We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Aflatoxins and ochratoxins are among the most important mycotoxins of all and producers of both types of mycotoxins are present inAspergillussectionFlavi, albeit never in the same species. Some of the most efficient producers of aflatoxins and ochratoxins have not been described yet. Using a polyphasic approach combining phenotype, physiology, sequence and extrolite data, we describe here eight new species in sectionFlavi. Phylogenetically, sectionFlaviis split in eight clades and the section currently contains 33 species. Two species only produce aflatoxin B1 and B2 (A. pseudotamariiandA. togoensis), and 14 species are able to produce aflatoxin B1, B2, G1 and G2: three newly described speciesA. aflatoxiformans, A. austwickiiandA. cerealisin addition toA. arachidicola,A. minisclerotigenes,A. mottae, A. luteovirescens(formerlyA. bombycis), A. nomius, A. novoparasiticus, A. parasiticus, A. pseudocaelatus, A. pseudonomius, A. sergiiandA. transmontanensis. It is generally accepted thatA. flavusis unable to produce type G aflatoxins, but here we report on Korean strains that also produce aflatoxin G1 and G2. One strain ofA. bertholletiuscan produce the immediate aflatoxin precursor 3-O-methylsterigmatocystin, and one strain ofAspergillus sojaeand two strains ofAspergillus alliaceusproduced versicolorins. Strains of the domesticated forms ofA. flavusandA. parasiticus,A. oryzaeandA. sojae, respectively, lost their ability to produce aflatoxins, and from the remaining phylogenetically closely related species (belonging to theA. flavus-,A. tamarii-,A. bertholletius- andA. nomius-clades), onlyA. caelatus,A. subflavusandA. tamariiare unable to produce aflatoxins. With exception ofA. togoensisin theA. coremiiformis-clade, all species in the phylogenetically more distant clades (A. alliaceus-,A. coremiiformis-,A. leporis- andA. avenaceus-clade) are unable to produce aflatoxins. Three out of the four species in theA. alliaceus-clade can produce the mycotoxin ochratoxin A:A. alliaceus s.str. and two new species described here asA. neoalliaceusandA. vandermerwei. Eight species produced the mycotoxin tenuazonic acid:A. bertholletius,A. caelatus, A. luteovirescens,A. nomius, A. pseudocaelatus,A. pseudonomius, A. pseudotamariiandA. tamariiwhile the related mycotoxin cyclopiazonic acid was produced by 13 species:A. aflatoxiformans, A. austwickii, A. bertholletius, A. cerealis, A. flavus, A. minisclerotigenes, A. mottae, A. oryzae, A. pipericola, A. pseudocaelatus,A. pseudotamarii, A. sergiiandA. tamarii. Furthermore,A. hancockiiproduced speradine A, a compound related to cyclopiazonic acid. SelectedA. aflatoxiformans, A. austwickii, A. cerealis, A. flavus, A. minisclerotigenes, A. pipericolaandA. sergiistrains produced small sclerotia containing the mycotoxin aflatrem. Kojic acid has been found in all species in sectionFlavi, exceptA. avenaceusandA. coremiiformis. Only six species in the section did not produce any known mycotoxins:A. aspearensis,A. coremiiformis, A. lanosus, A. leporis, A. sojaeandA. subflavus. An overview of other small molecule extrolites produced inAspergillussectionFlaviis given.

Novel species of fungi described in this study include those from various countries as follows: Australia: Apiognomonia lasiopetali on Lasiopetalum sp., Blastacervulus eucalyptorum on Eucalyptus adesmophloia, Bullanockia australis (incl. Bullanockia gen. nov.) on Kingia australis, Caliciopsis eucalypti on Eucalyptus marginata, Celerioriella petrophiles on Petrophile teretifolia, Coleophoma xanthosiae on Xanthosia rotundifolia, Coniothyrium hakeae on Hakea sp., Diatrypella banksiae on Banksia formosa, Disculoides corymbiae on Corymbia calophylla, Elsinoë eelemani on Melaleuca alternifolia, Elsinoë eucalyptigena on Eucalyptus kingsmillii, Elsinoë preissianae on Eucalyptus preissiana, Eucasphaeria rustici on Eucalyptus creta, Hyweljonesia queenslandica (incl. Hyweljonesia gen. nov.) on the cocoon of an unidentified microlepidoptera, Mycodiella eucalypti (incl. Mycodiella gen. nov.) on Eucalyptus diversicolor, Myrtapenidiella sporadicae on Eucalyptus sporadica, Neocrinula xanthorrhoeae (incl. Neocrinula gen. nov.) on Xanthorrhoea sp., Ophiocordyceps nooreniae on dead ant, Phaeosphaeriopsis agavacearum on Agave sp., Phlogicylindrium mokarei on Eucalyptus sp., Phyllosticta acaciigena on Acacia suaveolens, Pleurophoma acaciae on Acacia glaucoptera, Pyrenochaeta hakeae on Hakea sp., Readeriella lehmannii on Eucalyptus lehmannii, Saccharata banksiae on Banksia grandis, Saccharata daviesiae on Daviesia pachyphylla, Saccharata eucalyptorum on Eucalyptus bigalerita, Saccharata hakeae on Hakea baxteri, Saccharata hakeicola on Hakea victoria, Saccharata lambertiae on Lambertia ericifolia, Saccharata petrophiles on Petrophile sp., Saccharata petrophilicola on Petrophile fastigiata, Sphaerellopsis hakeae on Hakea sp., and Teichospora kingiae on Kingia australis. Brazil: Adautomilanezia caesalpiniae (incl. Adautomilanezia gen. nov.) on Caesalpina echinata, Arthrophiala arthrospora (incl. Arthrophiala gen. nov.) on Sagittaria montevidensis, Diaporthe caatingaensis (endophyte from Tacinga inamoena), Geastrum ishikawae on sandy soil, Geastrum pusillipilosum on soil, Gymnopus pygmaeus on dead leaves and sticks, Inonotus hymenonitens on decayed angiosperm trunk, Pyricularia urashimae on Urochloa brizantha, and Synnemellisia aurantia on Passiflora edulis. Chile: Tubulicrinis australis on Lophosoria quadripinnata. France: Cercophora squamulosa from submerged wood, and Scedosporium cereisporum from fluids of a wastewater treatment plant. Hawaii: Beltraniella acaciae, Dactylaria acaciae, Rhexodenticula acaciae, Rubikia evansii and Torula acaciae (all on Acacia koa). India: Lepidoderma echinosporum on dead semi-woody stems, and Rhodocybe rubrobrunnea from soil. Iran: Talaromyces kabodanensis from hypersaline soil. La Réunion: Neocordana musarum from leaves of Musa sp. Malaysia: Anungitea eucalyptigena on Eucalyptus grandis × pellita, Camptomeriphila leucaenae (incl. Camptomeriphila gen. nov.) on Leucaena leucocephala, Castanediella communis on Eucalyptus pellita, Eucalyptostroma eucalypti (incl. Eucalyptostroma gen. nov.) on Eucalyptus pellita, Melanconiella syzygii on Syzygium sp., Mycophilomyces periconiae (incl. Mycophilomyces gen. nov.) as hyperparasite on Periconia on leaves of Albizia falcataria, Synnemadiella eucalypti (incl. Synnemadiella gen. nov.) on Eucalyptus pellita, and Teichospora nephelii on Nephelium lappaceum. Mexico: Aspergillus bicephalus from soil. New Zealand: Aplosporella sophorae on Sophora microphylla, Libertasomyces platani on Platanus sp., Neothyronectria sophorae (incl. Neothyronectria gen. nov.) on Sophora microphylla, Parastagonospora phoenicicola on Phoenix canariensis, Phaeoacremonium pseudopanacis on Pseudopanax crassifolius, Phlyctema phoenicis on Phoenix canariensis, and Pseudoascochyta novae-zelandiae on Cordyline australis. Panama: Chalara panamensis from needle litter of Pinus cf. caribaea. South Africa: Exophiala eucalypti on leaves of Eucalyptus sp., Fantasmomyces hyalinus (incl. Fantasmomyces gen. nov.) on Acacia exuvialis, Paracladophialophora carceris (incl. Paracladophialophora gen. nov.) on Aloe sp., and Umthunziomyces hagahagensis (incl. Umthunziomyces gen. nov.) on Mimusops caffra. Spain: Clavaria griseobrunnea on bare ground in Pteridium aquilinum field, Cyathus ibericus on small fallen branches of Pinus halepensis, Gyroporus pseudolacteus in humus of Pinus pinaster, and Pseudoascochyta pratensis (incl. Pseudoascochytagen. nov.) fromsoil. Thailand: Neoascochyta adenii on Adenium obesum, and Ochroconis capsici on Capsicum annuum. UK: Fusicolla melogrammae from dead stromata of Melogramma campylosporum on bark of Carpinus betulus. Uruguay: Myrmecridium pulvericola from house dust. USA: Neoscolecobasidium agapanthi (incl. Neoscolecobasidium gen. nov.) on Agapanthus sp., Polyscytalum purgamentum on leaf litter, Pseudopithomyces diversisporus from human toenail, Saksenaea trapezispora from knee wound of a soldier, and Sirococcus quercus from Quercus sp. Morphological and culture characteristics along with DNA barcodes are provided.

The phylogeny of the genera Periconiella, Ramichloridium, Rhinocladiella and Veronaea was explored by means of partial sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and ITS2). Based on the LSU sequence data, ramichloridium-like species segregate into eight distinct clusters. These include the Capnodiales (Mycosphaerellaceae and Teratosphaeriaceae), the Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and five ascomycete clades with uncertain affinities. The type species of Ramichloridium, R. apiculatum, together with R. musae, R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new species isolated from Strelitzia, Musa and forest soil, respectively, reside in the Capnodiales clade. The human-pathogenic species R. mackenziei and R. basitonum, together with R. fasciculatum and R. anceps, cluster with Rhinocladiella (type species: Rh. atrovirens, Herpotrichiellaceae, Chaetothyriales), and are allocated to this genus. Veronaea botryosa, the type species of the genus Veronaea, also resides in the Chaetothyriales clade, whereas Veronaea simplex clusters as a sister taxon to the Venturiaceae (Pleosporales), and is placed in a new genus, Veronaeopsis. Ramichloridium obovoideum clusters with Carpoligna pleurothecii (anamorph: Pleurothecium sp., Chaetosphaeriales), and a new combination is proposed in Pleurothecium. Other ramichloridium-like clades include R. subulatum and R. epichloës (incertae sedis, Sordariomycetes), for which a new genus, Radulidium is erected. Ramichloridium schulzeri and its varieties are placed in a new genus, Myrmecridium (incertae sedis, Sordariomycetes). The genus Pseudovirgaria (incertae sedis) is introduced to accommodate ramichloridium-like isolates occurring on various species of rust fungi. A veronaea-like isolate from Bertia moriformis with phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is placed in a new genus, Rhodoveronaea. Besides Ramichloridium, Periconiella is also polyphyletic. Thysanorea is introduced to accommodate Periconiella papuana (Herpotrichiellaceae), which is unrelated to the type species, P. velutina (Mycosphaerellaceae).

Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.