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The genus Dendriscosticta(Ascomycota: Peltigerales) encompasses several distinctive lichen‐forming fungal species restricted to the Northern Hemisphere. Most are flagship species of old‐growth forests with good air quality. A global phylogeny of the genus based on multilocus sequence data (ITS, RPB1, EF‐1α, MCM7), model‐based phylogenetic methods, and morphological and chemical assessments, reveals a high level of cryptic speciation often associated with restricted geographical distribution and/or chemical characters. Using sequence‐based species delimitation approaches, we circumscribe two main clades referred to as the D. wrightiiclade, with five unequivocal species, including D. gelidasp. nov., and the D. praetextataclade, with eight putative species, including D. phyllidiatasp. nov. The absence of recently collected material of D. hookericomb. nov. from the type locality unfortunately prevents assignment of this epithet to one of the five supported lineages sharing this morphotype. Three new combinations are proposed: D. hookeri, D. insinuanscomb. nov. and D. yatabeanacomb. nov. Epitypes are designated for D. wrightiiand D. yatabeana. Species diversity within the genus increased from four to nine. Our morphological assessment confirmed that Stictaand Dendriscostictacan be readily distinguished by the presence of excipular algae whereas the structure of the lower surface pores is not a reliable diagnostic feature.

The genus Wetmoreanawas studied using quantitative integrative taxonomy methods to resolve the genus delimitation and explore its taxonomy diversity at the species level. As a result, the genus Fulgogasparreais synonymized with Wetmoreana, and the latter includes 15 formally described species, one subspecies, and three further, thus far undescribed species: W. appressa, W. awasthiicomb. nov., W. bahiensissp. nov., W. brachylobacomb. nov., W. brouardii, W. chapadensiscomb. nov., W. circumlobatasp. nov., W. decipioides, W. intensacomb. nov., W. ochraceofulvacomb. nov., W. rubrasp. nov., W. sliwaesp. nov., W. sliwaessp. subparvilobasubsp. nov., W. subnitidacomb. nov., W. texana, and W. variegatasp. nov. Eleven of 19 examined taxa are newly placed within this genus or confirmed to belong to it. Two species, W. awasthiiand W. intensa, are transferred to Wetmoreanawithout additional analysis but based on previous studies. The W. brouardiiand W. ochraceofulvaspecies complexes are discussed in detail.Additionally, Caloplaca muelleriand C. rubinavar. evolutiorare transferred to Squamulea, and the latter is elevated to the species rank.

ABSTRACTMembers of the poorly investigated family Teloschistaceae in South America, mostly from Bolivia and Peru, were examined using molecular and morphological data here for the first time. In recent phylogenetic reclassifications of Teloschistaceae, South American representatives were poorly represented but shown to belong to subfamilies Teloschistoideae and Xanthorioideae. In this study, we expanded the sampling of South American taxa and investigated mainly the lobate, sublobate, and squamulose members of Caloplacas.l., using morphological characters and a molecular phylogeny based on a combined three-locus data set (one mitochondrial and two nuclear loci). Building upon new phylogenies at the family and subfamily levels (Teloschistoideae), we propose here three new genera: Andina, Aridoplaca, and Cinnabaria, with the type species Andina citrinoides, Aridoplaca peltata, and Cinnabaria boliviana. We also propose to reduce Tarasginiato synonymy with Sirenophilaand Tayloriellinato synonymy with Villophoraand introduce three new combinations: Dufourea ottolangei, D. volkmarwirthii, and Villophora erythrosticta. Scutaria andinais reported as new to Bolivia. A critical revision of the subfamily Brownlielloideae confirmed recent findings that it is an artifactual taxon based on a “chimeric” data set, with the type genus being part of Teloschistoideae.

Aims: The objective of this paper was to test the hypothesis that epiphytic lichen metacommunities in the Brazilian Atlantic Forest are hierarchically structured and not only correspond to forest formations and their floristic subdivisions, but also reflect the main geopolitical regions in the study area (Northeast, Southeast, South) and particularly the division of the Atlantic Forest, along a latitudinal gradient, into a tropical and a subtropical-temperate zone north and south of the Tropic of Capricorn. Study area: Atlantic Forest in Brazil. Methods: We employed niche distribution modeling for 245 species of four large and representative families of epiphytic lichens in the study area, using a stacked species approach to model metacommunity structure via quantitative methods of community analysis (clustering and ordination techniques). To account for sampling bias, we performed background manipulation via a bias layer. Results: We detected a hierarchical structure with three main clusters (A, B, C) subdivided into ten subclusters. Both the main clusters and each of the subclusters correlated strongly with environmental variables and latitude and featured statistically significant, characteristic indicator species, and the subclusters matched floristic subdivisions of the main forest formations recognized in the study area. There was a significant correlation of the three main clusters with the three geopolitical regions in the study area which after all also reflect ecogeographical features. The main separation between the two northern (A, B) and the southern cluster (C) almost precisely followed the division of the Atlantic Forest by the Tropic of Capricorn, supports the notion that the latter is an important delineator in biome formation, reflected by epiphytic lichen metacommunities. Conclusion: We conclude that modeling metacommunities via a stacked species approach is a powerful tool, also to elaborate baseline data for future monitoring of metacommunities in relation to climate change. Abbreviations: DEF = Forest types distinguished within this area include dense ombrophyllous or evergreen forest; OEF = open ombrophyllous or evergreen forest; MEF = mixed ombrophyllous or evergreen forest; SSF = seasonal semideciduous forest; SDF = seasonal deciduous forest; RE = restingas; MA = mangroves; BA = Brejos de Altitude

Traditional taxonomic studies provide only a limited understanding of species richness within a group. Their usefulness for assessing species diversity could also be limited as many lack sufficient sampling and/or fail to integrate different data types for assessing species boundaries. To explore the challenges and limitations of estimating species richness in lichens, we employed an integrative taxonomic approach to elucidate diversification patterns of the genus Sticta(Peltigeraceae) in Puerto Rico. Specimens were collected throughout the island, and a six‐locus dataset was generated to infer phylogenetic relationships among Puerto Rican Stictaand their continental counterparts. Phylogenetic analysis was combined with species delimitation methods and analysis of morpho‐anatomical characters to assess diversity patterns and clarify species‐level taxonomy. We found that Stictais represented by 16 species in Puerto Rico and that at least 11 (69%) of them are potentially endemic to the island. We describe eight of these in this work: S. borinquensissp. nov., S. corymbosasp. nov., S. densiphyllidiatasp. nov., S. guilartensissp. nov., S. harrisiisp. nov., S. parvilobatasp. nov., S. ripariasp. nov., and S. tainorumsp. nov. These species do not cluster in a monophyletic assemblage but are scattered over the broader Stictaphylogeny, indicating at least eight separate dispersal events. Putative endemic species were found to have close allies occurring in South America. Careful re‐examination of material revealed phenotypical characters that separate most species, suggesting low levels of cryptic diversity. We highlight that integrating molecular methods and other sources of information in species discovery along with comprehensive sampling efforts can greatly enhance our knowledge about diversity patterns in poorly studied groups and regions. Furthermore, species and ecosystems in the Caribbean are being threatened by substantial human‐driven changes (e.g., deforestation, climate change). Consequences of these impacts include reduction in already restricted habitats and potential extinction. We argue that studies analyzing species diversity within a phylogenetic framework could better inform conservation efforts aimed at addressing these challenges.

