Trapelia is a small genus of worldwide distribution. Trapelia coarctata has long been regarded as a morphologically variable species and phylogenetic studies have suggested that it is non-monophyletic, or at least that species are frequently misidentified. The phylogenetic relationships of freshly-collected material of Trapelia were studied using ITS, mitochondrial SSU rDNA and to a small extent also beta-tubulin sequence data, together with chemical and morphological characters. Sequence data combined with morphology and chemistry confirm that the diversity of the genus at species-level has been underestimated. Trapelia coarctata is defined in a more restricted way and many specimens previously referable to this taxon are assigned to the reinstated species T. elacista, which differs in subtle morphological characters including a crack separating the thallus and apothecium in well-developed thalli. Trapelia involuta is reinstated as a separate, though closely related, species to T. glebulosa based on sequence data, morphology and chemistry, and is lectotypified. Trapelia collaris is a distinctive species described as new from Great Britain which has an extensive, cracked thallus with abruptly thickening marginal areoles arising on an inconspicuous prothallus, relatively small apothecia (rarely exceeding 300 µm diameter) and contains 5-O-methylhiascic acid as the major secondary substance. Trapelia obtegens is shown to include frequent non-sorediate morphs which have doubtless been misidentified as other species. The number of species of Trapelia considered to occur in Europe is thus raised from five to eight. The genus is newly reported for the Falkland Islands where seven species occur: T. coarctata, T. placodioides, T. sitiens sp. nov. (with a thin, extensive thallus, sessile apothecia, 5-O-methylhiascic acid as the major secondary substance and the presence of conidiomata), T. tristis sp. nov. (with relatively small apothecia up to 460 µm diameter, presence of gyrophoric acid as the major substance and an absence of conidiomata) and three unidentified species represented by very sparse material. All the species studied, with the possible exception of the three unidentified species, can usually be distinguished by morphological features, particularly the method of development of the thallus and the shape and distribution of the areoles, but morphological variation in response to microhabitat variation is likely to make a proportion of specimens difficult to assign to species in the absence of sequence data.

Bacidina mendax, described here as a new lichen species, appears to be common and widespread, at least in Central Europe. Analyses of the ITS rDNA region and the morphology of specimens showed an intraspecific variation in the new taxon. It differs from B. neosquamulosa in the lack of a subsquamulose thallus, and from B. caligans in its longer and only slightly curved to apically hooked conidia and lack of a granular (sorediate) thallus. Since ITS rDNA data support the inclusion of Bacidia pycnidiata Czarnota & Coppins in the genus Bacidina, a new combination is proposed.

The lichen species of the genus Thamnolia, with their striking wormlike thalli and frequent occurrence in arctic and tundra environments, have often been debated with regard to the use of chemistry in lichen taxonomy. Phylogenetic studies have arrived at different conclusions as to the recognition of species in the genus, but in a recent study based on the analyses of six nuclear markers (genes or noncoding regions) of a worldwide sample of Thamnolia, we showed the existence of three well-supported lineages with two different chemistries and geographical distributions. Here, we present two analyses based on ITS and three markers, respectively, which were extended from the study mentioned above to include type specimens and additional Thamnolia strains and taxa. In these analyses the same three clades were retrieved. A putative DEAD-box helicase is used here for the first time as an informative phylogenetic marker to provide taxonomic resolution at species level. The distribution of morphological and chemical characters across the phylogeny was analyzed and it was concluded that three morphologically cryptic, but genetically well supported, species occur: T. vermicularis s. str., T. subuliformis s. str. and T. tundrae sp. nov. Thamnolia vermicularis s. str. contains individuals with uniform secondary chemistry (producing thamnolic acid) and a rather limited distribution in the European Alps, Tatra Mts and the Western Carpathians, a distribution which might result from glacial survival in an adjacent refugium/refugia. Thamnolia subuliformis s. str. is widely distributed in all hemispheres and the samples contain two chemotypes (either with thamnolic or squamatic acids). Thamnolia tundrae is described as new; it produces baeomycesic and squamatic acids, and has a distribution limited to the arctic tundra of Eurasia extending to the Aleutian Islands in North America. It may have survived the latest glaciation in coastal refugia near its present distribution. Thus, secondary chemistry alone is not suitable for characterizing species in Thamnolia, secondary chemistry and geographical origin are informative, and the ITS region can be confidently used for species recognition. Nomenclatural notes are given on several other names that have been used in Thamnolia.

