Population genetics investigates the distribution of genetic variation in natural populations and the genetic differentiation among populations. Lichen-forming fungi are exciting subjects for population genetic studies due to their obligate symbiosis with a green-algal and/or cyanobacterial photobiont, and because their different reproductive strategies could influence fungal genetic structures in various ways. In this review, first, I briefly summarize the results from studies of chemotype variation in populations of lichen-forming fungi. Second, I compare and evaluate the DNA-based molecular tools available for population genetics of lichen-forming fungi. Third, I review the literature available on the genetic structure of lichen fungi to show general trends. I discuss some fascinating examples, and point out directions for future research.

The Caloplaca citrina group in the Nordic countries, except Iceland, is analysed with regard to morphology, anatomy, ecology, and chemistry. Their genetic relationship is also analysed using the ITS ribosomal DNA gene. The results show that there are at least five species within what has been called C. citrina, of which four are closely related to one another and to several non-sorediate species. Three of these, C. citrina, C. flavocitrina and C. arcis have previously been recognized at specific or varietal level some time during the last two centuries, whereas the fourth species, C. dichroa, is described as new. The fifth species, C. phlogina, is not related to the other species but shows a close relationship to the Xanthoria candelaria group. The species are described and illustrated in colour. Distribution maps are given for the study area and a key to sorediate, yellow to orange species occurring in the Nordic countries, except Iceland, is also provided.

The Tabernas badlands in semiarid south-east Spain is one of the driest regions in Europe with a mean annual precipitation of c. 240 mm. The landscape is deeply dissected, with canyons, ramblas and sparsely vegetated eroded badland slopes. The vegetation is predominantly a biological soil crust consisting of different types of lichen-rich communities, one of the more conspicuous being dominated by Diploschistes diacapsis (Ach.) Lumbsch. This lichen is mainly restricted to the north- facing slopes, where it forms extensive whitish carpets and probably plays an important role in preventing erosion of the slopes and allowing plant colonization. South-facing slopes are much more eroded and generally lack vegetation. %The photosynthetic performance of north (shade) and south-facing (sun) populations of D. diacapsis was studied to determine if these different populations showed any adaptations to the microclimatic conditions of their individual habitats. The response of CO2 exchange to light intensity, temperature and water content was measured under controlled conditions in the laboratory. Dry weight-based net photosynthetic rates were higher in the southern-exposed population but quantum efficiency, and light compensation points were similar. Thallus weight per unit area (LMA) was considerably higher for shade specimens but maximum water content and optimal water content were very similar and chlorophyll content on a dry weight basis was also similar. Chlorophyll content on an area basis was higher in the northern-exposed population and always much larger than those reported in other studies on the same species (up to 8 times larger) with the result that NP values on a chlorophyll basis were relatively low. The larger LMA meant that shade thalli stored more water per unit area which should ensure longer active periods than sun thalli. The results support a strategy pair of high NP and short active time versus low NP and long active time, both having been reported for other soil crust species. However, the visibly larger biomass of the shade D. diacapsis suggests that the lichen is at the limit of its adaptability in these habitats.

Induction of secondary compounds in three reindeer lichens (Cladonia arbuscula, C. rangiferina and C. stellaris) was studied under controlled conditions in a growth chamber. Acetone rinsed (secondary compounds removed) lichen mats were subjected to three light regimes (PAR, PAR+UV-A and PAR+UV-A+UV-B), each combined with simulated herbivory (clipping). After 4 weeks, lichen extracts were analyzed by HPLC for any synthesized secondary compounds. UV-B induced the synthesis of usnic acid in C. arbuscula and C. stellaris and melanic pigments in C. rangiferina. Atranorin, fumarprotocetraric acid and perlatolic acid were not influenced by light quality. None of the identified compounds were significantly influenced by clipping. In conclusion, all three lichen species responded to UV-B radiation by developing cortical UV-B absorbing pigments that might function as protective screens. However, the experiment did not produce evidence for a herbivore-deterrent role of compounds studied.

A comparative review of 57 Lepraria species and 2 varieties is provided together with species descriptions and a key. Lecanora leuckertiana is transferred to Lepraria. In addition some putative taxa by different authors are discussed.

Practically most of the taxonomists working on vascular plants and fungi are using the so-called taxonomic species concept, relying largely on morphological criteria or other observable patterns of discontinuity and assuming that these patterns are reflecting the underlying genetic integrity of species. Such a concept is described in detail here for the genus Usnea. The typologicalview versus the populational view of species are discussed. The diagnostic value of characters used by previous and recent taxonomists of the genus is analysed. The fact that Usnea has such a bad taxonomic reputation is discussed. The use by J. Motyka, author of the world monograph published in the thirties, of characters that are strongly modified by environmental factors together with a typological view of species are thought to be mainly responsible for this. More than 770 names have been published worldwide so far and it is suggested that around 50% are to be considered as synonyms.

