Showing papers in "Fungal Diversity in 2017"

Notes for genera: Ascomycota

Abstract: Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).

Fungal diversity notes 603–708: taxonomic and phylogenetic notes on genera and species

Abstract: This is the sixth in a series of papers where we bring collaborating mycologists together to produce a set of notes of several taxa of fungi. In this study we introduce a new family Fuscostagonosporaceae in Dothideomycetes. We also introduce the new ascomycete genera Acericola, Castellaniomyces, Dictyosporina and Longitudinalis and new species Acericola italica, Alternariaster trigonosporus, Amarenomyces dactylidis, Angustimassarina coryli, Astrocystis bambusicola, Castellaniomyces rosae, Chaetothyrina artocarpi, Chlamydotubeufia krabiensis, Colletotrichum lauri, Collodiscula chiangraiensis, Curvularia palmicola, Cytospora mali-sylvestris, Dictyocheirospora cheirospora, Dictyosporina ferruginea, Dothiora coronillae, Dothiora spartii, Dyfrolomyces phetchaburiensis, Epicoccum cedri, Epicoccum pruni, Fasciatispora calami, Fuscostagonospora cytisi, Grandibotrys hyalinus, Hermatomyces nabanheensis, Hongkongmyces thailandica, Hysterium rhizophorae, Jahnula guttulaspora, Kirschsteiniothelia rostrata, Koorchalomella salmonispora, Longitudinalis nabanheensis, Lophium zalerioides, Magnibotryascoma mali, Meliola clerodendri-infortunati, Microthyrium chinense, Neodidymelliopsis moricola, Neophaeocryptopus spartii, Nigrograna thymi, Ophiocordyceps cossidarum, Ophiocordyceps issidarum, Ophiosimulans plantaginis, Otidea pruinosa, Otidea stipitata, Paucispora kunmingense, Phaeoisaria microspora, Pleurothecium floriforme, Poaceascoma halophila, Periconia aquatica, Periconia submersa, Phaeosphaeria acaciae, Phaeopoacea muriformis, Pseudopithomyces kunmingnensis, Ramgea ozimecii, Sardiniella celtidis, Seimatosporium italicum, Setoseptoria scirpi, Torula gaodangensis and Vamsapriya breviconidiophora. We also provide an amended account of Rhytidhysteron to include apothecial ascomata and a J+ hymenium. The type species of Ascotrichella hawksworthii (Xylariales genera incertae sedis), Biciliopsis leptogiicola (Sordariomycetes genera incertae sedis), Brooksia tropicalis (Micropeltidaceae), Bryochiton monascus (Teratosphaeriaceae), Bryomyces scapaniae (Pseudoperisporiaceae), Buelliella minimula (Dothideomycetes genera incertae sedis), Carinispora nypae (Pseudoastrosphaeriellaceae), Cocciscia hammeri (Verrucariaceae), Endoxylina astroidea (Diatrypaceae), Exserohilum turcicum (Pleosporaceae), Immotthia hypoxylon (Roussoellaceae), Licopolia franciscana (Vizellaceae), Murispora rubicunda (Amniculicolaceae) and Doratospora guianensis (synonymized under Rizalia guianensis, Trichosphaeriaceae) were re-examined and descriptions, illustrations and discussion on their familial placement are given based on phylogeny and morphological data. New host records or new country reports are provided for Chlamydotubeufia huaikangplaensis, Colletotrichum fioriniae, Diaporthe subclavata, Diatrypella vulgaris, Immersidiscosia eucalypti, Leptoxyphium glochidion, Stemphylium vesicarium, Tetraploa yakushimensis and Xepicula leucotricha. Diaporthe baccae is synonymized under Diaporthe rhusicola. A reference specimen is provided for Periconia minutissima. Updated phylogenetic trees are provided for most families and genera. We introduce the new basidiomycete species Agaricus purpurlesquameus, Agaricus rufusfibrillosus, Lactifluus holophyllus, Lactifluus luteolamellatus, Lactifluus pseudohygrophoroides, Russula benwooii, Russula hypofragilis, Russula obscurozelleri, Russula parapallens, Russula phoenicea, Russula pseudopelargonia, Russula pseudotsugarum, Russula rhodocephala, Russula salishensis, Steccherinum amapaense, Tephrocybella constrictospora, Tyromyces amazonicus and Tyromyces angulatus and provide updated trees to the genera. We also introduce Mortierella formicae in Mortierellales, Mucoromycota and provide an updated phylogenetic tree.

An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence

Abstract: The previous phylogenies of Sordariomycetes by M.E. Barr, O.E. Eriksson and D.L. Hawksworth, and T. Lumbsch and S. Huhndorf, were mainly based on morphology and thus were somewhat subjective. Later outlines by T. Lumbsch and S. Huhndorf, and Maharachchikumbura and co-authors, took into account phylogenetic evidence. However, even these phylogenetic driven arrangements for Sordariomycetes, were somewhat subjective, as the arrangements in trees depended on many variables, such as number of taxa, different gene regions and methods used in the analyses. What is needed is extra evidence to help standardize ranking in the fungi. Estimation of divergence times using molecular clock methods has been proposed for providing additional rational for higher ranking of taxa. Thus, in Sordariomycetes, a divergence period (i.e. 200–300 MYA) can be used as criteria to judge when a group of related taxa evolved and what rank they should be given. In this paper, we provide an updated classification of accepted subclasses, orders of Sordariomycetes and use divergence times to provide additional evidence to stabilize ranking of taxa in the class. We point out and discuss discrepancies where the phylogenetic tree conflicts with the molecular clock.

Ranking higher taxa using divergence times: a case study in Dothideomycetes

Abstract: The current classification system for the recognition of taxonomic ranks among fungi, especially at high-ranking level, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split; and Pleosporales, the largest order of Dothideomycetes with 55 families, to establish family divergence times. We have assembled a multi-gene data set (LSU, SSU, TEF1 and RPB2) from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes lineages. Two separated datasets were analysed: (i) 272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis, and (ii) 191 taxa representing 55 families of Pleosporales were included for the family level analysis. Our results indicate that divergence times (crown age) for most orders (20 out of 32, or 63%) are between 100 and 220 Mya, while divergence times for most families (39 out of 55, or 71%) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this added approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi. In this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders, namely Bezerromycetales and Wiesneriomycetales and these are treated as synonyms of Tubeufiales while Asterotexiales is treated as a synonym of Asterinales. In addition, we provide an updated phylogenetic assessment of Dothideomycetes previously published as the Families of Dothideomycetes in 2013 with a further ten orders and 35 families.

A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective

Abstract: In this paper, we provide a phylogenetic overview of Basidiomycota and related phyla in relation to ten years of DNA based phylogenetic studies since the AFTOL publications in 2007 We selected 529 species to address phylogenetic relationships of higher-level taxa using a maximum-likelihood framework and sequence data from six genes traditionally used in fungal molecular systematics (nrLSU, nrSSU, 58S, tef1-α, rpb1 and rpb2) These species represent 18 classes, 62 orders, 183 families, and 392 genera from the phyla Basidiomycota (including the newly recognized subphylum Wallemiomycotina) and Entorrhizomycota, and 13 species representing 13 classes of Ascomycota as outgroup taxa We also conducted a molecular dating analysis based on these six genes for 116 species representing 17 classes and 54 orders of Basidiomycota and Entorrhizomycota Finally we performed a phyloproteomics analysis from 109 Basidiomycota species and 6 outgroup taxa using amino-acid sequences retrieved from 396 orthologous genes Recognition of higher taxa follows the criteria in Zhao et al (Fungal Divers 78:239–292, 2016): (i) taxa must be monophyletic and statistically well-supported in molecular dating analyses, (ii) their respective stem ages should be roughly equivalent, and (iii) stem ages of higher taxa must be older than those of lower level taxa The time-tree indicates that the mean of stem ages of Basidiomycota and Entorrhizomycota are ca 530 Ma; subphyla of Basidiomycota are 406–490 Ma; most classes are 358–393 Ma for those of Agaricomycotina and 245–356 Ma for those of Pucciniomycotina and Ustilaginomycotina; most orders of those subphyla split 120–290 Ma Monophyly of most higher-level taxa of Basidiomycota are generally supported, especially those taxa introduced in the recent ten years: phylum Entorrhizomycota, classes Malasseziomycetes, Moniliellomycetes, Spiculogloeomycetes, Tritirachiomycetes and orders Amylocorticiales, Golubeviales, Holtermanniales, Jaapiales, Lepidostromatales, Robbauerales, Stereopsidales and Trichosporonales However, the younger divergence times of Leucosporidiales (Microbotryomycetes) indicate that its order status is not supported, thus we propose combining it under Microbotryales On the other hand, the families Buckleyzymaceae and Sakaguchiaceae (Cystobasidiomycetes) are raised to Buckleyzymales and Sakaguchiales due to their older divergence times Cystofilobasidiales (Tremellomycetes) has an older divergence time and should be amended to a higher rank We however, do not introduce it as new class here for Cystofilobasidiales, as DNA sequences from these taxa are not from their respective types and thus await further studies Divergence times for Exobasidiomycetes, Cantharellales, Gomphales and Hysterangiales were obtained based on limited species sequences in molecular dating study More comprehensive phylogenetic studies on those four taxa are needed in the future because our ML analysis based on wider sampling, shows they are not monophyletic groups In general, the six-gene phylogenies are in agreement with the phyloproteomics tree except for the placements of Wallemiomycotina, orders Amylocorticiales, Auriculariales, Cantharellales, Geastrales, Sebacinales and Trechisporales from Agaricomycetes These conflicting placements in the six-gene phylogeny vs the phyloproteomics tree are discussed This leads to future perspectives for assessing gene orthology and problems in deciphering taxon ranks using divergence times

