There is still a high diversity of lichen-forming fungi that remains undescribed, especially cryptic lineages at the species level. Integrating morphological, chemical, and DNA sequence data has proved useful in corroborating species descriptions and delimitations. Here we reviewed morphological features, secondary metabolites and the DNA sequences of ITS, mtSSU and nuLSU markers to study the diversity of Xanthoparmelia in southern Africa. A total of 37 species were recorded. Three of these appear undescribed, and we therefore describe them here as new: Xanthoparmelia nimisii, with a sorediate thallus and broad lobes, is well supported as a clade separate from X. annexa; X. pseudochalybaeizans with a white medulla is phylogenetically distinct from the otherwise similar X. chalybaeizans; and X. sipmaniana, well supported as a separate clade from the similar X. hypoprocetrarica. In addition, the separation of Xanthoparmelia capensis and X. tinctina requires further studies.

Recent studies have demonstrated that species boundaries among the lichen-forming fungi are in need of revision with the discovery of cryptic species in numerous clades, especially in parmelioid lichens. Here we focus on addressing the species boundaries in Canoparmelia texana, a sorediate species with a pantropical distribution that extends into temperate regions. We extracted DNA sequences of the nuclear ribosomal internal transcribed spacer region (ITS), large subunit (nuLSU) and mitochondrial small subunit (mtSSU) from samples mostly collected in Kenya, and analyzed them in a phylogenetic framework. We illustrate that our samples of the species as currently circumscribed do not form a monophyletic group but fall into two distinct clades, with the apotheciate C. nairobiensis nested within. Both of the discovered lineages have a wide distributional range and are common in Kenya, and Parmelia albaniensis C. W. Dodge is resurrected to accommodate one of the clades; consequently a new combination, Canoparmelia albaniensis (C. W. Dodge) Divakar & Kirika comb. nov., is proposed.

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.

Lichens of the Ramalina siliquosa complex dominate seashore cliffs in Europe and South-East Asia, but their taxonomy has been vigorously debated for over a century. On many cliffs, they exhibit a bewildering zonation of chemotypes that resembles the classic zonation of organisms that occupy the littoral zone below. Do the chemotypes represent separate species, or infraspecific variation? To better understand the systematics of this group, sequences from four genetic loci (ITS, IGS, RPB1 and RPB2) were obtained for 59 samples from Denmark, France, Iceland, Norway, UK, Japan and Korea, including all major chemotypes. Maximum likelihood analysis of these sequences, together with sequences from 36 other Ramalina species, reveals that the complex comprises two distinct phylogenetic lineages, each including multiple chemotypes. These two putative species-level lineages correspond to the currently accepted taxa R. cuspidata and R. siliquosa. There is no evidence that these two taxa are phylogenetic sister species. Consequently, the explanation of this chemotype complex as an example of ‘sibling speciation’ is rejected. Specimens traditionally called ‘R. siliquosa’ from South-East Asia form a third clade, identified here as R. semicuspidata, with an additional, divaricatic acid chemotype. Other results include a robustly supported clade of Ramalina species that produce medullary depsides and depsidones; this clade includes another well-supported clade of south-eastern United States coastal plain and tropical Ramalina species. By contrast, large, strap-shaped Ramalina species that lack medullary depsides and depsidones occur in separate lineages. In addition, close relationships between the following groups of species are indicated: R. farinacea with R. subfarinacea; R. fraxinea with R. leptocarpha, R. menziesii and R. subleptocarpha; R. sinensis with R. unifolia. Furthermore, a new, variolaric acid-only chemotype is reported for R. farinacea, and a new, acid-deficient chemotype is reported for a more broadly circumscribed R. culbersoniorum.