In two lichen species, Hypogymnia physodes and Lecanora conizaeoides, often used as model organisms for pollution-sensitive and pollution-tolerant epiphytic lichens, respectively, the hypothesis was tested that the toxitolerance of the Trebouxia photobiont limits the tolerance of the entire lichen symbiosis. Being lecanoralean-trebouxioid associations, H. physodes and L. conizaeoides represent the most common type of lichens. Photobionts of both lichen species deriving from microhabitats with varying supply of S and heavy metals were identified using nuclear ITS nrDNA sequencing. The photobiont of L. conizaeoides was identified as T. simplex, whereas the photobiont of H. physodes belongs to an undescribed Trebouxia species, related to T. jamesii subsp. angustilobata and provisionally named as T. hypogymniae Hauck & Friedl ined. Since T. hypogymniae ined. is also known from Lecidea silacea, which is characteristic of rock and slag with high heavy metal content, a high sensitivity of this alga to pollutants is unlikely to be a key factor for the relatively low toxitolerance of H. physodes. Furthermore, the photobiont cannot be crucial for the extremely high toxitolerance of L. conizaeoides, as T. simplex is also known from pollution-sensitive lichens of the fruticose genus Pseudevernia. These findings suggest that the photobiont is not generally a key factor determining pollution sensitivity in the most common type of lichen symbiosis. The high specificity for T. simplex in L. conizaeoides in existing populations of L. conizaeoides suggest that already established thalli could be a source of photobiont cells for re-lichenization.

The localization of psoromic acid and copper in partly green, copper-rich specimens of Lecidella bullata and Tephromela testaceoatra collected in Norway was studied by optical microscopy, scanning electron microscopy, and electron probe microanalysis. Infrared absorption spectroscopy of lichen material and of a synthetic copper-psoromic acid complex, and the other techniques, provide evidence that complexing of copper by psoromic acid occurs within specific areas of these lichens and this leads to their unusual colouration. In contrast, a specimen of copper-rich Lecanora cascadensis, which contains psoromic and usnic acids, does not contain such a complex. From the evidence obtained it is suggested that taxonomists should pay attention to the impact of rock and lichen chemistry on the appearance of lichen thalli.

The pH of 192 thin, even-aged twigs from 4 height levels of 12 randomly selected trees within a boreal Picea abies canopy naturally exposed to rainfall with a high pH (>5·2) was measured. The largest variation in bark pH was due to the height above the ground. However, a highly significant horizontal variation between trees was also found, apparently due to small-scale soil variations. The biomass of alectorioid lichens increased with increasing height above die ground to at least 12 m, a height interval with fairly constant pH values. The uppermost twigs had an unusually high pH and an abnormal species composition for P. abies, with dominance of the foliose Melanelia exasperatula. The canopy hosted several cyanobacterial lichens, but these were scattered and had low biomass, restricted to lower branches of the trees with the highest bark pH.

Temperate rainforests are a poorly researched habitat with respect to lichen ecophysiology in comparison to desert and polar regions. The evergreen, broadleaf forests provide a dim, moist environment that is relatively stable throughout the year. Lichens are abundant in both quantity and species diversity with the large foliose genera Sticta and Pseudocyphellaria normally being dominant, visually and in terms of biomass. These lichens exhibit a great diversity of both form and habitat range. Physiological and morphological adaptation has also been demonstrated. Pseudocyphellaria dissimilis shows changes in thallus water storage capacity with evaporative demand and is also highly shade-adapted. The species has the lowest light saturation and compensation values for photosynthesis yet known for lichens (20 and 1-μmol m−2s−1, PAR, respectively). Unexpectedly it is also highly desiccation-sensitive with some thalli being killed after only 20 h exposure to 15% relative humidity. Photobiont versatility is also a feature of these genera. Photosymbiodemes occur, i.e. a single thallus containing both green algal and cyanobacterial sectors. Because the different sectors have the same fungal partner and grow in the same habitat, it is possible to investigate whether particular physiological traits are photobiont determined. The ability to recover photosynthetic activity in humid air is confined to thalli with green algal photobionts whilst the inability of thalli containing cyanobacterial photobionts to tolerate high light stress may be related to their lack of a protective xanthophyll cycle.

As part of a comprehensive study on lecideoid lichens in Antarctica, we investigated the photobiont diversity and abundance in 119 specimens of lecideoid lichens from 11 localities in the continental and maritime Antarctic. A phylogeny of these photobiont ITS sequences, including samples from arctic, alpine and temperate lowland regions, reveals the presence of five major Trebouxia clades in Antarctic lecideoid lichens. Two clades are formed by members of the T. jamesii and T. impressa aggregates but for all other clades no close match to any known Trebouxia species could be found in sequence databases. One genetically uniform and well-supported Trebouxia clade was found only in the climatically unique cold desert regions of the Antarctic (preliminarily called Trebouxia sp.URa1), where it is preferentially associated with the highly adapted Antarctic endemic lichen Lecidea cancriformis. Levels of genetic photobiont diversity differ slightly, but insignificantly among ecological regions of the Antarctic and do not decrease towards regions with more unfavourable ecological conditions. The genetic diversity of photobionts varies among mycobiont species. Most pairwise comparisons reveal that these differences are insignificant, probably due to the small sample size for most species. The Antarctic lichens studied here are predominantly not specific for a single photobiont species or lineage, except for Lecidella greenii and L. siplei. These two species are preferably associated with Trebouxia sp. URa2, although in the sampling areas of both species, a pool of several other photobionts is available. Lecidea cancriformis associates with the highest diversity of photobionts followed by L. andersonii.