ABSTRACTOcellularia(Graphidaceae) is a genus of crustose lichens comprising c.200 species, four known from Australia and New Zealand. Based on recent collections from northern North Island, we describe a fifth species Ocellularia jacinda-arderniae, which is a member of the O. bicuspidatacomplex. This complex is characterised by peculiar, appendiculate ascospores and a psoromic acid chemistry. Two further undescribed species of this complex, one from North Island and one from South Island, are discussed but left undescribed pending further study. Based on our findings, we provide a revised assessment of New Zealand Ocellularia. Of the four species included in the most recent Flora of New Zealand Lichens from 2007, three do not belong in that genus and the identification of the fourth is incorrect; instead, the following four taxa are recognised: O. jacinda-arderniae, O.aff. dolichotata, O.aff. bicuspidata(a) (South Island; OTA 58820) and O.aff. bicuspidata(b) (North Island; UNITEC 10818). This leads to the somewhat unusual situation that a presumably known genus biota in New Zealand is entirely replaced by names of a new species and three provisional identifications. The following new combination is introduced: Schizotrema concentricum(Stirt.) Lücking comb. nov. In addition, the name Thelotrema manosporum(C. Knight.) Hellb. is given as the correct name for the New Zealand taxon previously identified as T. monosporumNyl., and the name T. monosporoidesNyl. [syn.: O. monosporoides(Nyl.) Hale] is established as a taxonomic synonym of T. manosporum, leaving two New Zealand species of Thelotremawith large, brown ascospores, namely T. manosporumand T. saxatileC. Knight. The situation of the genus Ocellulariahighlights the need for detailed taxonomic revision of understudied lichen groups in New Zealand, especially as these and related genera in the Graphidaceae are excellent indicators of forest health and can be used for monitoring purposes.

Seven proposals to modify the provisions of the International Code of Nomenclature for algae, fungi, and plants(ICN) at the 11thInternational Mycological Congress (IMC11) in July 2018 had been received by the proscribed date of 1 March 2018. These proposals are formally presented together here. The topics addressed relate to the clarification of the meaning of “original material” in relation to the typification of sanctioned names, the indication of the nomenclatural status of sanctioned names in author citations, the use of DNA sequences as nomenclatural types, and the possibility of including repository identifiers as an alternative to author citations. A synopsis of the proposals will be provided during April, and the mycological community will be invited to provide a guiding vote up to 10 June 2018. Final decisions on these proposals are to be made following debate at the Fungal Nomenclature Session of IMC11.

We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167–175, 2018) and Thines et al.(IMA Fungus9: 177–183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code(Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code.We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with ‘false negatives” surpassing “false positives”; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Codethat would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatusstatus of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as “nom. seq.” (nomen sequentiae).Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungifollowing evaluation based on strict quality control of the underlying studies based on established rules or recommendations.

There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungicould help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Codenever aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample (’bag’ type), (2) the DNA extract, (3) fluorescent in situhybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Codeand the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types. or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, ‘hijacking’ species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.

Lineages with broad, intercontinental distributions can provide insight into factors that influence diversity across both temporal and geographic scales. Lichens are well known for distinct biogeographic distribution patterns, including a high number of lineages with intercontinental distributions. The lichen-forming fungal genus Oropogon, from one of the largest families of lichen-forming ascomycetes, Parmeliaceae, occurs in both Asia and the Neotropics. How this genus obtained this disjunct distribution is not currently known. To better understand factors shaping diversity in Oropogon, we (i) estimated the timing of diversification of major clades within this genus; (ii) inferred the historical biogeography of Oropogon; and (iii) identified factors that potentially affected the distribution and evolution of this genus. Our results suggest that the genus originally radiated during the early Miocene, with subsequent diversification events occurring during the middle Miocene. Ancestral area reconstructions for Oropogonsuggest that the genus was either widespread with subsequent separate diversification in Asia and America or originated in the New World (America), with subsequent migration to Asia. We hypothesize that the Mi-1 glaciation impacted diversification of Oropogonspecies in Asia, and that the rise of major mountain ranges, such as the Himalayas, helped promote diversification in Oropogonin the Old World.