Microfungi on Tectona grandis (teak) in Northern Thailand

Abstract: To date there is virtually no information available concerning the fungi associated with Tectona grandis (teak) (Lamiaceae) in Thailand. In this study, samples of microfungi were collected from both asymptomatic stems and dead wood, and symptomatic branches, stem and leaves of T. grandis from 27 sites in six provinces (Chiang Mai, Chiang Rai, Phayao, Phitsanulok, Phrae and Uttaradit Provinces). Morphology and combined multi-gene phylogeny (CAL, GAPDH, ITS, LSU, RPB2, SSU, TEF1 and TUB) were used to identify taxa. A total of 270 collections, representing 28 fungal species residing in 12 families, 7 orders and 21 genera, with three species of uncertain taxonomic placement were identified. Of these, one family, three genera and 14 species are new to science. The new family, Pseudocoleodictyosporaceae is introduced based on its distinct lineage in the Dothideomycetes and its unique morphology as compared to Roussoellaceae and Torulaceae. The new genera are Neooccultibambusa, Pseudocoleodictyospora and Subglobosporium. The newly described species are Diaporthe neoraonikayaporum, D. tectonendophytica, D. tectonae, D. tectonigena, Hermatomyces tectonae, H. thailandica, Manoharachariella tectonae, Neooccultibambusa chiangraiensis, Pseudocoleodictyospora sukhothaiensis, Ps. tectonae, Ps. thailandica, Rhytidhysteron tectonae, Subglobosporium tectonae and Tubeufia tectonae. Fourteen species are known published taxa including Alternaria tillandsiae, Berkleasmium talaumae, Boerlagiomyces macrospora, Ceratocladium purpureogriseum, Fusarium solani, Helicoma siamense, Lasiodiplodia theobromae, Macrovalsaria megalospora, Paradictyoarthrinium diffractum, Phaeoacremonium italicum, Sphaeropsis eucalypticola, Stachybotrys levispora, St. renispora and Thaxteriellopsis lignicola. Epitypifications or reference specimens are designated for Boerlagiomyces macrospora and Macrovalsaria megalospora. Macrovalsaria megalospora is transferred from Botryosphaeriaceae to Dothideomycetes genus, incertae sedis based on taxonomy and phylogenetic analysis, which indicate it is distinct from Botryosphaeriaceae. All fungal species represent first reports on T. grandis in Thailand. New taxa and taxa incertae sedis, as well as known taxa which are established as reference specimens or epitypes, are presented with phylogenetic tree analyses, habitat, known distribution, material examined, full descriptions, notes and figures. Information is also provided for known taxa to add to the body of knowledge and to assist those wishing to study fungi occurring on T. grandis in future.

Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi

Abstract: Although classification at supra-specific ranks is inherently arbitrary, comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Different circumscriptions of the hyper-diverse lichen-forming fungal family Parmeliaceae and widely different generic circumscriptions among authors have been proposed. For this study, we use a recently developed temporal approach that uses time-calibrated chronograms to identify temporal bands for specific ranks in Parmeliaceae and allied groups with the overarching goal of establishing a consistent, stable classification. A data set of 330 species, representing 73 genera in the family and 52 species of related families was used to address the circumscription of Parmeliaceae and its genera following the proposed temporal approach. Based on the results of this study, we propose a revised, temporal-based classification for Parmeliaceae, including all clades that share a common ancestor 102.13–112.88 Ma for families and a time window of 29.45–32.55 Ma for genera. Forty-five of the currently accepted genera in Parmeliaceae were supported in their current circumscription. Two subfamilies are accepted within Parmeliaceae: Protoparmelioideae Divakar et al. subfam. nov., including Protoparmelia and the resurrected genus Maronina, and Parmelioideae, including the bulk of genera in the family. The new genus Austromelanelixia Divakar et al. is proposed to accommodate a clade of southern Hemisphere species previously included in Melanelixia. Eumitria and tentatively Dolichousnea are resurrected as genera separate from Usnea. The following genera are reduced to synonymy: Allocetraria, Cetrariella, Usnocetraria, and Vulpicida with Cetraria; Arctocetraria, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Tuckermanella, and Tuckermannopsis with Nephromopsis; and the lichenicolous genera Nesolechia and Raesaenenia with the lichen-forming genera Punctelia and Protousnea, respectively. A total of 47 new combinations and three new names at the species level are proposed.

The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday

Abstract: The history of assigning ranks to fungi, as well as the relative importance of using divergence time estimates is reviewed. The paper pays tribute to the major mycological players, and especially to David Hawksworth on his 70th birthday and his contribution to fungal ranking in Systema Ascomycetum from 1982 to 1998. Following the conclusion of the latter series, the ranking continued with the Outlines of Ascomycota in 2007 and 2010 and more recently with specific classes in 'Towards an outline of Sordariomycetes' and 'Families of Dothideomycetes'. Earlier classifications based on phenotype were certainly more subjective; however, remarkably many of these old arrangements have stood the test of time. More recently, phylogenetic analyses have provided evidence towards a natural classification, resulting in significant changes in many lineages. The classification arrangements however, are still subjective and dependent on the taxa analysed, resulting in different taxonomic interpretations and schemes, particularly when it comes to ranking. Thus, what have been considered as genera by some, have been introduced as families by others. More recently, estimation of divergence times using molecular clock methods have been used as objective evidence for higher ranking of taxa. A divergence period (i.e. 200-300 MYA) can be used as a criterion to infer when a group of related taxa evolved and what rank they should be given. We compiled data on divergence times for various higher ranking taxa in the Kingdom Fungi. The kingdom evolved 1000-1600 MYA (Stenian-Calymmian), while the presently accepted phyla evolved between 358 and 541 MYA (Devonian-Cambrian). Divergence times for subphyla are generally between 358 and 485 MYA (Devonian-Ordovician), those of classes 145-358 MYA (Jurassic-Carboniferous), subclasses 66-358 MYA (Cretaceous-Carboniferous), orders 23-252 MYA (Paleogene-Triassic), families 2.8-145 MYA (Neogene-Cretaceous), and genera 2.8-66 MYA (Neogene-Paleogene). Thus, there are wide discrepancies in the times different taxa diverged. We provide an overview over Ascomycota, showing how application of temporal banding could affect the recognition of higher taxa at certain rank levels. We then use Sordariomycetes as an example where we use divergence times to provide additional evidence to stabilize ranking of taxa below class level. We propose a series of evolutionary periods that could be used as a guide to determine the various higher ranks of fungi: phyla[550 MYA, subphyla 400-550 MYA; classes 300-400 MYA; subclasses 250-300 MYA, orders 150-250 MYA, and families 50-150 MYA. It is proposed that classification schemes and ranking of taxa should, where possible, incorporate a polyphasic approach including phylogeny, phenotype, and estimate of divergence times.