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.

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.

Myriospora signyensis Purvis, Fdez-Brime, M. Westb. & Wedin is described from Signy Island, South Orkney Islands, Antarctica, where it occurs predominantly on quartz mica schist. This represents the first record of the genus for Antarctica. The distinctive interrupted photobiont arrangement places it within the genus Myriospora (formerly known as the ‘Acarospora’ smaragdula group, or Silobia). The new species is characterized by having large, distinctly elevated, sessile apothecia with a prominent margin and a thallus that is usually lobed at the margins and variously orange-red, rust-coloured or brown-pigmented. Molecular phylogenetic analyses inferred with strong support that M. signyensis is closely related to M. scabrida which is similar in having a lobed, imbricate thallus with large and frequently somewhat raised apothecia, but which differs in never being rusty red, by frequently having a larger number of apothecia per areole/squamule and by having a thick and distinctive thalline epinecral layer. Myriospora signyensis is otherwise most similar to M. dilatata but the thallus of M. dilatata is never imbricate-lobate and the ascomata of M. signyensis have larger and more distinctly raised and sessile apothecia. A worldwide key to the 10 species currently recognized in the genus is presented.

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.

Lichen thalli represent the most conspicuous examples of fungal-algal interactions. Studies that describe phycobiont diversity within entire thalli are based mainly on Sanger sequencing. In some lichen species, this technique could underestimate the intrathalline coexistence of multiple microalgae. In this study different multi-tool approaches were applied to two lichen taxa, Circinaria hispida and Flavoparmelia soredians, to detect algal coexistence. Here, we combined Sanger sequencing, a specific polymerase chain reaction (PCR) primer, 454-pyrosequencing, phycobiont isolation and ultrastructural characterization. Furthermore, we compared pyrenoid ultrastructural features of lichenized phycobionts with microalgae isolated in culture. An improved methodology was used to isolate and propagate phycobionts which, in combination with fast genetic identification, resulted in a considerable reduction in time and cost to complete the process. This isolation method, coupled with a specific PCR primer, allowed for the detection of coexisting algae in C. hispida (four Trebouxia lineages). 454-pyrosequencing detected only a fraction of such diversity, while Sanger sequencing identified only the primary phycobiont. Ultrastructural features of the isolated algae were observed by transmission electron microscopy; the maintenance of the pyrenoid characteristics suggested the existence of different Trebouxia lineages. In F. soredians a single Trebouxia lineage was identified using all these approaches.

In cases of lichens with algal coexistence, a combination of different molecular and ultrastructural approaches may be required to reveal the underlying algal diversity within a single thallus. The approach proposed in this study provides information about the relationship between molecular and ultrastructural data, and represents an improvement in the delimitation of taxonomic features which is needed to recognize intrathalline Trebouxia diversity.

Chlorophyll a fluorescence is often used to estimate various types of damage in lichens. In order to optimize the output and improve interpretations of such measurements the protocol for pretreatment and measuring is important. To study the effects of measurement conditions, the lichens Lobaria pulmonaria, L. scrobiculata, Xanthoria parietina and Parmelia sulcata were first stressed by high light intensities at 600 or 1000 µmol photons m−2 s−1 for 4 h. Then various conditions during recovery or pretreatment were used to optimize the detection of more lasting damage. Recovery from photoinhibition was incomplete in darkness, whereas light as low as 0·2 or 1·0 µmol m−2 s−1 resulted in complete recovery if the recovery period was long enough. Additionally, low intensity light given for1·5 h after one day in darkness caused rapid and complete recovery. In conclusion, before measuring maximal PSII efficiency (Fv/Fm) with chlorophyll fluorescence, it is important to let lichens recover in low intensity light and not in darkness, to optimize recovery from photoinhibition; dark adaptation can only be recommended if the photoinhibition status of the lichens is of interest.