Although lichens develop their highest biomass in cool-temperate climates, lichen fungi may form highly diverse assemblages in tropical lowland rain forests. The reasons for such high species richness are not well known. The present study tested the hypothesis that lichen diversity in the northern Atlantic rain forest mainly depends on habitat diversity and conservation status of forest fragments. To this end, the known lichen biota of 23 forest remnants in the region was analyzed. We identified 784 species, with 11 taxa newly reported from Brazil and 44 from Bahia. The vast majority (711) are principally corticolous, while 53 are saxicolous and 20 terricolous. The most frequent species in terms of site occurrence were found at 13 sites, whereas over half of the taxa (462) were only found at a single site. This coincides with an overall low average sampling score, with only six sites being moderately well to well sampled. The number of species per site varied between 5 and 371. Multiple linear regression of species richness with the parameters, site extension, habitat diversity, sampling effort, conservation status, and elevation, was strong and highly significant, with site extension, habitat diversity, and sampling effort being the best predictors for species richness. Site ordination based on species composition suggested a correlation with conservation status and species richness, as well as site extension and habitat diversity. There was no overall correlation between species composition and geographical location of sites along a north–south gradient, but an underlying pattern was detected, suggesting some species turnover along a macroecological gradient. A predictive model using a combined score from the five parameters resulted in a strong and highly significant linear correlation with observed species richness. Using a quantitative, site-based method, we predicted a minimum of 44 and a maximum of 583 species per studied site and we estimated the overall richness for the northern Atlantic rain forest to be 1017 species. Traditional estimators (Chao 1, Chao 2, Jackknife 1, Jackknife 2, Bootstrap) resulted in predicted values ranging between 971 and 1527 species overall. The results of the study are relevant for conservation priorities, as they show that well-conserved areas with a higher habitat diversity (e.g., including transitional forest types and open areas) are an important component preserving the original diversity of the Atlantic Rain Forest, accounting for a large part of the extant biodiversity of this biome.

We present a taxonomic revision of the lichenized basidiomycete genus Acantholichen, species of which produce a characteristic blue-gray, microsquamulose thallus with spiny apical hyphal cells known as acanthohyphidia. Since its discovery, the genus was thought to be monospecific, only including the generic type, A. pannarioides. However, a detailed morphological and anatomical study of recently collected specimens from the Galápagos, Costa Rica, Brazil and Colombia, combined with a molecular phylogenetic analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and 28S of the nuc rDNA and RPB2 sequences, revealed a much more diverse and widespread species assemblage. Based on the results of these analyses, we describe five new species in the genus: A. albomarginatus, A. campestris, A. galapagoensis, A. sorediatusand A. variabilis. We also provide an identification key to all species, anatomical and morphological descriptions, photographs and a table comparing main characters of each species.

Based on new collections of Graphidaceae originating from Horton Plains National Park in Sri Lanka, six new species are described: Chapsa thambapanni Weerakoon, Jayalal & Lücking, differing from C. laemensis in the larger ascomata and ascospores produced in numbers of 2–4 per ascus; Fissurina lumbschiana Weerakoon, Jayalal & Lücking, differing from F. consentanea in the larger, comparatively short, gaping ascomata; F. tuberculifera Weerakoon, Jayalal & Lücking, differing from F. insidiosa in the tuberculate thallus and the larger, more emergent ascomata with tuberculate margins, as well as the amyloid ascospores and psoromic acid chemistry; Graphis mahaeliyensis Weerakoon, Jayalal & Lücking, differing from G. subintermedians in the single-spored asci with larger ascospores; Thelotrema heladiwense Weerakoon, Jayalal & Lücking, differing from T. weberi and T. subweberi in the transversely septate ascospores and presence of a unique, unknown secondary compound; and Topeliopsis subtuberculifera Weerakoon, Jayalal & Lücking, differing from T. tuberculifera in the large, basally constricted thallus verrucae, the substipitate ascomata with bumpy margins and wider pore, and the narrower ascospores. The rather unique lichen biota encountered in the Horton Plains National Park, as exemplified by these new taxa, underlines the recognition of this area as one of the world heritage sites in Sri Lanka. Nevertheless, further extensive field work is necessary to document the overall lichen biota in the park.

