This study investigated the molecular, chemical and morphological variation in the Usnea pectinata aggregate using 42 specimens, 22 from Tanzania and 20 from São Tomé and Príncipe. A total of 31 sequences (13 ITS, 13 nuLSU and 5 RPB1) were generated. The results are presented in two phylogenies: first a three-markers ‘backbone’ phylogeny for the U. pectinata aggregate, where six distinct, strongly supported subclades indicate considerable genetic variation in the dataset; and second, an ITS phylogeny with 47 terminals along with a mapping of morphological and chemistry data. Several well-supported monophyletic clades were recovered in both phylogenies and these may well represent separate species in the complex referred to here as the U. pectinata aggregate. Three morphotypes characterized by axis pigmentation and four by branch shape were noted. Six chemotypes were observed.

Of the c. 900 lichen species known from Kenya, 178 belong to the parmelioid clade. Several of these parmelioid taxa require further revisionary studies. An identification key to the species of the parmelioid clade, based on updated nomenclature, is produced to support the practical work in collecting and selecting certain parmelioid lichens for further research. A new combination Parmotrema nyasense (C. W. Dodge) R. S. Egan comb. nov. in Egan et al., Bibliotheca Lichenologica 110, 383 (2016) is published here by R. S. Egan.

The species of the Parmelia saxatilis complex occurring in the Iberian Peninsula were revised. Eight species are accepted, including a new species found in southern Spain, described as P. rojoi A. Crespo, V. J. Rico & Divakar. The new species, which forms a sister-group relationship with P. saxatilis s. str., is rare in the Iberian Peninsula and is restricted to higher altitudes of northern and central Spain. Parmelia rojoi differs from P. saxatilis by generally narrower isidia and a more fragile thallus. The segregation of the new species is also supported by ITS (rDNA) and Mcm7 (MS456) phylogeny and multispecies coalescent-based approaches, including StarBEAST and BP&P. Furthermore, the divergence of P. rojoi is dated back to the Pleistocene, c. 2.13 Ma. A key to the identification of species from the P. saxatilis complex with their diagnostic features is provided. All species of the complex known from Europe are also found in the Iberian Peninsula. We hypothesize that P. rojoi is a relict species that survived the Pleistocene glaciations in refugia in Spain and has been unable to extend its distributional range in postglacial periods.

The results of the first molecular phylogenetic study of Pseudephebe are presented; a three-locus phylogeny. The genus is confirmed as monophyletic within the alectorioid clade of Parmeliaceae. Two major clades were recovered, which can be assigned to the two traditional taxa, P. minuscula and P. pubescens, with modifications of the species delimitation, especially the variable P. minuscula. These species are cryptic and cannot be confidently distinguished morphologically due to phenotypic convergence. Therefore, the use of P. pubescens aggr. is recommended for samples not molecularly analyzed. Contrary to previous studies, specimens of both species might have indistinct pseudocyphellae and also contain lichen substances; norstictic acid was detected in c. 60% of specimens tested. An SSU 1516 Group I intron is usually present in P. minuscula but always absent in P. pubescens. The species-level nomenclature is summarized and sequenced reference specimens (RefSpec) for both Pseudephebe species are selected. Sequences from Bryoria mariensis established that this name was a synonym of P. minuscula.

Bryoria araucana sp. nov. is described from Chile on the basis of morphological, chemical and molecular data. It has a grey to dark greyish brown pendent thallus with the base usually black, branching angles mainly obtuse, terminal branches with few lateral branchlets acutely inserted, fumarprotocetraric acid, and often protocetraric and confumarprotocetraric acids. It is morphologically similar to the Northern Hemisphere B. trichodes, but lacks soralia and has inconspicuous concolorous or slightly darker pseudocyphellae. Bryoria glabra is also reported for the first time from the Southern Hemisphere. New phylogenetic data based on ITS, mtSSU and MCM7 analyses suggest that Bryoria sect. Bryoria is polyphyletic and needs revision.

