This is the opening paper in the special issue of Fungal Diversity, which collates the data on defining species. Defining and recognizing species has long been a controversial issue. Since Darwin's proposed origin of species, over 30 species criteria have been brought forth and used to define species boundaries. In recent times, phylogenetic analyses based on multiple loci have been extensively used as a method to define species boundaries. However, only a few mycologists are aware that phylogenetic species criteria can mask discordances among fungal groups, leading to inaccurately defined species boundaries. In the current review, we discuss species recognition criteria, how and where these criteria can be applied along with their limitations and derived alternatives. In order to delimit fungal species, authors need to take into account not only the phylogenetic and phenotypic coherence, but also the timing of events that lead to fungal speciation and subsequent diversifications. Variations in the rate of phenotypic diversifications and convergent fungal evolution make it difficult to establish a universal species recognition criterion. The best practice can only be defined in the context of each fungal group. In this review, we provide a set of guidelines, encouraging an integrative taxonomic approach for species delimitation that can be used to define fungal species boundaries in the future. The other papers in this special issue deal with fungal speciation in Ascomycota, Dothideomycetes, Basidiomycota, basal fungi, lichen-forming fungi, plant pathogenic fungi, and yeasts.

Fungi play vital roles in ecosystems as endophytes, pathogens and saprobes. The current estimate of fungal diversity is highly uncertain, ranging from 1.5 to 12 million, but only around 150,000 species have been named and classified to date. Since the introduction of DNA based methods for species identification, the number of newly described taxa has increased from approximately 1000 to around 2000 yearly. This demonstrates the importance of DNA based methods to identify and distinguish species, especially cryptic species. Many novel species from recent studies have been found in historically understudied regions and habitats, but these still represent only a small percentage of the estimated species. In this paper, we examine 16 genera from the top 40 most speciose genera as listed in Species Fungorum as case studies to examine the diversity of taxa in each genus. The genera treated herein are Cercospora, Diaporthe, Meliola, Passalora, Phyllachora, Phyllosticta, Pseudocercospora, Ramularia (ascomycetes) and Cortinarius, Entoloma, Inocybe, Marasmius, Psathyrella, Puccinia, Russula, Uromyces (basidiomycetes). We critically evaluate the number of species in these genera and correlate these numbers with the number of entries in GenBank. We introduce 18 new species Apiospora multiloculata, Candolleomyces thailandensis, Cortinarius acutoproximus, Cortinarius melleoalbus, Cortinarius pacificus, Cortinarius parvoacetosus, Diaporthe guizhouensis, Entoloma pseudosubcorvinum, Inocybe meirensongia, Marasmius albulus, Marasmius obscuroaurantiacus, Meliola camporesii, Phyllachora siamensis, Phyllosticta doitungensis, Picipes yuxiensis, Pseudocercospora vignae, Puccinia maureanui and Russula inornata. We also introduce a new record of Candolleomyces cladii-marisci and Inocybe iringolkavensis. We discuss the genera Colletotrichum and Pleurotus that are speciose, but do not occur in the top 40. We hypothesize whether there might be more species in these genera and discuss why these genera have some of the largest number of species.

The recent realistic estimate of fungal numbers which used various algorithms was between 2.2 and 3.8 million. There are nearly 100,000 accepted species of Fungi and fungus-like taxa, which is between 2.6 and 4.5% of the estimated species. Several forums such as Botanica Marina series, Fungal Diversity notes, Fungal Biodiversity Profiles, Fungal Systematics and Evolution—New and Interesting Fungi, Mycosphere notes and Fungal Planet have enhanced the introduction of new taxa and nearly 2000 species have been introduced in these publications in the last decade. The need to define a fungal species more accurately has been recognized, but there is much research needed before this can be better clarified. We address the evidence that is needed to estimate the numbers of fungi and address the various advances that have been made towards its understanding. Some genera are barely known, whereas some plant pathogens comprise numerous species complexes and numbers are steadily increasing. In this paper, we examine ten genera as case studies to establish trends in fungal description and introduce new species in each genus. The genera are the ascomycetes Colletotrichum and Pestalotiopsis (with many species or complexes), Atrocalyx, Dothiora, Lignosphaeria, Okeanomyces, Rhamphoriopsis, Thozetella, Thyrostroma (relatively poorly studied genera) and the basidiomycete genus Lepiota. We provide examples where knowledge is incomplete or lacking and suggest areas needing further research. These include (1) the need to establish what is a species, (2) the need to establish how host-specific fungi are, not in highly disturbed urban areas, but in pristine or relatively undisturbed forests, and (3) the need to establish if species in different continents, islands, countries or regions are different, or if the same fungi occur worldwide? Finally, we conclude whether we are anywhere near to flattening the curve in new species description.

The cosmopolitan plant genus Clematis contains many climbing species that can be found worldwide. The genus occurs in the wild and is grown commercially for horticulture. Microfungi on Clematis were collected from Belgium, China, Italy, Thailand and the UK. They are characterized by morphology and analyses of gene sequence data using an integrated species concept to validate identifications. The study revealed two new families, 12 new genera, 50 new species, 26 new host records with one dimorphic character report, and ten species are transferred to other genera. The new families revealed by multigene phylogeny are Longiostiolaceae and Pseudomassarinaceae in Pleosporales (Dothideomycetes). New genera are Anthodidymella (Didymellaceae), Anthosulcatispora and Parasulcatispora (Sulcatisporaceae), Fusiformispora (Amniculicolaceae), Longispora (Phaeosphaeriaceae), Neobyssosphaeria (Melanommataceae), Neoleptosporella ( Chaetosphaeriales , genera incertae sedis) , Neostictis (Stictidaceae), Pseudohelminthosporium (Neomassarinaceae), Pseudomassarina (Pseudomassarinaceae), Sclerenchymomyces (Leptosphaeriaceae) and Xenoplectosphaerella (Plectosphaerellaceae). The newly described species are Alloleptosphaeria clematidis , Anthodidymella ranunculacearum , Anthosulcatispora subglobosa , Aquadictyospora clematidis , Brunneofusispora clematidis , Chaetosphaeronema clematidicola , C. clematidis , Chromolaenicola clematidis , Diaporthe clematidina , Dictyocheirospora clematidis , Distoseptispora clematidis , Floricola clematidis , Fusiformispora clematidis , Hermatomyces clematidis , Leptospora clematidis , Longispora clematidis , Massariosphaeria clematidis , Melomastia clematidis , M. fulvicomae , Neobyssosphaeria clematidis , Neoleptosporella clematidis , Neoroussoella clematidis , N. fulvicomae , Neostictis nigricans, Neovaginatispora clematidis , Parasulcatispora clematidis , Parathyridaria clematidis, P. serratifoliae , P. virginianae , Periconia verrucose , Phomatospora uniseriata , Pleopunctum clematidis , Pseudocapulatispora clematidis , Pseudocoleophoma clematidis , Pseudohelminthosporium clematidis , Pseudolophiostoma chiangraiense , P. clematidis , Pseudomassarina clematidis , Ramusculicola clematidis , Sarocladium clematidis , Sclerenchymomyces clematidis , Sigarispora clematidicola , S. clematidis , S. montanae , Sordaria clematidis , Stemphylium clematidis , Wojnowiciella clematidis , Xenodidymella clematidis , Xenomassariosphaeria clematidis and Xenoplectosphaerella clematidis. The following fungi are recorded on Clematis species for the first time: Angustimassarina rosarum , Dendryphion europaeum , Dermatiopleospora mariae , Diaporthe ravennica , D. rudis , Dichotomopilus ramosissimum , Dictyocheirospora xishuangbannaensis , Didymosphaeria rubi - ulmifolii , Fitzroyomyces cyperacearum , Fusarium celtidicola , Leptospora thailandica , Memnoniella oblongispora , Neodidymelliopsis longicolla , Neoeutypella baoshanensis , Neoroussoella heveae , Nigrograna chromolaenae , N. obliqua , Pestalotiopsis verruculosa , Pseudoberkleasmium chiangmaiense , Pseudoophiobolus rosae , Pseudoroussoella chromolaenae , P. elaeicola , Ramusculicola thailandica , Stemphylium vesicarium and Torula chromolaenae . The new combinations are Anthodidymella clematidis (≡ Didymella clematidis ), A. vitalbina (≡ Didymella vitalbina ), Anthosulcatispora brunnea (≡ Neobambusicola brunnea ), Fuscohypha kunmingensis (≡ Plectosphaerella kunmingensis ), Magnibotryascoma rubriostiolata (≡ Teichospora rubriostiolata ), Pararoussoella mangrovei (≡ Roussoella mangrovei ), Pseudoneoconiothyrium euonymi (≡ Roussoella euonymi ), Sclerenchymomyces jonesii (≡ Neoleptosphaeria jonesii ), Stemphylium rosae (≡ Pleospora rosae) , and S. rosae - caninae (≡ Pleospora rosae - caninae ). The microfungi on Clematis is distributed in several classes of Ascomycota. The analyses are based on morphological examination of specimens, coupled with phylogenetic sequence data. To the best of our knowledge, the consolidated species concept approach is recommended in validating species.

The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora , Bambusicola , Beltrania , