1803 by Robert Brown, has been rediscovered. The species has proved to belong to the genus Glonium (Hysteriaceac), previously not known to contain species associated with algae. The new combination Glonium circumserpens (Nyl.) Kantvilas & Coppins is proposed. The anatomy, morphology and ecology of the species are described. Problems regarding the provenance of several lichen specimens collected by Robert Brown are discussed.

A revision of several specimens of Catillaria mediterranea Hafellner revealed that two species can be recognized: C. mediterranea s. str., which has 8–16 spores per ascus, grows on foliose and fruticose lichens, and has a Mediterranean- Macaronesian, montane distribution, and C. praedicta Tretiach & Hafellner sp. nov., which has (16-) 24–32 (-48) spores per ascus, occurs on shrubs in coastal Mediterranean maquis, and has a Mediterranean, maritime distribution. The systematic affinities of the two species with the 8-spored C. nigrodavata (Nyl.) Schuler are briefly discussed.

A new lichenicolous ascomycete, Arthonia diorygmae, is described from the thallus and ascomata of Diorygma junghuhnii. The new species is characterized by rounded to irregular, applanate to convex ascomata up to 0·3 mm in diameter, a slightly whitish pruinose disc, transversely 1-septate, hyaline to greyish ascospores (13–)14–15(–21)×5–7 µm, and its lichenicolous habitat. It is known from the subtropical region of the Western Ghats in India and appears to be widespread due to the large distribution of the host species.

Non-photochemical quenching (NPQ) plays an important role in protecting photosynthetic organisms from photoinhibition by dissipating excess light energy as heat. However, excess NPQ can greatly reduce the quantum yield of photosynthesis at lower light levels. Recently, there has been considerable interest in understanding how plants balance NPQ to ensure optimal productivity in environments in which light levels are rapidly changing. In the present study, chlorophyll fluorescence was used to study the induction and relaxation of non-photochemical quenching (NPQ) in the dark and the induction of photosynthesis in ten species of lichens, five sampled from exposed and five sampled from shaded habitats. Here we show that the main difference between sun and shade lichens is the rate at which NPQ relaxes in the dark, rather than the speed that photosynthesis starts upon illumination. During the first two minutes in the dark, NPQ values in the five sun species declined only by an average of 2%, while by contrast, in shade species the average decline was 40%. For lichens growing in microhabitats where light levels are rapidly changing, rapid relaxation of NPQ may enable their photobionts to use the available light most efficiently.

Chimeras with green algae are reported for the first time from a lichen outside the Peltigerales, viz. the cyanophilous Lichinomycete Phyllopeltula corticola. The species is reported here to be pantropical, based on additional collections from Hawaii, Puerto Rico, Thailand and the Philippines.

A monograph of the genus Placomaronea is presented; all species described earlier are revised, a total of six species is recognized, and an identification key is presented. In addition to the three previously known species, P. candelarioides, P. lambii and P. mendozae, three new species are described: Placomaronea kaernefeltii is a large rosette-like species known from one locality in northernmost Chile; Placomaronea fuegiana is a bullate, areolate species described from Tierra del Fuego, Argentina; Placomaronea minima is a small, areolate to minutely lobate species described from Chile and Argentina, and is the first species of Placomaronea to be reported from the African continent. In a phylogenetic analysis of nuclear ITS rDNA, Placomaronea is shown to form a monophyletic group within the Candelariales.

The saxicolous species, Pertusaria weii Q. Ren (Pertusariaceae, Ascomycota) from China, is described as new to science. Diagnostic characters for the new species are a brownish, marginally unzoned thallus; numerous, solitary and lecanorate verrucae with heavily pruinose discs that are black; a strongly K+ violet epithecial reaction; 1-spored cylindrical asci with single, smooth-walled, untrimmed and ovoid spores; and, the presence of stictic acid. It grows on calcareous rock and is known only from the Tianshan Mountains in Western China.

Using an ITS mutation rate as calibration reference, a three-locus timetree was generated for the genus Lobaria and its most important clades. The timetree resolved most clades with strong support and gave an estimate of the diversification time for Lobaria during the early Oligocene. A fossil impression from a 12–24 million-year-old Miocene deposit is hypothesized here to belong to an ancestral Lobaria species. Additionally, the age estimate indicates that the paleoclimate and the closing or opening of the Bering Strait played a major role in shaping the current distribution of most Lobaria species. It is hypothesized that the Bering land bridge acted as a major highway during warm-temperate climate periods, but as a barrier during Arctic climate times.

Six species of Pyxine have been reported from Europe (including the Azores), but only two, Pyxine sorediata (syn. P. endochrysoides) and P. subcinerea (syn. P. chrysanthoides), are now accepted, the remaining four being excluded for various reasons. Buellia convexa is found to be a synonym of B. pulverulenta.