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.

We present a phylogenetic revision of the Sticta filix morphodeme in New Zealand. This non-monophyletic group of early diverging clades in the genus Sticta is characterized by a stalked thallus with a green primary photobiont and the frequent formation of a dendriscocauloid cyanomorph. Traditionally, three species have been distinguished in New Zealand: S. filix (Sw.) Nyl., S. lacera (Hook. f. & Taylor) Müll. Arg. and S. latifrons A. Rich., with two cyanomorphs separated under the names Dendriscocaulon dendriothamnodes Dughi ex D. J. Galloway (traditionally associated with S. latifrons) and D. dendroides (Nyl.) R. Sant. ex H. Magn. (traditionally associated with S. filix). Sticta lacera was not included in the present study due to the lack of authentic material (all specimens originally identified under that name and sequenced clustered with S. filix); S. filix was confirmed as a distinct species whereas S. latifrons s. lat. was shown to represent two unrelated species, S. latifrons s. str. and the reinstated S. menziesii Hook. f. & Taylor. The cyanomorphs of S. filix and S. latifrons are not conspecific with the types of the names D. dendriothamnodes and D. dendroides, respectively; the D. dendriothamnodes cyanomorph belongs to the Australian taxon Sticta stipitata C. Knight ex F. Wilson, which is not present in New Zealand, whereas the D. dendroides cyanomorph corresponds to a previously unrecognized species with unknown chloromorph, recombined here as Sticta dendroides (Nyl.) Moncada, Lücking & de Lange. Thus, instead of three species (S. filix, S. lacera, S. latifrons) with their corresponding cyanomorphs, five species are now distinguished in this guild in New Zealand: S. dendroides (cyanomorph only), S. filix (chloro- and cyanomorph), S. lacera (chloromorph only), S. latifrons (chloro- and cyanomorph) and S. menziesii (chloro- and cyanomorph). A key is presented for identification of the chloromorphs and the dendriscocauloid cyanomorphs of all species. Semi-quantitative analysis suggests that species in this guild are good indicators of intact forest ecosystems in New Zealand and that the two newly recognized species, S. dendroides and S. menziesii, appear to perform particularly well in this respect. The use of lichens as bioindicators of environmental health is not yet established in New Zealand and so, based on our results, we make the case to develop this approach more thoroughly.

Descriptions, illustrations, discussion and an identification key are presented for six saxicolous and terricolous species of the lichen genus Bacidia De Not. occurring in temperate Australia and Tasmania. Three species are described as new to science: B. lithophila Kantvilas from northern Tasmania, characterized by having only brown apothecial pigments and 3–5-septate, acicular ascospores, 23–35×1·5–2·0 µm; B. littoralis Kantvilas from Tasmania, South Australia (Kangaroo Island) and New South Wales, characterized by green and brown apothecial pigments and acicular, 3–7-septate ascospores, 24–48×2·0–3·5 µm; and B. maccarthyi Kantvilas from New South Wales, with pruinose apothecia and long, filiform, 17–25-septate ascospores, 65–115×2·5–4·0 µm. Three further species are reported for the region for the first time: B. bagliettoana (A. Massal. & de Not.) Jatta (Tasmania), B. curvispora Coppins & Fryday (Tasmania) and B. scopulicola (Nyl.) A. L. Sm. (Tasmania, Victoria).

Temperature preferences and small-scale distribution patterns of four Dermatocarpon taxa in the catchment areas of two Bulgarian rivers were analyzed. Taxa with an overall alpine or arctic-alpine distribution were restricted to microhabitats with the lowest water and rock surface temperatures. A trend for increasing Dermatocarpon rivulorum thallus diameter and colony size (aggregates of thalli) with decreasing temperature was identified. Data on pH and conductivity of the water for the study sites are provided for all taxa. Dermatocarpon arnoldianum is reported for the first time from Bulgaria, confirmed by ITS sequence data, and its known range extends to South-East Europe. All previous records of D. rivulorum from Bulgaria were based on misidentified specimens of D. arnoldianum. Freshwater taxa of Dermatocarpon are proposed as a tool for monitoring the biological effects of temperature changes due to global climate change. Thallus and colony size are recommended as additional features for monitoring populations of threatened Dermatocarpon species.

The genus Coenogonium Ehrenb. in Tasmania comprises seven species. New to science are: C. atherospermatis Kantvilas, Rivas Plata & Lücking, endemic to Tasmania and characterized by pale yellowish beige apothecia and relatively small ascospores, 6–8·5×2·5–3 µm; C. urceolatum Kantvilas, Rivas Plata & Lücking, likewise endemic to Tasmania and characterized by orange, urceolate apothecia, 0·3–0·4 mm wide, and uniseriate ascospores, 8·5–11×2·5–3 µm; and C. australiense Kantvilas & Lücking, recorded from Tasmania, South Australia and New South Wales, and characterized by orange apothecia, 0·5–2 mm wide, and relatively broad ascospores, 10–14×3–4·5 µm. Also treated are C. lutescens (Vĕzda & Malcolm) Malcolm (Tasmania and New Zealand) and three widespread taxa, namely C. implexum Nyl. (Southern Hemisphere), C. luteum (Dicks.) Kalb & Lücking and C. pineti (Schrad. ex Ach.) Lücking & Lumbsch (both subcosmopolitan). All species are described in full from Tasmanian collections and illustrated, and their ecology, variation and affinities to related species are discussed. The Tasmanian taxa are also discussed in the context of the Australasian lichen biota.

