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.

The past and present occurrence of Usnea longissima has been investigated at 31 localities in an area of eastern central Sweden. A marked decline was found which is due to different forestry practices, and, to a minor extent, air pollution. The species is confined to old spruce forests, mainly located on north-facing slopes with a slightly oceanic climate. The population size showed a large variation both within and between seven investigated localities. Specific habitat demands and low dispersal ability make U. longissima very sensitive to environmental disturbances.

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).

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.

The utility of plastic cover slips as a substratum for in situ study of lichen developmental stages is further explored in a neotropical foliicolous lichen community and in a European temperate corticolous community. Twenty-one months after placement in the tropical forest, the cover slips bore foliicolous lichen thalli with several species producing characteristic ascocarps and ascospores, indicating the suitability of the substratum for completion of the life cycle of these lichens. On cover slips placed within the temperate corticolous community, lichen propagules anchored to the substratum with relatively short attachment hyphae but did not develop further within the one year observation period. Intimately intermixed microbial communities of short-celled, mainly pigmented fungi and chlorophyte algae developed upon the transparent substratum. Among the algae, Trebouxia cells, often in groups showing cell division and without associated lichenizing hyphae, were commonly observed. The potential significance of the free-living populations in the life cycle of Trebouxia and in those of Trebouxia-associated lichen fungi is discussed.

A recent survey of epiphytic lichens in the Jardin du Luxembourg has shown there to be a marked improvement in the air quality of Paris over the past decade. Recolonization by at least 11 lichen species has occurred during that period. It has taken almost 100 years for epiphytic lichens to re-establish in the Jardin du Luxembourg, where William Nylander in the 1890s was able to amply confirm his far reaching hypothesis, made 30 years earlier, on the direct relationship between lichen survival and air pollution.

Chlorophyll a fluorescence was measured every three months from December 2003 to December 2004 in ten, randomly selected thalli of the epiphytic lichen Punctelia subrudecta (Nyl.) Krog occurring in a deciduous, thermophilous downy oak wood in southern Tuscany (central Italy). In situ measurements were carried out with a photosynthesis yield analyser Mini-PAM (Walz, Effeltrich, Germany) on the same measuring points of 30-minute dark-adapted, fully hydrated thalli. The results show a remarkable seasonal change in Fo, Fm, and Fv/Fm, probably caused by a long-term physiological-structural adaptation of the photobiont to the gradual modification of the climatic conditions of each measurement period and the light regime of the understorey. However, P. subrudecta is also sensitive to rapid changes in microclimatic conditions as the PSII functionality is affected by the light regime of the days preceding the field measurements. Some critical observations on the statistical analysis of chlorophyll a fluorescence parameters are also made.

The development of isidia in thalli of Pseudevernia furfuracea from the Carnic Alps (North-eastern Italy), and the effects of these structures on CO2 gas exchanges were investigated. The ontogenetic events were studied by comparison of sections stained with different histochemical tests and SEM observations. A high cell turnover rate in both symbiotic partners is the first sign of isidium development, followed by an increased aplanosporogenesis of algae and growth of neighbouring medullary hyphae which become oriented upwards. Large nuclei and an intense cytoplasm activity characterize the mycobiont cells. The surface of very young isidia shows an irregular structure of spherical to ovoid protruding tips of perpendicular cortical hyphae, that are later organised in a pseudomeristematic area similar to that observed in the apex of growing lobes. CO2 gas exchange measurements carried out in the laboratory confirmed the high metabolic activity of isidia. At optimal water content and favourable light conditions, isolated isidia had rates of gross photosynthesis and dark respiration that were twice those of non-isidiate lobes. Isolated isidia also had a very low CO2 saturation point, probably because of their favourable surface/volume ratio, and a high light saturation, probably linked to their high content of photosynthetic pigments. The different roles played by isidia in the biology of Pseudevernia furfuracea, and particularly their rejuvenating effect on aged lobes, are discussed, and the presence of thalloconidia is briefly mentioned.

Available evidence indicates that basal regions of well-developed lichen mats are composed largely of dead or senescent thallus material. Marked vertical gradients in concentrations of N, P and K in thalli of mat lichens, together with results of N budget studies in Cladonia stellaris and Stereocaulon paschale, suggest that these key elements may be recycled internally to fund new growth at the apices. It is argued that nutrient recycling will increase rates of both apical growth and basal necromass production and that under steady-state conditions this will result in deeper mats and facilitate dominance sensu Grime; thus accumulation of necromass may be an ecological advantage in mat-forming lichens. Basal necromass of the N2-fixing S. paschale contains more N than necromass of the non-N2-fixing C. stellaris; this may be due in part to a greater allocation of N to irrecoverable fungal cell wall components in S. paschale and may underlie a greater requirement for N in this mycobiont.