Genetic diversity of green algal and cyanobacterial photobionts in Nephroma was examined by using nucleotide sequences of the ribosomal gene cluster. The lichens studied included both bipartite and tripartite species. There was very little variation in green algal-ITS sequences of N. arcticum and N. expallidum. Almost identical sequences were obtained from all thalli analysed and also from two tripartite Peltigera species. On the basis of SSU rDNA data the green algal photobionts of N. arcticum are closely related to the primary photobiont of P. britannica, and also to an endophytic alga of Ginkgo biloba. The SSU rDNA region of lichen-forming cyanobacteria was rather variable. A phylogenetic analysis indicated that the Nostoc specimens formed a monophyletic group and the strains were divided into two main groups. One clade included only cyanobionts of lichens, including those of all bipartite Nephroma species. The second group was genetically more heterogeneous and included mainly cyanobionts of terricolous cyanolichens, including those of both tripartite Nephroma species studied. The distinction between bi- and tripartite Nephroma species is significant as the mycobionts of tripartite species are not monophyletic. It implies that within Nephroma, evolutionary transitions between symbiosis types cannot have been achieved simply via an acquisition or loss of the green algal photobiont. As the Nostoc symbionts of bi- and tripartite species belong to different phylogenetic groups, an evolutionary change in green algal association has required a concurrent change in cyanobiont composition.

We estimated phylogeny in the lichen-forming ascomycete family Pannariaceae. We specifically modelled spatial (across-site) heterogeneity in nucleotide frequencies, as models not incorporating this heterogeneity were found to be inadequate for our data. Model adequacy was measured here as the ability of the model to reconstruct nucleotide diversity per site in the original sequence data. A potential non-orthologue in the internal transcribed spacer region (ITS) of Degelia plumbea was observed. We propose a revised generic classification for the Pannariaceae, accepting 30 genera, based on our phylogeny, previously published phylogenies, as well as available morphological and chemical data. Four genera are established as new: Austroparmeliella (for the ‘Parmeliella’ lacerata group), Nebularia (for the ‘Parmeliella’ incrassata group), Nevesia (for ‘Fuscopannaria’ sampaiana), and Pectenia (for the ‘Degelia’ plumbea group). Two genera are reduced to synonymy, Moelleropsis (included in Fuscopannaria) and Santessoniella (non-monophyletic; type included in Psoroma). Lepidocollema, described as monotypic, is expanded to include 23 species, most of which have been treated in the ‘Parmeliella’ mariana group. Homothecium and Leightoniella, previously treated in the Collemataceae, are here referred to the Pannariaceae. We propose 41 new species-level combinations in the newly described and re-circumscribed genera mentioned above, as well as in Leciophysma and Psoroma.

Soluble rocks undergo erosion by solution when rain falls on an unprotected rock surface. Lichens may act to protect the surface from such erosion, and the protected area may subsequently emerge from the surrounding lowering surface to form an area of higher relief. Specimens of Aspicilia calcarea and Diploschistes diacapsis act in this way on a gypsum surface, creating conical or rounded mounds up to 15 mm in height. In the case of Aspicilia, the lichen centre decays, re-exposing to surface solution the central area, which then corrodes to create a cratered gypsum cone. The gradient of the cone side-slopes is a function of the relative rates of lichen radial growth and rock surface lowering.

Recently, the number of cryptic species known has increased considerably, showing that species diversity has in many cases been underestimated in the past. Parmelia sulcata is a widely distributed species and one of the most common taxa in temperate Europe. The first intra-specific molecular studies on P. sulcata showed an unexpectedly high genetic variability. In the present work, we study the biodiversity of this taxon including specimens from four continents and using three molecular markers (nuITS, nuIGS rDNA, and partial β-tubulin gene). Two monophyletic groups of P. sulcata were encountered; one of these is epitypified as P. sulcata s. str and the other one is segregated as the new cryptic species P. encryptata sp. nov. Issues surrounding the lectotypification of Parmelia sulcata have also been elucidated.

Two new fossil species (Parmelia ambra Poinar, E.B. Peterson & Platt and P. isidiiveteris Poinar, E.B. Peterson & Platt) are described from Dominican amber. The potential evolutionary value of lichens preserved in amber is discussed.