While the phylogenetic position of Trypetheliaceae has been the subject of recent molecular studies, the relationships within this family have been little studied. Here we construct a detailed genus-level phylogeny of the family. We confirm previous morphology-based findings suggesting that a substantial proportion of genera are not monophyletic, and that an overemphasis has been placed on certain character state combinations which do not strictly reflect phylogenetic relationships. Specifically, patterns of ascospore septation, ostiole orientation and type of ascomatal aggregation are evolutionarily labile, and of limited utility for the delimitation of genera as currently circumscribed. We show that species from a number of genera including Astrothelium, Bathelium, Cryptothelium, Laureraand Trypetheliumtogether form a strongly supported group, referred to here as the “Astrothelium” clade. Species from Aptrootia, Architrypethelium, Campylothelium, Marcelaria(L. purpurina and L. cumingii groups), Pseudopyrenulaand species from the Trypethelium eluteriaegroup fall outside of the “Astrothelium” clade and each form monophyletic groups. In contrast, species from Arthopyrenia, Mycomicrotheliaand Polymeridiumfall outside of the “Astrothelium” clade, and do not form monophyletic groups. The data presented here validate earlier morphology-based findings suggesting generic delimitations are in need of revision, and provides a first step towards identifying the utility of individual characters and identifying which characters and character state combinations may be useful for future classification.

As a first step towards the production of a List of Protected Generic Names for Fungi, a without-prejudice list is presented here as a basis for future discussion and the production of a List for formal adoption. We include 6995 generic names out of the 17072 validly published names proposed for fungi and invite comments from all interested mycologists by 31 March 2014. The selection of names for inclusion takes note of recent major publications on different groups of fungi, and further the decisions reached so far by international working groups concerned with particular families or genera. Changes will be sought in the Codeto provide for this and lists at other ranks to be protected against any competing unlisted names, and to permit the inclusion of names of lichen-forming fungi. A revised draft will be made available for further discussion at the 10thInternational Mycological Congress in Bangkok in August 2014. A schedule is suggested for the steps needed to produce a list for adoption by the International Botanical Congress in August 2017. This initiative provides mycologists with an opportunity to place nomenclature at the generic level on a more secure and stable base.

AbstractSouth Korea is covered primarily by temperate vegetation; therefore, foliicolous lichens may not be expected to play an important role in its lichen flora. However, this study describes four foliicolous lichen species, Strigula concreta, S. macrocarpa, S. melanobapha, and S. subelegans, which are new to South Korea. These findings will lead to further research on foliicolous lichens and provide a better understanding of their distribution within the East Asian region. This is the first detailed report on foliicolous lichens and their distribution in South Korea.

In this paper, an extended molecular phylogeny was generated for the Ocellulariaclade, which includes about half of the species that were previously separated in the family Thelotremataceae. Three genes (mtSSU, nuLSU, RPB2), from a total of 270 OTUs with 136 ingroup species, were sequenced to evaluate whether the core genera, Ocellulariaand Myriotrema, form monophyletic clades or split into several lineages. Further, we tested the usefulness of phenotypic characters for circumscrib ing monophyletic groups. Besides a maximum likelihood analysis, we incorporated the novel method of morphology-based 'phylogenetic binning', which allowed us to weight the morphological characters in those taxa with molecular data available and then predict the phylogenetic classification for over 200 additional species for which no molecular data are currently available. Our results showed that the large genera Myriotrema, Ocellularia, and Stegobolusare polyphyletic. For some of the previously unrecognized lineages, older generic names are available (Rhabdodiscus, Ocellis, Stigmagora, Antrocarpum, Macropyrenium). Some previously separated genera, such as Ampliotremaand Gyrotrema, were found to be nested within a large clade currently recognized as Ocellularias.l. For this clade, no meaningful generic subdivision could be established based on the available data, and we proposed to recognize distinct subclades at the subgenus level. One new genus, Compositrema, was also discovered, and a second new genus, Glaucotrema, is established for the Myriotrema glaucophaenumgroup. Further, the genus Rhabdodiscusis reinstated formally. We found a high level of homoplasy (parallel evolution) of phenotype characters previously used for classification purposes, such as excipular carbonization, columella morphology, and ascospore size, septation, and pigmentation. Secondary chemistry, on the other hand, was remarkably uniform in most clades. Some clades also exhibit a high level of disparity of ascoma morphology. Thus, the very distinctive Gyrotrema-type apothecia occur in a clade nested within and genetically very similar to Ocellularias.str.