Phylogenetic and chemotaxonomic resolution of the genus Annulohypoxylon (Xylariaceae) including four new species

Abstract: This study deals with an extensive evaluation focusing on phylogenetic and chemotaxonomic infrageneric relationships of the genus Annulohypoxylon (Xylariaceae, Ascomycota), whose species are ubiquitously associated with seed plants as endophytes and saprotrophs in all forested areas of the world. Using evidence from phylogenetic, chemotaxonomic and morphological data, various varieties within the genus are raised to species level, leading to the new combinations for A. areolatum (≡ A. bovei var. microsporum), A. macrosporum (≡ A. leptascum var. macrosporum), and A. microdiscum (≡ A. moriforme var. microdiscum). Annulohypoxylon substygium nom. nov. is applied for A. stygium var. annulatum and the four new tropical and subtropical species A. massivum, A. violaceopigmentum, A. viridistratum and A. yungensis are introduced. Furthermore, A. leucadendri is excluded from the genus as its morphological characters disagree with the generic concept, the recently erected A. palmicola is synonymized with A. leptascum and A. austrobahiense has been reassigned to the genus Hypoxylon. In addition, the key taxa A. annulatum and A. truncatum have been reinvestigated and epitypes have been defined. For the first time, a dichotomous key to the genus is provided. A phylogenetic β-tubulin tree in conjunction with stromatal HPLC profiles clearly shows that Annulohypoxylon comprises two distinct lineages. The A. cohaerens/multiforme group might eventually warrant segregation into a new genus as further molecular data become available.

Turbo-taxonomy to assemble a megadiverse lichen genus: seventy new species of Cora (Basidiomycota: Agaricales: Hygrophoraceae), honouring David Leslie Hawksworth’s seventieth birthday