Eight new species of Pyrenulaceae are described as new to science from Brazil, Guyana and Puerto Rico. Pyrenula sanguineomeandrata Aptroot & Mercado Diaz (with a thallus with red, KOH+ purple pigmentation of lines or a reticulum, simple ascomata with vertical ostioles, a deep red inspersed, KOH+ orange hamathecium, and dark brown 3-septate ascospores 25–29×10–12 μm) and P. sanguineostiolata Aptroot & Mercado Diaz (with a thallus with deeply immersed simple ascomata with vertical ostioles, which are superficial and bright red, and 3-septate ascospores 25–28×9–12 μm) are described from submontane evergreen forests in Puerto Rico. Pyrenula biseptata Aptroot & M. Cáceres (with simple ascomata with vertical ostioles, an inspersed hamathecium and 2-septate ascospores 11–12×4·5–5·0 μm) and P. xanthinspersa Aptroot & M. Cáceres (with an ecorticate thallus containing lichexanthone, simple ascomata with vertical ostioles, not inspersed hamathecium and 3-septate ascospores 14–17×6·0–7·5 μm) are described from rainforest in Amazonian Brazil. Pyrenula subvariabilis Aptroot & Sipman (with fused ascomata with lateral ostioles and submuriform ascospores 17–20(–25)×6–9 μm) and Sulcopyrenula biseriata Aptroot & Sipman (with a thallus containing lichexanthone, simple ascomata with lateral ostioles and lozenge-shaped ascospores with 8 locules, (13–)15–17(–20)×8–10 (width)×6–7 (thickness) μm) are described from savannahs in Guyana. Special attention is paid to the genus Pyrgillus: two new species from the 3-septate core group of this small genus are described from Brazil, viz. P. aurantiacus Aptroot & M. Cáceres (with a corticate thallus containing lichexanthone, mazaedium with orange, KOH+ violet, UV+ red pruina and ascospores of 13–16×6·0–7·5 μm) and P. rufus Aptroot & M. Cáceres (with a corticate thallus containing lichexanthone, mazaedium with dark red, KOH+ orange, UV+ red pruina and ascospores of 15·0–17·5×5·0–6·5 μm). An updated key to the 3-septate species of Pyrgillus is provided.

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.

With more than 180 known species, Leptogium has its greatest richness in tropical regions. Only three species have so far been reported from Antarctica but extensive surveys in the Antarctic Maritime Islands have shown that this is an underestimate. Leptogium antarcticum (non-isidiate, with medulla composed of columnar hyphae), L. marcellii (non-isidiate, with medulla composed of a sponge-like arrangement of hyphae) and L. tectum (isidiate, with medulla composed of columnar hyphae) are described here as new to science. The new species are compared with those already reported for the genus in Antarctica, namely L. crispatellum, L. menziesii and L. puberulum, and an identification key is provided. Sequences of ITS and mrSSU regions were obtained from recently collected L. antarcticum, L. marcellii, L. puberulum and L. tectum specimens. Morphological and anatomical data were compared along with available genetic data in order to delimit these species more accurately, using an integrative approach.

Species conservation depends on accurate data, but for many lichens existing collections are geographically biased and contain many taxonomic errors. It is unclear whether ‘non-expert’, systematic monitoring schemes can address these sources of error, particularly for taxonomically challenging lichens (e.g. species requiring chemistry for accurate identification). In this case study we use the Alberta Biodiversity Monitoring Institute (ABMI), a large-scale, systematic, multi-taxon monitoring programme, to better understand the ecology and distribution of a putative rare species, Cladonia rei. Collections of C. rei from Alberta dating from 1947 suggested the species was broadly distributed but rare, with seven accessioned specimens. We used comparative morphology, thin-layer chromatography and habitat modelling to compare historical records against more recent material from ABMI surveys. Contrary to the historical collections, ABMI samples suggest C. rei is almost entirely limited to the dry mixed grassland, northern fescue grassland and aspen parkland natural regions, and that within these ecosystems it is relatively common. The typical ecotype exhibited included a persistent primary thallus, podetia with a persistent basal cortex, and secondary squamules; typically they lacked cups, well-developed apothecia and fumarprotocetraric acid, and ramifications were sparse. Cladonia rei was consistently found in pastures and undisturbed grasslands that hosted relatively rich communities of epigeic lichens, thus it does not appear to act as a pioneer in Alberta or to commonly occupy the anthropogenic niches documented elsewhere. In summary, large-scale, systematic, non-targeted monitoring employing novices redressed issues of sample bias through almost 300 C. rei collections, simultaneously improving the ecological understanding of a putative rare species.

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.