In order to confirm and investigate the extent of reported mismatches between chemotypes and molecular sequence data in Bryoria fuscescens s. lat., we examined 15 morphologically similar thalli from each of three Pinus forest sites in the Sistema Central of central Spain. Three thalli were rejected due to infections by Phacopsis huuskonenii (not previously published from Spain). The remaining 42 thalli represented nine ITS rDNA haplotypes and four chemotypes (by TLC): fumarprotocetraric and protocetraric acids; norstictic and connorstictic acids; psoromic acid; and fumarprotocetraric, protocetraric and psoromic acids. The molecular phylogenetic tree was characterized by extremely short branch lengths, often only with a single mutational difference, and a single haplotype could have different chemical products. In some cases, adjacent specimens represented different chemotypes, and three thalli appeared to be mixed individuals. Consistency of both molecular and chemical data within individual specimens was demonstrated by examining four different parts of each thallus, which showed only a difference in the location of psoromic acid in some. This is the first population-level study of this taxon, and so it is premature to propose taxonomic changes at this time. Further populations in different parts of the geographical range of this widespread complex now need to be analyzed, and more sensitive chemical analyses conducted, in order to understand the basis of the variability and determine the appropriate taxonomic treatment.

The phylogenetic position of the genus Pseudoparmelia was addressed using molecular data from five loci (mtSSU, nuLSU, ITS, Mcm7, RPB1), generated from three species and aligned with sequences from 293 samples representing all major clades of Parmeliaceae. Pseudoparmelia species form a well-supported monophyletic group that is the sister group of a clade consisting of the genera Relicina and Relicinopsis. These three genera share a thallus with a pored epicortex, isolichenan as cell wall polysaccharide, and relatively small ascospores. Morphological and chemical characters that distinguish Pseudoparmelia from the closely related Relicina and Relicinopsis are discussed. To further elucidate the relationships of these three genera, we assembled a second dataset including 15 additional samples of Relicina and Relicinopsis using three loci (mtSSU, nuLSU, ITS). All three genera are monophyletic but monophyly of Relicina lacks support and, in the mtSSU single locus tree, the genus is paraphyletic with Relicinopsis nested within. Additional studies including more Relicina species are necessary to test delimitation of the genera Relicina and Relicinopsis.

A key is given to the foliose and squamulose lichens known so far from Rondônia, including also corticolous crustose lichens with a chlorococcoid alga. The foliicolous Lecanorales found are also listed. The following four new corticolous Lecanorales are described from Rondônia: Calopadia granulosa with a granular, corticate thallus and ascospores 1 per ascus, 33–38×10·5–13·0 µm; Crustospathula amazonica with irregularly capitate to nearly globose, c. 0·2–0·4 mm diam. soralia on cartilaginous stalks; Flavoparmelia plicata with a thallus containing usnic and protocetraric acids, with laminal, irregular, globose to cylindrical isidia which are often easily abraded and showing the whitish medulla, but not sorediate or postulate; Physcidia striata with ascending squamules, without hypothallus, often with laminal isidia in defined areas towards lobe tips of some, usually sterile lobes, and often with biatorine apothecia with ascospores simple to 1-septate, (6·2–)7·5–10·0×(2·5–)3·0–3·5 µm. In the whole lichen flora of the lowland rainforest region of Rondônia, the following traits can be discerned: foliose lichens amount to only 17 species (2·7% of nearly 600), 33 (5·5%) are squamulose, while the vast majority (91·8%) are crustose. Cyanobacteria are present in only 6 (1%) species. A chlorococcoid alga present in c. 100 (16%), 12 of which (2%) have a myrmecioid alga. The remainder of the species, a staggering 83%, have trentepohlioid alga, including 6 (1%) with Phycopeltis. In neotropical lowland rainforest, the vast majority of the lichens are crustose and contain a trentepohlioid alga, and the Arthoniales, Graphidaceae and pyrenocarpous lichens are the main groups, each accounting for roughly a quarter of the lichen biodiversity.