Wooded meadows with a history of traditional land use over thousands of years support a great diversity of various taxa. Today, however, high-species-rich communities in wooded meadows are threatened because of the cessation of traditional management in large areas. We studied lichen communities on 136 deciduous trees (Betula spp., Fraxinus excelsior and Quercus robur) in 12 wooded meadows in three regions of Estonia, and assessed the effect of habitat change due to the abandonment of traditional management on epiphytic lichen species composition, considering factors on three spatial scales: regional, habitat and individual tree. The variation partitioning approach in partial Canonical Correspondence Analysis (pCCA) revealed that most of the variation in species composition is described by the species of host tree and tree bark pH. Other tree level variables, foremost tree diameter, described as much of the compositional variation as geographic location (region) or environmental conditions in wooded meadows. Of the environmental factors studied, woodland canopy cover is the strongest predictor of the change in epiphytic lichen species composition from the community type of semi-open wooded meadows to species-poor communities characteristic of secondary forest. General Linear Model (GLM) analysis of the abundance of the 35 most frequently observed lichen species revealed that more than half of them (21) are influenced by site openness (canopy cover and/or undergrowth density), showing that increasing canopy cover has a negative effect on the abundance of epiphytic lichen species characteristic of traditionally managed semi-open wooded meadows. The results emphasize that the preservation of large old deciduous trees of various species and the maintenance of the semi-open structure of stands are vitally important for the protection of epiphytic lichen communities in wooded meadows.

The cetrarioid core group has been the focus of numerous taxonomic and phylogenetic studies in recent years, yet the phylogenetic resolution and support among these clades remains unclear. Here we use four commonly employed loci to estimate if their use increases phylogenetic resolution and support. The present study largely confirms the topologies of previous studies, but with increased support. Approximately half of the genera in the cetrarioid core were not monophyletic. Melanelia sorediella was clustered within Cetrariella, and the combination Cetrariella sorediella (Lettau) V. J. Rico & A. Thell comb. nov. is made. Additionally, the genus Flavocetrariella was supported as part of Nephromopsis and is considered to be a synonym of the latter. Finally, a comparison of genetic distances shows that the maximum intrageneric genetic distance encompassed by many cetrarioid genera is lower than that of many other genera in Parmeliaceae.

To investigate the association between, and the reproductive modes of, mycobiont and photobiont in the lichen Parmotrema tinctorum, microsatellite markers (SSR markers) were developed for both bionts and genotypic analysis was performed for thalli in a Pinus thunbergii forest. In a within-thallus analysis, tissue pieces were sampled from many portions within each of five thalli. Within-thallus variation for both mycobiont and photobiont differed among the thalli investigated, suggesting that a single thallus can be derived from either a single mycobiont origin with or without occasional changes in the photobiont, or fusion of several independent thalli. In the within-tree analysis, thalli with the same genotypes were found on individual trees, suggesting the presence of short-distance isidium dispersal. In the within-stand analysis, genotypically similar photobionts tended to be associated with the same mycobiont genotype, suggesting the participation of local dispersal via isidia. The overall index of association (IA) for the mycobiont in the stand probably indicates the dominance of sexual reproduction, in contrast to that of the photobiont, where dominance of asexual reproduction is suggested. IA's of mycobiont and photobiont were also calculated for thalli collected from larger areas, where there is a signature for sexual reproduction for photobiont.

Ecological studies are essential in understanding the response of crustose lichens to habitat dynamics and developing effective conservation strategy. While the combined response of individual crustose species within a community will be tremendously complex, the overall result of individualistic change can be simplified using trait-based analyses. In this paper we examine the response of crustose species with contrasting reproductive traits (predominantly sexual vs asexual reproduction) and which occur within a closely defined habitat (as epiphytes on the lower bole of aspen) to environmental drivers measured at two different scales, i.e. between and within aspen stands. Our results point to the important effect of tree age and subsequent shifts in bark quality (pH) on the composition of the crustose community. However, shifts in community composition putatively controlled by bark quality comprise a change from a community dominated by sexual species to a community with mostly asexual crusts. Our results suggest therefore that variation within this crustose community may be driven by the combined effects of allogenic change (tree age and bark quality) and autogenic processes that are related to a species’ adaptive life-history traits.