Three new crustose lichen species are described from Sri Lanka. Chapsa pulchellaWijeyaratne, Lücking & Lumbsch is unique due to its bright red apothecial margin contrasting with the white-pruinose disc. Pyrenula ocellulataWijeyaratne, Lücking & Lumbsch resembles Pyrenula interductaand P. mastophoroidesin having an inspersed hymenium and medium-sized ascospores, but differs in its shiny, hemispherical perithecia with sharply delimited thalline cover. Thelotrema minisporumWijeyaratne, Lücking & Lumbsch is identical with Thelotrema lepadinumin morphology but its ascospores are much smaller and the thallus contains stictic acid.

Despite their potential shortcomings for phylogenetic inference, sometimes only morphological data are available for systematic classification. Computational methods are used to determine morphological site patterns congruent with the molecular tree in order to improve the accuracy of the classification of taxa for which only morphological data exist. Here, we used molecular site weight calibration as implemented in RAxML to weight morphological characters based on their distribution on a maximum likelihood tree inferred from molecular data. We subsequently conducted morphology-based 'phylogenetic binning' (= assignment of morphologically defined taxa that lack molecular data to branches of the molecular reference tree) based on the morphology of the taxa included in the tree. We applied this methodology to the lichen genus Graphiss.l. (Ascomycota: Ostropales: Graphidaceae), which was recently shown to represent two separate, distantly related lineages, Graphiss.str. and Allographa. Of 313 species of Graphisand Allographaincluded in the study, 16 were represented by molecular sequence data and morphology, and 297 by morphology only. Using maximum likelihood and maximum parsimony site weight calibration and morphology-based phylogenetic binning, 281–290 of the 297 species represented by morphological data only could be assigned to either Graphisor Allographawith strong support (90%–100%). Two species, G. saxisedaand G. evirescens, were found to represent species of the unrelated genus Carbacanthographis. Our results showed that assignment of taxa to clades based on morphological data only substantially improved with molecular site weight calibration. Both molecular site weight calibration and branch assignment to the molecular reference tree are implemented in the RAxML v.7.2.6 Windows executable and the RAxML v.7.2.8 open-source code.

Molecular phylogenetic analysis of the mitochondrial small subunit and nuclear large subunit ribosomal DNA revealed that the lichen genus Graphissensu Staiger represents two separate lineages. Graphiss.str. comprises the species of the G. scriptaand G. subserpentinagroups (‘Eugraphis’), as well as the G. striatulagroup sensu Lücking. For the segregate genus, the name AllographaChevall. is available, and this genus includes the G. acharii, G. dussii, G. marginata, G. nuda, and G. symplectagroups. The separation of both lineages is supported by principal component analysis species ordination based on phenotype characters, although the G. dussiiand G. subserpentinagroups appear phenotypically intermediate. Species formerly placed in Hemitheciumsubg. Hemitheciumsensu Staiger were shown to belong to at least four lineages, one nested within Graphis(H. implicatum), one within Allographa(H. chlorocarpum), one sister to Allographa(H. rufopallidum), and one nested within the Phaeographisclade (H. plicosum). Allographa is genetically close to the bulk of lirellate Graphidaceae (Diorygma, Glyphis, Pallidogramme, Phaeographis, Platygramme, Platythecium, Sarcographa, Thalloloma, Thecaria), whereas Graphiss.str. exhibits unique genetic apomorphies and takes a more isolated position.

Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.

The fungal order Ostropales is unique in Ascomycota for including both lichen-forming and non-lichenized species and species with optional nutritional strategies depending on substrate. To address the phylogenetic relationships within the order, we assembled a dataset of 78 ostropalean species, including all major clades and 23 taxa that are only optionally lichenized or non-lichenized. The analyses are based on sequences of the mtSSU and nuLSU rDNA and the protein-coding gene RPB2. A close relationship of Graphidaceae and Gomphillaceae is suggested with the latter possibly nested within Graphidaceae. Odontotremataceae is composed of two distantly related groups. Coenogoniaceae and Porinaceae are sister taxa, and their relation to Gyalectaceae is unresolved. Gyalecta is paraphyletic with Belonia and Pachyphiale nested within. A polyphyletic Belonia indicates that perithecioid ascomata evolved more than once in Gyalectaceae. The new family Sagiolechiaceae is proposed to accommodate Rhexophiale and Sagiolechia and Solorinellaceae is reinstated distinct from Gomphillaceae. Belonia and Pachyphiale are reduced to synonymy with Gyalecta. The distribution of phenotypical character states is discussed with selected character states mapped onto a phylogenetic tree. A special focus is given on lifestyles. Our phylogeny suggests that there is more plasticity in the evolution of life-styles in these fungi than was previously assumed.

As part of an ongoing comprehensive inventory of the Galapagos lichen flora, all species in the Graphidaceae from the archipelago have been revised using both historic and recent collections. A total of forty-two species is reported here, of which thirty-four were previously unknown from the archipelago and two are described as new to science: Graphis pedunculata, and Phaeographis striata. The new combinations Carbacanthographis saxiseda, Carbacanthographis saxorumand Phaeographis majorare made. Four previously reported species are based on misidentifications and thus removed from the checklist. Detailed descriptions are presented that include diagnostic characteristics to distinguish similar species. An identification key to all Galapagos Graphidaceae is provided and a preliminary assessment discusses known distribution and ecology for each of the species. Principal components analysis was used to assess ecology for thirty-nine species.

Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher fungi, Ascomycota and Basidiomycota, at between 390 million y and up to 1.5 billion y ago. Assuming that these inconsistencies stem from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500–650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.

Family concepts in lichen-forming fungi are poorly understood and were traditionally based on easily observable characters. An example is the family Thelotremataceae, a species-rich group of crustose, predominantly tropical lichens with over 1,000 described species. Its distinction from Graphidaceae is largely based on ascoma shape (round vs. lirelliform). Previous studies already indicated that the distinction of these families is doubtful. However, these studies only included a few taxa of Thelotremataceae. Hence we obtained 96 new partial sequences of nuclear and mitochondrial ribosomal DNA, mostly of Thelotremataceae. We performed maximum parsimony and Bayesian phylogenetic analyses of a combined dataset of 105 samples, representing 97 species. Our results indicate that Graphidaceae and Thelotremataceae cannot be separated, but form several lineages within one strongly supported monophyletic lineage. Monophyly of Graphidaceae and Thelotremataceae each in their present circumscription was rejected significantly using two independent alternative topology tests. Consequently, Thelotremataceae is reduced to synonymy with Graphidaceae. Further, numerous genera in Graphidaceae and Thelotremataceae were found to be para- or polyphyletic, including all genera currently placed in Thelotremataceae, with the sole exception of Diploschistes. In Graphidaceae, Graphisand Sarcographaare polyphyletic as currently circumscribed. However, since the topology within Graphidaceae s.l. largely lacks support and given the large number of species not yet studied, a thorough evaluation of the generic concept requires a larger dataset, including additional genes and taxa.

The recent uptake of the name SclerophytonomycesCif. & Tomas. sets a precedent for the potential use of 215 alternative generic names established by Ciferri and Tomaselli for lichen-forming fungi. It is generally believed that the intention of these authors was an alternative nomenclature for lichenized mycobionts, assuming that lichen names covered the entire symbiosis and were thus nomenclaturally incorrect. However, being aware of Art. 76 in the Stockholm Code(“… names given to lichens shall be considered as applying to their fungal components”; Art. 13 in subsequent Codes), the original idea of Ciferri and Tomaselli was not to replace these names, but to introduce a dual nomenclature that permitted separate naming of isolated fungal cultures, which appeared very different from the corresponding lichen mycobionts. Since Art. 76 did not allow such a dual nomenclature, the authors presented Proposal 46 to amend the Code, but at the same time published their new names separately. The names are conceptually illegitimate, but according to Art. 52.1, legitimacy is formally tied to the identity of the type specimens as governed by Art. 10.1. No type specimens were cited, yet the names are validly published since types were not required for valid publication of names prior to 1958. This has led to inconsistent interpretations of their use, and at least five generic names threaten more recently introduced generic names (Adelolecia, Allocetraria, Caleniopsis, Parmelina, Poeltinula), with about 100 species, many of which are widely distributed and well-known. About 75 of the 215 generic names were thought to be potentially available for use, because their presumed types are not types of previously published names of lichen genera. However, the species names cited as types of the 203 generic names published in the original paper lacked Latin diagnoses and so have no status under the Code, so the generic names are automatically typified under Art. 10.2 and 10.3 based on their diagnoses, which by use of the phrase “Ut in …” make direct reference to previously established generic names, and are thus formally illegitimate. Only three generic names are available for use because they are based on species with validly published names that are not the types of names of previously established genera of lichenized fungi: Coenomycogonium(based on Coenogonium interpositum), Dictyonematomyces(based on Dictyonema sericeum), and Mycocoenogonium(based on Coenogonium curvulum). However, these names are younger taxonomic synonyms of Coenogoniumand Dictyonema, respectively.

Frisch, A., K. Kalb & M. Grube: Contributions towards a new systematics of the lichen family Thelotremataceae. Bibliotheca Lichenologica 92, 556 pp., soft cover, 2006. J. Cramer in der Gebrüder Borntraeger Verlagsbuchhandlung, Berlin, Stuttgart. ISBN: 3-443-58071-8; Bednarek-Ochyra, H.: A taxonomic monograph of the moss genus Codriophorus P. Beauv. (Grimmiaceae). 2006, 273 pp. W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland. ISBN 83-89648-40-7.

The phylogeny and systematic position of Gomphillaceae was reconstructed using a combined Bayesian analysis of nuclear LSU rDNA and mitochondrial SSU rDNA sequences. Twenty-four partial sequences of 12 taxa (11 Gomphillaceae and one Asterothyriaceae) plus two new sequences of Stictis radiata(Ostropales outgroup) were generated and aligned with the corresponding sequences retrieved from GenBank, resulting in an alignment of 82 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. Our results confirm Gomphillaceae sensu Vezda and Poelt plus Asterothyriaceae to be a monophyletic group, with an unresolved relationship between the two families. Placement of Gomphillaceae and Asterothyriaceae within Ostropales sensu Kauff and Lutzoni, as sister of Thelotremataceae, also is strongly supported. Alternative hypotheses placing Gomphillaceae in Lecanorales (Cladoniaceae), Agyriales (Baeomycetaceae) or within bitunicate Ascomycota (Arthoniomycetes, Chaetothyriomycetes, Dothideomycetes) were rejected with our dataset. After recent synonymization of Dimerellawith Coenogonium(Ostropales: Coenogoniaceae), we propose the new combination Coenogonium pineti(one of our Ostropales outgroup taxa in this analysis).