The type collection of Parmelia goebelii (Bulbothrix goebelii) was discovered to be a mixture of several different Bulbothrix species. The true identity of B. goebelii is established and problems regarding the variability of this species discussed. The species B. papyrina, B. scortella and B. subdissecta, synonymized with B. goebelii by Hale, are resurrected as valid taxa. A detailed description of B. goebelii is presented, its lectotype is selected, and the characteristics of all four species discussed.

Morphological and chemical studies of Hypogymnia from the Himalayas revealed one new species, three species new to the region, and a previously unrecognized synonym. Hypogymnia crystallina, distinguished by its rimmed holes in the lobe axils, a pruinose disc, POL+ epihymenium, and distinctive chemistry (zeorin, hypoprotocetraric acid, usnic acid and atranorin) is described as new. Hypogymnia pseudohypotrypa (Asah.) A. Singh is synonymized with H. thomsoniana and a second location is reported for the recently described H. sikkimensis. Hypogymnia bitteri, H. mundata, and H. subarticulata are reported as new to India. A total of 17 species of the genus Hypogymnia are accepted for the Himalayan region of India and Nepal, with one additional species from southern India. A key is given to the species known from this region.

Two new species of Anzia are described from Sri Lanka: A. mahaeliyensis characterized by a white, single-layered medulla and pale tipped isidia, and A. flavotenuis by a two-layered medulla with the upper layer yellow and the lower part white, a central chondroid axis and isidia with brown-black tips. Morphological and chemical characters used to distinguish species of Anzia are discussed and DNA sequences (ITS) are provided for the two new species. Characteristic features and worldwide distribution of the genus are also outlined.

The phylogenetic relationships of the genus Bryoria were examined using ITS, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and mitochondrial SSU rDNA sequence data in addition to 20 chemical and morphological characters. This first comprehensive molecular study to assess Bryoria phylogeny includes representatives from all the traditionally recognized four sections. Combined cladistic analyses of 88 Bryoria specimens representing at least 25 species resulted in highly resolved phylogenies. Based on the results, a new infrageneric classification for the genus is proposed. Five sections are recognized, largely corresponding to the existing classification, with the addition of section Americanae. The study shows that while most species with an erect growth-form are clearly monophyletic, current species status of many pendent taxa can be questioned.

This article traces the changing systems in the classification of the parmelioid lichens from the early 19th century to the present day. Molecular phylogenetic approaches have enabled the relative importance of traditionally used characters to be objectively re-assessed, and led to the realization of the significance of others that had previously been passed over or dismissed; for example, differences in ascospore and conidium types or the cell-wall constituents. Information on the different characters employed is presented and assessed. It is concluded that characters related to thallus form or chemical products prove to be less informative at the generic level than has sometimes been assumed. Features requiring further study are identified, and in the light of experience in this group, lichenologists should be cautious in translating their results into formal taxonomies.

We used a genetic distance approach in conjunction with molecular phylogeny to establish species boundaries and detect cryptic lineages in the Parmotrema reticulatum – P. pseudoreticulatum complex. The phylogeny of specimens from a broad geographic distribution was reconstructed from the internal transcribed spacer region. Pairwise genetic distances were calculated and compared to an intraspecific range defined for the parmelioid lichens to circumscribe species-level groups. Our results showed that P. reticulatum and P. pseudoreticulatum are polyphyletic, being comprised of at least seven well-supported lineages. In contrast, the genetic distance approach revealed ten cryptic lineages within the P. reticulatum – P. pseudoreticulatum complex. Neither morphology nor geography was conclusive in attempting to corroborate these genetic lineages. However FST indices suggest significant genetic differentiation between these lineages. Our results suggest that the morphology-based circumscriptions underestimated species in Parmotrema and that, in some cases, genetic distances may be used as an additional tool to determine species boundaries in morphologically cryptic species complexes. The most significant contribution of the present study is the application of a fast and accurate method to identify problematic groups and candidate species using the ITS locus with a genetic distances approach.

Additions and corrections to the checklist published in 2008 are presented. Ten additional species are recognized: Allantoparmelia almquistii, Asahinea chrysantha, Hypogymnia bryophila, Hypotrachyna afrorevoluta, Melanelixia glabratula, Parmelia encryptata, Parmelina atricha, P. cryptotiliacea, Parmotrema cinereopruinata, and Punctelia rudecta. Myelochroa subaurulenta is deleted, and Xanthoparmelia perezdepazii is also noted as newly described from the Canary Islands. In addition, Cavernularia hultenii is now placed in Hypogymnia, the Canoparmelia crozalsiana group is included within Parmotrema, and Parmelinopsis is treated as a synonym of Hypotrachyna. The typification of the name Lichen quercinus is also corrected with the designation of the original figure as lectotype, and the new combination Hypotrachyna cryptochlora comb. nov. (syn. Parmelia cryptochlora) is made.

The phylogenetic placement of the genus Maronina was studied, based chiefly on phenotypic characters such as thallus colour and anatomy, secondary chemistry, the anatomy of the excipulum and the ascus-type. DNA sequence data of mitochondrial and nuclear ribosomal loci from some of the species support the hypothesis that Maronina is nested within Protoparmelia. Hence, Maronina is reduced to synonymy with Protoparmelia. Comparison of genetic distances suggests that the two varieties within M. orientalis should be regarded as distinct species. Consequently, the new combinations Protoparmelia australiensis (Hafellner & R. W. Rogers) Kantvilas et al., P. corallifera (Kantvilas & Papong) Kantvilas et al., P. hesperia (Kantvilas & Elix) Kantvilas et al., P. multifera (Nyl.) Kantvilas et al., and P. orientalis (Kantvilas & Papong) Kantvilas et al. are proposed.

This study focuses on European Usnea species with sorediate shrubby thalli, with the aim to evaluate the morphological and chemical separation of species in the light of molecular data. Twenty-two Usnea species, including widely distributed taxa such as U. diplotypus, U. fulvoreagens, U. glabrescens, U. lapponica, U. subfloridana, U. substerilis and U. wasmuthii, were included in the study using Bayesian and maximum parsimony analyses of nuclear ITS and beta-tubulin sequences. The analyses showed that: 1) most taxa that are morphologically well delimited are also distinct by means of molecular characters, 2) shrubby taxa in the section Usnea that are difficult to determine by traditional characters form a group of closely related but still genetically distinct entities, except U. diplotypus and U. substerilis which appear to be polyphyletic. The branch lengths differed largely between two parts of the ITS tree (sections Usnea and Ceratinae). Usnea intermedia is proposed as the sexually reproducing counterpart for the sorediate U. lapponica. Additionally, some new chemotypes of Usnea species were determined.

Two asexual reproductive strategies of the common lichen Pseudevernia furfuracea are described. Although the species propagates mainly by isidia, some specimens also show the development of soralia. Morphological, chemical and molecular analyses were performed on three such sorediate specimens from the Canary Islands, Morocco and Turkey. Maximum parsimony, maximum likelihood and Bayesian analyses indicate that: a) sorediate samples represent only a morphological variant of the reproductive mode and b) the separation of taxa (at species level or below) on the basis of their containing either olivetoric acid or physodic and oxyphysodic acids is not appropriate. In addition, a phylogenetic reconstruction of the genus Pseudevernia is presented for the first time. The tree shows two sister monophyletic clades, one containing American species (P. intensa, P. cladonia, P. consocians), and the second encompassing the P. furfuracea samples (including sorediate specimens). The biological and taxonomic significance of soralia in sorediate samples is discussed.

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.

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).