A first hypothesis for the phylogeny of Lecanora subgen. Placodium is presented by using molecular data. Previous evolutionary ideas and classification concepts for this group with non-molecular data are re-investigated using DNA sequence data from the nuclear ITS and 5.8S regions. Using Protoparmelia as an outgroup, the Lecanora subfusca group together with the L. rupicola group appear as a sister group to assemblages with lobate species. Subgen. Placodium as currently accepted, is not monophyletic. Molecular data suggest that the Lecanora dispersa group and the L. polytropa group are widened by lobate species and there is evidence from the ITS data that the monotypic genus Arctopeltis Poelt is closely related to the L. dispersa group. A congruence between molecular data and secondary chemistry supports the broader concept of the L. dispersa group suggested by the molecular data.

Although several lichen inventories exist for European ultramafic sites, only four surveys of serpentine lichens for North America have been published to date. Of those, only one has been conducted in California. We conducted a survey of saxicolous lichens from ultramafic rocks (including nephrite, partially serpentinized peridotite, and serpentinite) and non-ultramafic rocks (including silica-carbonate, shale, and sandstone) at the New Idria serpentinite mass, San Benito County, California. X-ray Fluorescence Analysis of the rocks from which the lichens were collected revealed significant elemental differences between the ultramafic and non-ultramafic rocks for 26 of the 32 major and trace elements analyzed. We identified a total of 119 species of lichenized and lichenicolous fungi; 60 species were restricted to ultramafic substrata, 19 to silica-carbonate, and 15 to shale and sandstone. Only 4 species were shared in common. A permutational multivariate analysis of variance (perMANOVA) test revealed significant differences in lichen assemblages between ultramafic and non-ultramafic rocks at the species level but not at the generic level, with species richness (alpha-diversity) significantly greater at the ultramafic sites. We suggest that, although differences in geochemistry clearly influence the lichen community composition, other factors, especially substratum age and the physical characteristics of the rock, are of equal, if not greater, importance. Of all the species collected, six, Buellia aethalea, B. ocellata, Caloplaca oblongula, Rhizocarpon saurinum, Thelocarpon laureri, and Trapelia obtegens, are reported new to California, along with an apparently previously undescribed Solenopsora sp. The rest of the species encountered are relatively frequent in the lichen flora of southern and central California, except Aspicilia praecrenata, a rare California endemic that we collected on both ultramafic and non-ultramafic rocks.

Maximum parsimony analysis of nuclear SSU rDNA sequences was utilized to infer the phylogenetic relationships of representatives of the macrolichen families Cladoniaceae, Sphaerophoraceae, and Stereocaulaceae (Lecanorales subord. Cladoniineae, Ascomycotina). Farris’ parsimony jackknifing, and a similar jackknife strategy with branch-swapping and multiple addition sequences in PAUP*, were performed to assess branch support. The results indicate that the Sphaerophoraceae should be emended to include Neophyllis (formerly Cladoniaceae or Stereocaulaceae) and Austropeltum (formerly Stereocaulaceae), and it is suggested that the type of boundary tissue present is a synapomorphy for the family. The families Sphaerophoraceae and Bacidiaceae form a clade, together with Psora decipiens, Tephromela atra and Scoliciosporum umbrinum. The Cladoniaceae should be emended to include Pilophorus, and the genera Metus, Cladia and Heterodea should also be included in the family. The sometimes-recognized families Cladiaceae and Heterodeaceae are shown to be derived from within Cladoniaceae. The Stereocaulaceae is recircumscribed to accommodate Stereocaulon only. Neither the possession of podetia/ pseudopodetia, a dimorphic, cladoniiform thallus, nor the presence of cephalodia, is a morphological synapomorphy for a monophyletic group in our analysis. Optimising ascus structures onto one of the most parsimonious trees suggest that tube-like apical structures may well be primitive characteristics within the Lecanorales. The two lecanoralean suborders Lecanorineae and Cladonineae are both paraphyletic groups in the present analysis. It is pointed out that if further studies confirm that Stereocaulon is the sister-group to the Cladoniaceae, as circumscribed here, then there may be no reason to accept the two families Cladoniaceae and Stereocaulaceae as distinct. Branch-swapping and several random-addition sequencesimprove resolution, adding several supported groups in the topology, and improve support values for groups already supported by parsimony jackkniring analyses, and we suggest a procedure for implementing this by using PAUP*

Molecular phylogenetic analyses based on nuclear ITS rDNA and mitochondrial SSU rDNA sequences from 32 specimens representing Parmotrema pseudoreticulatum, P. reticulatum and P. clavuliferum from Africa, Asia, Australia, and Europe are reported. Samples from western Europe and South Africa formed an independent monophyletic group, which belongs to P. pseudoreticulatum, a species not accepted by some recent authors, that has only been reported from Portugal, Spain and Morocco. In contrast, P. reticulatum and P. clavuliferum, both widely distributed taxa, formed a monophyletic clade, supporting the synonymy already proposed on the basis of morphological features.