An account of thelotremoid species of Graphidaceae in India is provided, which includes 124 species in 24 genera. Ocellularia and Thelotrema are the most diverse genera represented by 34 and 18 species, respectively. Type specimens were re-examined and additional samples studied morphologically and chemically. One new species, Ocellularia upretii S. Joshi, Divakar, Lumbsch & Lücking, is described; it is characterized by a greyish green thallus, porinoid ascomata, brown proper exciple, simple, carbonized columella, clear hymenium, transversely septate, amyloid ascospores of 110–125×15–20 µm and an absence of secondary metabolites. Asteristion australianum, Astrochapsa mirabilis, Cruentotrema cruentatum, C. kurandense, Ocellularia violacea and Thelotrema adjectum are reported as new to the country, and Astrochapsa mirabilis, Melanotrema submicrosporoides, Ocellularia annuloelevata, O. subkeralensis and Rhabdodiscus verrucoisidiatus are proposed as new combinations. Diploschistes awasthii, Ocellularia gupeti, O. leucina, O. mahabalei, Thelotrema confertum and T. verrucorugosum are synonymized under D. scruposus, O. neomasonhalei, O. urceolaris, O. thelotremoides, Chapsa leprocarpoides and T. rugatulum, respectively, with Ocellularia canariana and O. verrucomarginata reduced to synonymy with O. allosporoides.

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.

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.

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.

Macro-morphological features traditionally used to segregate genera in Parmeliaceae have been shown to be highly plastic, placing limits on their taxonomic value. Here we aim to elucidate the evolutionary relationships of the genera Relicina and Relicinopsis and reassess the phenotypic features traditionally used to separate these genera. To this end, we gathered ribosomal DNA sequences of ITS, nuLSU and mtSSU and analyzed them in a phylogenetic framework. Relicina was recovered as paraphyletic, with Relicinopsis nested within, and three different clades were identified within Relicina. Alternative hypothesis tests significantly rejected the monophyly of Relicina. Our results indicate that the presence or absence of bulbate cilia is of limited taxonomic value in this clade. Based on differences in conidia, however, we propose to accept Relicinopsis as a subgenus within Relicina as Relicina subgen. Relicinopsis (Elix & Verdon) Kirika, Divakar & Lumbsch. It is proposed that five new combinations of species previously classified in Relicinopsis be placed in Relicina.

Five new species and one new record of Astrothelium (Trypetheliaceae) are reported from Thailand. Phylogenetic analysis of four DNA loci (ITS, nuLSU, mtSSU rDNA and RPB1) demonstrated the placement of the new species within Astrothelium, as well as their distinction from similar or related taxa. The new species are: A. flavocoronatum, with a yellow pigment surrounding the ostiole, and 3-septate ascospores 22–28×8·0–9·5 µm; A. macrostiolatum, with large whitish ostiolar area, a hamathecium inspersed with small oil droplets, and 9–11-septate ascospores 80–100×17–19 µm; A. neglectum, with lichexanthone on the thallus and pseudostromata, a non-inspersed hamathecium and 3–5-septate ascospores 21–25×7·5–9·5 µm; A. neovariolosum, with inspersed hamathecium and 3-septate ascospores 17–23×6–7 µm; and A. siamense, with inspersed hamathecium and 4–7-septate ascospores 30–50×10·5–12·0 µm. Astrothelium aenascens is reported from Thailand for the first time.