Abstract: Following a large-scale phylogenetic study of the lichenized genus Cora (Basidiomycota: Agaricales: Hygrophoraceae), we formally describe 70 new species, honouring the seventieth birthday of David Leslie Hawksworth, one of the preeminent figures in mycology and lichenology in the past 50 years. Based on an updated phylogeny using the ITS fungal barcoding locus, we now recognize 189 taxa in a genus that until recently was considered to represent a single species; including this contribution, 92 of these are formally recognized, including five taxa based on historical names or collections that have not been sequenced. Species of Cora can be recognized by a combination of morphological (size, colour, lobe configuration, surface hairs, hymenophore size and shape), anatomical (thallus thickness, cortex structure, photobiont type, hyphal papillae), and ecogeographical features (substrate, habitat, distribution), and a keytable allowing the identification of all accepted taxa is provided. The new species are: Cora accipiter Moncada, Madrinan & Lucking spec. nov., C. applanata Moncada, Soto-Medina & Lucking spec. nov., C. arachnodavidea Moncada, Dal Forno & Lucking spec. nov., C. arborescens Dal Forno, Chaves & Lucking spec. nov., C. arcabucana Moncada, C. Rodriguez & Lucking spec. nov., C. aturucoa Lucking, Moncada & C. Vargas spec. nov., C. auriculeslia Moncada, Yanez-Ayabaca & Lucking spec. nov., C. barbifera Moncada, Patino & Lucking spec. nov., C. boleslia Lucking, E. Morales & Dal Forno spec. nov., C. caliginosa Holgado, Rivas Plata & Perlmutter spec. nov., C. campestris Dal Forno, Eliasaro & Spielmann spec. nov., C. canari Nugra, Dal Forno & Lucking spec. nov., C. caraana Lucking, Martins & Lucheta spec. nov., C. casasolana Moncada, R.-E. Perez & Lucking spec. nov., C. caucensis Moncada, M. Gut. & Lucking spec. nov., C. celestinoa Moncada, Cabrera-Amaya & Lucking spec. nov., C. comaltepeca Moncada, R.-E. Perez & Herrera-Camp. spec. nov., C. corani Lucking, E. Morales & Dal Forno spec. nov., C. corelleslia Moncada, A. Suarez-Corredor & Lucking spec. nov., C. crispoleslia Moncada, J. Molina & Lucking spec. nov., C. cuzcoensis Holgado, Rivas Plata & Perlmutter spec. nov., C. dalehana Moncada, Madrinan & Lucking spec. nov., C. davibogotana Lucking, Moncada & Coca spec. nov., C. davicrinita Moncada, Madrinan & Lucking spec. nov., C. davidia Moncada, L. Vargas & Lucking spec. nov., C. dewisanti Moncada, A. Suarez-Corredor & Lucking spec. nov., C. dulcis Moncada, R.-E. Perez & Lucking spec. nov., C. elephas Lucking, Moncada & L. Vargas spec. nov., C. fuscodavidiana Lucking, Moncada & L. Vargas spec. nov., C. garagoa Simijaca, Moncada & Lucking spec. nov., C. gigantea Lucking, Moncada & Coca spec. nov., C. gomeziana Dal Forno, Chaves & Lucking spec. nov., C. guajalitensis Lucking, Robayo & Dal Forno spec. nov., C. hafecesweorthensis Moncada, Lucking & R. Pelaez spec. nov., C. haledana Dal Forno, Chaves & Lucking spec. nov., C. hawksworthiana Dal Forno, P. Nelson & Lucking spec. nov., C. hochesuordensis Lucking, E. Morales & Dal Forno spec. nov., C. hymenocarpa Lucking, Chaves & Lawrey spec. nov., C. imi Lucking, Chaves & Lawrey spec. nov., C. itabaiana Dal Forno, Aptroot & M. Caceres spec. nov., C. leslactuca Lucking, Moncada & R. Pelaez spec. nov., C. maxima Wilk, Dal Forno & Lucking spec. nov., C. minutula Lucking, Moncada & Yanez-Ayabaca spec. nov., C. palaeotropica Weerakoon, Aptroot & Lucking spec. nov., C. palustris Dal Forno, Chaves & Lucking spec. nov., C. parabovei Dal Forno, Kukwa & Lucking spec. nov., C. paraciferrii Lucking, Moncada & J.E. Hern. spec. nov., C. paraminor Dal Forno, Chaves & Lucking spec. nov., C. pastorum Moncada, Patino & Lucking spec. nov., C. pichinchensis Paredes, Jonitz & Dal Forno spec. nov., C. pikynasa J.-M. Torres, Moncada & Lucking spec. nov., C. pseudobovei Wilk, Dal Forno & Lucking spec. nov., C. pseudocorani Lucking, E. Morales & Dal Forno spec. nov., C. putumayensis L.J. Arias, Moncada & Lucking spec. nov., C. quillacinga Moncada, F. Ortega & Lucking spec. nov., C. rothesiorum Moncada, Madrinan & Lucking spec. nov., C. rubrosanguinea Nugra, Moncada & Lucking spec. nov., C. santacruzensis Dal Forno, Bungartz & Yanez-Ayabaca, spec. nov., C. schizophylloides Moncada, C. Rodriguez & Lucking spec. nov., C. smaragdina Lucking, Rivas Plata & Chaves spec. nov., C. soredavidia Dal Forno, Marcelli & Lucking spec. nov., C. subdavicrinita Moncada, J. Molina & Lucking spec. nov., C. suturifera Nugra, Besal & Lucking spec. nov., C. terrestris Dal Forno, Chaves & Lucking spec. nov., C. terricoleslia Wilk, Dal Forno & Lucking spec. nov., C. udebeceana Moncada, R. Pelaez & Lucking spec. nov., C. urceolata Moncada, Coca & Lucking spec. nov., C. verjonensis Lucking, Moncada & Dal Forno spec. nov., C. viliewoa Lucking, Chaves & Soto-Medina spec. nov., and C. yukiboa Mercado-Diaz, Moncada & Lucking spec. nov. Furthermore, the taxonomic status of the recently described or recognized species C. arachnoidea, C. aspera, C. ciferrii, and C. reticulifera, is revised.

Microfungi on Tamarix

Abstract: Tamarix species are small trees that grow in various natural habitats and have a wide geographic distribution. Microfungal species previously found on Tamarix and recently collected in Italy and Russia were identified based on morphological characters and analyses of gene sequence data. The sexual morph of the coelomycetous genus Homortomyces was collected for the first time and is described and illustrated. A new family, Homortomycetaceae (Dothideomycetes, families incertae sedis) is introduced to accommodate Homortomyces. Two new genera Neomicrosphaeropsis (Didymellaceae) and Tamaricicola (Pleosporaceae) are introduced in this paper. Phoma tamaricicola was recollected and is placed in Neomicrosphaeropsis based on morphology and molecular data. Ten new species, Cytospora italica, C. unilocularis, Diaporthe ravennica, Eutypella tamaricis, Neomicrosphaeropsis italica, N. novorossica, N. rossica, Keissleriella tamaricicola, Paracamarosporium tamaricis and Tamaricicola muriformis are introduced, while Alternaria tenuissima, Dothiorella sarmentorum, Neofusicoccum luteum, Paraepicoccum amazonense, Pleospora herbarum and Pseudocamarosporium propinquum are reported for the first time on Tamarix spp. with descriptions and illustrations. Multi-gene analyses show that Paraepicoccum amazonense should be placed in Pleosporineae, Pleosporales, where it is closely related to Camarosporium sensu stricto. Several herbarium specimens were studied to illustrate other fungal species recorded on Tamarix species. A comprehensive account of microfungi on Tamarix is provided, which includes a list with data from the literature, as well as those identified in the present study. The taxonomic placement of most taxa discussed in this study is based on a modern taxonomic framework based on analysis of multi-gene sequence data.

Phylogeny, taxonomy and diversification events in the Caliciaceae

Abstract: Although the high degree of non-monophyly and parallel evolution has long been acknowledged within the mazaediate Caliciaceae (Lecanoromycetes, Ascomycota), a natural re-classification of the group has not yet been accomplished. Here we constructed a multigene phylogeny of the Caliciaceae-Physciaceae clade in order to resolve the detailed relationships within the group, to propose a revised classification, and to perform a dating study. The few characters present in the available fossil and the complex character evolution of the group affects the interpretation of morphological traits and thus influences the assignment of the fossil to specific nodes in the phylogeny, when divergence time analyses are carried out. Alternative fossil assignments resulted in very different time estimates and the comparison with the analysis based on a secondary calibration demonstrates that the most likely placement of the fossil is close to a terminal node rather than a basal placement in the Calicium clade. Our dating analysis show two successive events giving rise to main clades of mazaediate taxa within the Caliciaceae, in the Upper-Lower Cretaceous boundary and in the Paleocene. As a result of this study, Cyphelium is synonymized with Calicium, Acolium is resurrected, and the new genera Allocalicium and Pseudothelomma are described. Twelve new combinations are proposed: Acolium karelicum, Acolium marcianum, Allocalicium adaequatum, Calicium carolinianum, Calicium lecideinum, Calicium lucidum, Calicium notarisii, Calicium pinicola, Calicium trachyliodes, Pseudothelomma occidentale, Pseudothelomma ocellatum and Thelomma brunneum. A key for the mazaedium-producing Caliciaceae is included.

Evidence for the polyphyly of Encoelia and Encoelioideae with reconsideration of respective families in Leotiomycetes

Abstract: This study focuses on the genus Encoelia and the subfamily Encoelioideae in the morphologically and ecologically diverse Helotiales. The 28S and 18S rDNA as well as tef1, rpb1 and rpb2 were sequenced for 70 species. Phylogenetic analyses revealed Encoelia and Encoelioideae to be highly polyphyletic, with species distributed among eight major lineages. Encoelia fascicularis and E. pruinosa belonged to Sclerotiniaceae and were combined in a new genus, Sclerencoelia. Rutstroemiaceae comprised E. tiliacea and Dencoeliopsis johnstonii, both accepted in Rutstroemia. The type of Encoelia, E. furfuracea, was closely related to species of Velutarina, Cenangiopsis and Crumenulopsis. These species together with members of Hemiphacidiaceae formed a clade conforming to the emended concept of Cenangiaceae, introduced here. Another resurrected family, Cordieritidaceae, comprised E. fimbriata, E. heteromera and species of Ameghiniella, Cordierites, Diplocarpa and Ionomidotis, characterised by inamyloid asci and a positive ionomidotic reaction. Encoelia glauca showed closest affinities with Chlorociboria species in Chlorociboriaceae. A new genus, Xeropilidium, with sporodochial and pycnidial synanamorphs, was described for the distinct encoelioid member of the Chaetomellaceae, previously known as E. fuckelii. Morphological and ecological synapomorphies were distinguished from convergent characters to delimit monophyletic taxa including encoelioid fungi. Incorporation of public sequences from various biological samples in ITS rDNA analyses allowed identification of sequenced organisms at species, genus, or family level and added information on the ecology of seversal taxa. Members of Cenangiaceae appeared to be widespread as endophytes. Inclusion of encoelioid genera in Chaetomellaceae and Sclerotiniaceae added xylicolous saprotrophs to these families.

DISCOMYCETES: the apothecial representatives of the phylum Ascomycota

Abstract: Discomycetes are an artificial grouping of apothecia-producing fungi in the phylum Ascomycota. Molecular-based studies have revealed that the discomycetes can be found among ten classes of Ascomycota. The classification of discomycetes has been a major challenge due to the lack of a clear understanding of the important morphological characters, as well as a lack of reference strains. In this review, we provide a historical perspective of discomycetes, notes on their morphology (including both asexual and sexual morphs), ecology and importance, an outline of discomycete families and a synoptical cladogram of currently accepted families in Ascomycota showing their systematic position. We also calculated evolutionary divergence times for major discomycetous taxa based on phylogenetic relationships using a combined LSU, SSU and RPB2 data set from 175 strains and fossil data. Our results confirm that discomycetes are found in two major subphyla of the Ascomycota: Taphrinomycotina and Pezizomycotina. The taxonomic placement of major discomycete taxa is briefly discussed. The most basal group of discomycetes is the class Neolectomycetes, which diverged from other Taphrinomycotina around 417 MYA (216–572), and the most derived group of discomycetes, the class Lecanoromycetes, diverged from Eurotiomycetes around 340 MYA (282–414). Further clarifications based on type specimens, designation of epitypes or reference specimens from fresh collections, and multi-gene analyses are needed to determine the taxonomic arrangement of many discomycetes.

Towards a natural classification of Annulatascaceae -like taxa: introducing Atractosporales ord. nov. and six new families

Abstract: Species with relatively small, membraneous, black ascomata, with or without long necks, unitunicate, cylindrical asci with apical rings and fusiform, hyaline ascospores with or without mucilaginous sheaths are common in freshwater habitats in tropical and temperate regions. Many of these taxa have originally been recorded as Annulatascaceae-like taxa. Twenty genera have been included in the family Annulatascaceae, mostly based on morphological characters, while molecular work and phylogenetic analyses are lacking for many genera. In this study, nine new Annulatascaceae-like taxa collected from Thailand were morphologically examined. Pure cultures obtained from single ascospores were used in molecular studies. The nine new strains and several other strains of Annulatascaceae-like Sordariomycetes species were used to establish phylogenetic and evolution relationships among the taxa, based on combined LSU, SSU, ITS and RPB2 sequence data. Phylogenetic analyses provide evidence to introduce one new order and six new families, to accommodate taxa excluded from Annulatascaceae sensu stricto. A new order Atractosporales is established based on the molecular study, including three new introduced families Conlariaceae, Pseudoproboscisporaceae and Atractosporaceae. Conlariaceae is introduced for the genus Conlarium which comprises two species, Conlarium duplumascosporun and a new Hyphomycetous asexual morph taxon Conlarium aquaticum which has subglobose or irregular, brown, clathrate, muriform conidia. Pseudoproboscisporaceae includes Pseudoproboscispora and Diluviicola, while Atractosporaceae includes the genera Rubellisphaeria and Atractospora. Barbatosphaeria, Xylomelasma and Ceratostomella form a distinct stable lineage which is introduced as a new family Barbatosphaeriaceae in Diaporthomycetidae families incertae sedis. A new family Lentomitellaceae is introduced in Diaporthomycetidae families incertae sedis, to accommodate the genus Lentomitella. Woswasiaceae is introduced to accommodate Woswasia, Xylochrysis and Cyanoannulus in Diaporthomycetidae families incertae sedis. Three new species of Fluminicola viz. F. saprophytica, F. thailandensis and F. aquatica are introduced. A new sexual morph, Dictyosporella thailandensis, is reported and Dictyosporella is excluded from Annulatascaceae and placed in Diaporthomycetidae genera incertae sedis. The first sexual morph of Sporidesmium, S. thailandense is also described. The new species Atractospora thailandensis, Diluviicola aquatica and Pseudoproboscispora thailandensis are also introduced. Platytrachelon is added to Papulosaceae based on phylogenetic analysis and morphological characters. Aquaticola, Fusoidispora and Pseudoannulatascus are excluded from Annulatascaceae and placed in Diaporthomycetidae genera incertae sedis. Mirannulata is accommodated in Sordariomycetes, genera incertae sedis.

Cantharellus (Cantharellales, Basidiomycota) revisited in Europe through a multigene phylogeny

Abstract: Resolving species delimitation issues of European Cantharellus is crucial to correctly name chanterelles around the globe. Thirty names referring to Cantharellus s. str. have been described in Europe, some of which are used in other continents. Based on combined analyses of ITS2, LSU, RPB2 and TEF-1, merely eight species are here recognized in Europe applying the genealogical concordance phylogenetic species recognition criteria, one of which, C. roseofagetorum, is described as new. Morphological characters used in species delimitation are mapped and their variability evaluated. The colour of the hymenophore in young specimens is found to be a rather constant morphological character of taxonomic use. European species of Cantharellus are morphologically distinguished by unique combinations of characters, such as the presence of a pink pileal coating, pileus and hymenophore colour when young, and in some cases, the mean spore length and ecology. Eighteen type specimens from Europe are sequenced. Based on revised species concepts sixteen novel taxonomic synonyms are here proposed for European chanterelles: C. alborufescens (= C. henrici, C. ilicis, C. lilacinopruinatus), C. amethysteus (= C. cibarius subsp. squamulosus, C. cibarius var. umbrinus, C. rufipes), C. cibarius (= C. cibarius var. atlanticus, C. parviluteus), C. ferruginascens (= C. cibarius var. flavipes), C. friesii (= C. ignescens), C. pallens (= C. cibarius var. albidus, C. cibarius var. bicolor, C. subpruinosus), and C. romagnesianus (= C. pseudominimus, C. lourizanianus, C. romagnesianus var. parvisporus). The type of Cantharellus, C. cibarius, is epitypified. Descriptions, colour illustrations and a key to all European species are provided.