Fuscopannaria leucosticta is a rare and understudied cyanolichen with an interesting and unusual distribution in tertiary relict hotspots worldwide. There is a relatively large population in eastern North America, where it occurs mostly throughout the Appalachian Mountains and reaches its northernmost extent in New Brunswick and Nova Scotia, Canada. The ability to detect this species, and thus determine its habitat requirements, is critical for understanding how it might be affected by human-induced environmental degradation. Maximum entropy modelling with MaxEnt was used to predict the distribution of suitable habitat for this species in Nova Scotia using 62 presence locations, 1405 pseudo-absence locations and four environmental covariates: depth to water table (a proxy for relative soil moisture), distance to the coast and mean annual temperature and precipitation. Our predictive maps identify important habitat features and areas of high suitability in Nova Scotia with an area under the curve value of 0·85. The predicted distribution of this lichen was most affected by temperature. This study elucidates locations as well as species-habitat relationships for F. leucosticta, providing land managers with baseline data that can aid in the discovery of additional populations and provide a better understanding of its ecological requirements which will support the development of sound conservation strategies for this rare lichen.

The lichen family Ophioparmaceae contains three genera: Boreoplaca, Hypocenomyce and Ophioparma. The genus Hypocenomyce is reported here for the first time for China, being represented by the species Hypocenomyce scalaris which is distributed in south-western China. For the genus Ophioparma, one new species is described in this paper, namely Ophioparma pruinosa Li S. Wang & Y. Y. Zhang sp. nov., which is characterized by a pruinose thallus and the presence of usnic acid. Ophioparma araucariae is also reported as new for the Chinese lichen biota. Previous reports of O. lapponica in China are recognized as misidentifications of O. ventosa. Descriptions, keys and phylograms are provided for these species.

How growth is distributed within the morphologically diverse thalli of lichens is still poorly known and the anatomical mechanisms involved are not well understood. This work applies electron microscopy (SEM and TEM) to examine cell- and tissue-level events in the umbilicate thallus of Lasallia pustulata, whose pattern of expansion was the subject of a previous field study. Stacks of epinecral tissue accumulating at the thallus surface showed broadening bases and recurring rupture attributable to diffuse expansion of the living tissue below. Cortical cells, dividing anticlinally, adjoined septa to previous septa, indicating parenchymatous divisions. These observations are all consistent with previous contentions that mature, organized tissues within the thallus are capable of continued diffuse growth. They provide a developmental explanation for the morphology of the epinecral layer and suggest that anatomical characteristics may be helpful in recognizing diffuse growth patterns. Parenchymatous cell divisions, believed until recently to never occur in lichen thallus tissues, are shown to play a developmental role in the diffuse growth of the umbilicate lichen thallus.

Epiphytic lichens are increasingly included in forest biodiversity monitoring schemes, but most of the standardized guidelines consider only lichens colonizing a small part of tree trunks (1·0–1·5 m) and overlook other important microhabitats, such as fallen branches and stumps. In this paper, we present results of a small-scale pilot study to evaluate the possible advantage of including four distinct microhabitats in standardized procedures for assessing epiphytic lichen diversity. Trunk bases, trunks between 100 and 150 cm above the ground, stumps, and fallen branches were each sampled with a different standardized sampling method along a forest age gradient in temperate deciduous forests of the Caucasian region. Plot-level species richness was contrasted between the standardized sampling procedures of different substrata and a non-probabilistic floristic sampling. The interactions between sampling procedure and stand age were analysed using linear mixed models, and non-metric multidimensional scaling (NMDS) and multi-response permutation procedures (MRPP) were used for comparing species composition. Overall, 97 species were recorded, their richness increasing with increasing stand age. Results were consistent across the gradient of stand age and demonstrated that the adoption of standardized sampling procedures which include stumps and fallen branches in addition to tree trunks would increase the capability of maximizing species capture. This approach would allow researchers to evaluate lichen patterns by simultaneously considering the response of different communities sensitive to different stand-related factors. Despite the likelihood that a non-probabilistic floristic survey would give a more exhaustive picture of the plot-level lichen diversity, standardized sampling procedures that include tree trunks, fallen branches and stumps are likely to represent a reasonable trade-off between exhaustiveness and cost-effectiveness.

Atranorin is a secondary metabolite found in many lichens. This compound can act as a photo-buffer, supporting its use as a marker of metabolic response to changes in light. In preliminary trials, atranorin was found to be unstable over time when in solution, potentially precluding its usefulness in this capacity. The present study tests the stability of atranorin in different extraction solvents and at different pH values over time using HPLC analysis. We found that atranorin is most stable in acetonitrile, among six tested solvents, and that the presence of strong acid or a strong base destabilizes the compound. We propose that atranorin breaks down through transesterification in methanol and ethanol until an equilibrium is reached, while a strong base breaks down atranorin through saponification and under acidic conditions, atranorin concentration significantly increases with time. Although atranorin levels were found to be stable in whole thallus extracts from fresh lichens using a leaching method, chemicals isolated using chromatographic separation showed similar breakdown to an atranorin standard. In future work on lichens atranorin should be extracted in acetonitrile or acetone without an added base or acid to yield the greatest stability and thus provide more accurate concentration values of atranorin with time using HPLC. The interactions of atranorin with acid and with chloroform need further study.