Based on separately obtained and analyzed molecular data and within the framework of a global revision of the family Trypetheliaceae, 21 new species are described, from the Neotropics and tropical Asia, in the genera Architrypethelium (1), Astrothelium (15), Bathelium (1), Nigrovothelium (1), Trypethelium (1), and Viridothelium (2), namely: Architrypethelium lauropaluanum Lücking, M. P. Nelsen & Marcelli sp. nov., differing from A. hyalinum in the perithecia immersed between coarse thallus verrucae and in the additional ascospore septa; Astrothelium aurantiacocinereum Lücking, Naksuwankul & Lumbsch sp. nov., differing from A. aeneum in the prominent, well-delimited, trypethelioid pseudostromata and the absence of pigment on the thallus surface, as well as in the barely lichenized thallus; A. carassense Lücking, M. P. Nelsen & Marcelli sp. nov., differing from A. purpurascens in orange, K+ red pseudostroma pigment and the slightly larger ascospores; A. cryptolucens Lücking, M. P. Nelsen & N. Salazar sp. nov., differing from A. carrascoense in the inspersed hymenium; A. fijiense Lücking, Naksuwankul & Lumbsch sp. nov., differing from A. cinereorosellum in the presence of lichexanthone on the well-delimited pseudostromata and in the slightly shorter ascospores; A. laevithallinum Lücking, M. P. Nelsen & Marcelli sp. nov., differing from A. endochryseum in the smooth thallus; A. leucosessile Lücking, M. P. Nelsen & Aptroot sp. nov., differing from A. phlyctaena in the conspicuous, sessile pseudostromata; A. macrostomoides Lücking, M. P. Nelsen & Benatti sp. nov., differing from A. macrostomum in the larger ascospores; A. megacrypticum Lücking, M. P. Nelsen & N. Salazar sp. nov., differing from A. longisporum in the single-spored asci and larger ascospores; A. nicaraguense Lücking, M. P. Nelsen & T. Orozco sp. nov., differing from A. gigantosporum in the smaller ascospores; A. norisianum Lücking, M. P. Nelsen & Aptroot sp. nov., differing from A. sepultum in the distinct, well-delimited pseudostromata; A. obtectum Lücking, M. P. Nelsen & Benatti sp. nov., differing from A. nigrocacuminum in the smaller ascospores; A. sordithecium Lücking, M. P. Nelsen & Marcelli sp. nov., differing from A. leucothelium in the inspersed hymenium and the absence of lichexanthone from the thallus surface outside the pseudostromata; A. subendochryseum Lücking, M. P. Nelsen & Marcelli sp. nov., differing from A. endochryseum in the absence of pigment in the pseudostromata and the lateral thallus cover of the pseudostromata; A. subinterjectum Lücking, M. P. Nelsen & Jungbluth sp. nov., differing from A. obtectum in the smaller pseudostromata and smaller ascospores, and from A. interjectum in the diffuse pseudostromata and smaller ascospores; Bathelium porinosporum Lücking, M. P. Nelsen & Gueidan sp. nov., differing from other Bathelium species in the 3-septate, euseptate ascospores; Nigrovothelium bullatum Lücking, Upreti & Lumbsch sp. nov., differing from N. tropicum in the bullate thallus; Trypethelium tolimense Lücking, Moncada & M. Gut. sp. nov., differing from T. xanthoplatystomum in the absence of a yellow-orange pigment on the pseudostromata and the K+ yellow (not K+ red) medullary pigment; Viridothelium tricolor Lücking, M. P. Nelsen & N. Salazar sp. nov., characterized by black perithecia with a lateral ostiole immersed in white pseudostromata strongly contrasting with the surrounding brown thallus, in combination with 2-spored asci and large, muriform ascospores; and V. vonkonratii Lücking, Naksuwankul & Lumbsch sp. nov., differing from V. virens in larger ascospores and mostly solitary ascomata. All species are illustrated and their taxonomy and phylogenetic relationships are discussed. ITS barcoding sequences are reported for five specimens of Bathelium porinosporum.

We provide an expanded and updated, 2-locus phylogeny (mtSSU, nuLSU) of the lichenized fungal family Trypetheliaceae, with a total of 196 ingroup OTUs, in order to further refine generic delimitations and species concepts in this family. As a result, the following 15 clades are recognized as separate genera, including five newly established genera: Aptrootia, Architrypethelium, Astrothelium (including the bulk of corticate species with astrothelioid ascospores; synonyms: Campylothelium, Cryptothelium, Laurera), Bathelium s. str. (excluding B. degenerans and relatives which fall into Astrothelium), the reinstated Bogoriella (for tropical, lichenized species previously placed in Mycomicrothelia), Constrictolumina gen. nov. (for tropical, lichenized species of Arthopyrenia), Dictyomeridium gen. nov. (for a subgroup of species with muriform ascospores previously placed in Polymeridium), Julella (provisionally, as the type species remains unsequenced), Marcelaria (Laurera purpurina complex), Nigrovothelium gen. nov. (for the Trypethelium tropicum group), Novomicrothelia gen. nov. (for an additional species previously placed in Mycomicrothelia), Polymeridium s. str., Pseudopyrenula, Trypethelium s. str. (T. eluteriae group), and Viridothelium gen. nov. (for the Trypethelium virens group). All recognized genera are phenotypically characterized and a discussion on the evolution of phenotypic features in the family is given. Based on the obtained phylogeny, species delimitations are revised and the importance of characters such as thallus morphology, hymenial inspersion, and secondary chemistry for taxonomic purposes is discussed, resulting in a refined species concept.