Towards a natural classification of Ophiobolus and ophiobolus-like taxa; introducing three novel genera Ophiobolopsis, Paraophiobolus and Pseudoophiobolus in Phaeosphaeriaceae (Pleosporales)

Abstract: Ophiobolus is a large genus of Phaeosphaeriaceae comprising more than 350 possible species, most of which are saprobes on herbaceous plants in Europe and North America. Ophiobolus species are polyphyletic and the type of Ophiobolus is not represented in GenBank. Therefore, an increased taxon sampling of ophiobolus-like taxa and epitypification of the type species, O. disseminans is reported. Multigene phylogenetic analyses of combined LSU, SSU, TEF1-α and ITS sequence data position O. disseminans in a sister clade with O. ponticus and several Entodesmium species in Phaeosphaeriaceae with high support. Therefore, Entodesmium is synonymized under Ophiobolus. Premilcurensis with it type species, P. senecionis also clusters within the Ophiobolus clade and is synonymized under Ophiobolus. Ophiobolus rossicus sp. nov. is introduced and a reference specimen is designated for O. ponticus. Other ophiobolus-like taxa (Ophiobolus sensu lato) can be distinguished as three main groups, which are introduced as new genera. Ophiobolopsis is introduced to accommodate the new species, Ophiobolopsis italica. The new genus Paraophiobolus is introduced to accommodate P. arundinis sp. nov. and P. plantaginis comb. nov. This genus is characterized by hyaline to pale yellowish ascospores, some green-yellowish at maturity, with a swollen cell, terminal appendages and ascospores not separating into part spores. Pseudoophiobolus gen. nov. is introduced to accommodate six new species and two new combinations, viz. Ps. achilleae, Ps. erythrosporus, Ps. galii, Ps. italicus, Ps. mathieui, Ps. rosae, Ps. subhyalinisporus and Ps. urticicola. Pseudoophiobolus is characterized by subhyaline to pale yellowish or yellowish ascospores, with a swollen cell, lack of terminal appendages and ascospores that do not separate into part spores and is related to Nodulosphaeria. An updated tree for Phaeosphaeriaceae based on multigene analysis is also provided.

High levels of endemism among Galapagos basidiolichens.

Abstract: This study is a re-assessment of basidiolichen diversity in the Galapagos Islands. We present a molecular phylogenetic analysis, based on 92 specimens from Galapagos, using two nuclear ribosomal DNA markers (ITS and nuLSU). We also re-examined the morphology and anatomy of all sequenced material. The molecular results confirm our previous assessment that all Galapagos basidiolichens belong to the Dictyonema clade, which in Galapagos is represented by four genera: Acantholichen, Cora, Cyphellostereum, and Dictyonema. Most species previously reported from Galapagos in these genera were at the time believed to represent widely distributed taxa. This conclusion, however, has changed with the inclusion of molecular data. Although almost the same number of species is distinguished, the phylogenetic data now suggest that all are restricted to the Galapagos Islands. Among them, six species are proposed here as new to science, namely Cora galapagoensis, Cyphellostereum unoquinoum, Dictyonema barbatum, D. darwinianum, D. ramificans, and D. subobscuratum; and four species have already been described previously, namely Acantholichen galapagoensis, Cora santacruzensis, Dictyonema pectinatum, and D. galapagoense, here recombined as Cyphellostereum galapagoense. Our analysis is set on a very broad phylogenetic framework, which includes a large number of specimens (N = 826) mainly from Central and South America, and therefore strongly suggests an unusually high level of endemism previously not recognized. This analysis also shows that the closest relatives of half of the basidiolichens now found in Galapagos are from mainland Ecuador, implying that they reached the islands through the shortest route, with all species arriving on the islands through independent colonization events.

Dismantling Marchandiomphalina into Agonimia (Verrucariaceae) and Lawreymyces gen. nov. (Corticiaceae): setting a precedent to the formal recognition of thousands of voucherless fungi based on type sequences

Abstract: Based on an unexpected result of obtaining molecular sequence data from tropical representatives of the genus Normandina, we revised the biological concept of the neotropical taxon Marchandiomphalina foliacea. The obtained data let us conclude that M. foliacea is not a basidiomycete, as originally proposed, but belongs in Verrucariaceae, in the genus Agonimia, including its perithecia which had been identified with the lichenicolous Norrlinia peltigericola. The ITS (and nuLSU) sequences previously obtained from M. foliacea, seemingly confirming its status as a basidiomycete, are from an unmanifested lichenicolous fungus, present also in numerous specimens of Normandina. ITS data suggest the presence of seven lineages that can be recognized at the species level, forming two clusters: one cluster of three lineages found in thalli of M. foliacea, and a second cluster of four lineages found in thalli of Normandina. This pattern is similar to what has recently been found in the basidiomycete genus Cyphobasidium occurring predominantly in Parmeliaceae lichens. We propose the combination of Omphalina foliacea into the genus Agonimia, as Agonimia foliacea (P.M. Jorg.) Lucking & Moncada, comb. nov., and place Marchandiomphalina in synonymy with Agonimia. To formally recognize the unnamed lichenicolous basidiomycete present in Agonimia and Normandina thalli, we take advantage of provision ICN Art. 40.5 in the Code and describe the unmanifested fungus as a new genus, with seven new species, even if no physical type specimens can be preserved (except for the corresponding host lichens which, however, do not show the features of the fungus): Lawreymyces Lucking & Moncada, gen. nov. (Type: L. palicei), with L. bogotensis Lucking & Moncada, sp. nov., L. columbiensis Lucking & Moncada, sp. nov., L. confusus Lucking & Moncada, sp. nov., L, foliaceae Lucking & Moncada, sp. nov., L. palicei Lucking & Moncada, sp. nov., L. pulchellae Lucking & Moncada, sp. nov., and L. spribillei Lucking & Moncada, sp. nov. This opens the door to the formal recognition of thousands of species of voucherless fungi detected through environmental sequencing techniques under the current Code.