The diversity of the Trypethelium eluteriae group in Thailand was studied using molecular (ITS and mtSSU rDNA sequences), morphological, and chemical data. Three species were recognized, T. eluteriae, T. platystomum, and T. subeluteriae, with the latter two being new records for Thailand. The separation of the three species, which have sometimes been regarded as synonymous, is supported by molecular and phenotypic characters. The chemical profiles of the three species are distinct, while ascospore size, often used to distinguish species in the group, shows some overlap.

One new species and six new records of the crustose lichenized genus Graphis are reported from Thailand. Graphis koratensis Pitakpong, Kraichak & Lücking sp. nov. is characterized by lirelline ascocarps with whitish grey or grey-green pruina along the slit, transversely septate ascospores, and the presence of norstictic acid. Phylogenetic analyses with two loci (mtSSU and nuLSU) show the distinct position of this new species within the genus. Six new records for Thailand are reported, including G. cincta (Pers.) Aptroot, G. jejuensis K. H. Moon et al., G. nigrocarpa Adaw. & Makhija, G. renschiana (Müll. Arg.) Stizenb., G. seminuda Müll. Arg., and G. subserpentina Nyl.

The Cladonia furcata complex treated here comprises C. farinacea, C. furcata, C. multiformis, C. scabriuscula, C. stereoclada, and C. subrangiformis. The well-known taxonomic complexity of this group is caused by wide phenotypic variation and high morphological similarity among the species, for which reason we investigated the distribution in the phylogeny of the phenotypic characters traditionally used to distinguish the species in this complex. A phylogenetic analysis of the C. furcata complex is presented here, based on three loci (ITS rDNA, IGS rDNA and RPB2), representing specimens from a broad geographical range (Europe, North America and New Zealand). The phylogenetic reconstructions were performed using Maximum Likelihood and Bayesian analyses. In addition, 14 features traditionally used for species delimitation within this complex were mapped onto the Bayesian phylogeny. All the species currently accepted, with the exception of C. stereoclada, turned out to be polyphyletic. Most of the phenotypic characters studied are highly homoplasious with the exception of the podetium type. The solid podetia represent a diagnostic character of C. stereoclada.

Based on collections focusing on Graphidaceae made in 2012 at Bukit Timah Nature Reserve (BTNR) in Singapore, seven new species are described: Astrochapsa sipmanii, differing from A. astroidea in the olive-brown thallus and thick and coarse apothecial pruina; Fissurina duplomarginata, differing from F. insidiosa by the double margin of the lirellae and the more greenish, rough thallus; Graphis bukittimaensis, differing from G. phaeospora in the erumpent lirellae with lateral thalline margin and the consistently 1-spored asci; G. singaporensis, differing from G. novopalmicola in the much smaller ascospores and in the immersed, densely branched lirellae with thin lateral thalline margin; Ocellularia subudupiensis, differing from O. udupiensis in the presence of three unknown secondary substances and in the comparatively rough thallus surface; O. gueidaniana, characterized by small, transversely septate, hyaline ascospores, prominent, carbonized but ecolumellate apothecia, and two unknown chemical substances resembling metabolites in the stictic acid chemosyndrome; and O. rivasplatana, differing from O. exigua in the larger, broad-pored apothecia with black-rimmed margin and filled with a black-topped columella. Nineteen species are recognized as new records for Singapore. The substantial diversity of Graphidaceae in this reserve suggests that many more taxa are awaiting discovery, even in such a highly urbanized location.

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.

The genus Hypogymnia is morphologically characterized by swollen lobes, a hollow medulla, perforations in the lower surface, and the absence of rhizines. In our studies on Hypogymnia spp. we found rhizines and hapters were occasionally present on the lower surface of 35 species. Morphology and anatomy of the appendage-organs were studied using dissecting, compound, and scanning electron microscopy and compared with rhizines found in the related genus Arctoparmelia. Two types of rhizine-like structures were found in Hypogymnia: slender and elongated rhizines, and thick and short hapters, both of which were few in number and sparsely distributed on the lower surface. There are no obvious differences in the morphology of rhizines between Arctoparmelia and Hypogymnia, except that rhizines are abundant in Arctoparmelia. Within Parmeliaceae, Hypogymnia belongs to the hypogymnioid clade together with the genera Arctoparmelia, Brodoa, and Pseudevernia, most of which are considered to lack rhizines. The occurrence of rhizines in Hypogymnia is consistent with the placement of Arctoparmelia in the hypogymnioid clade based on molecular data.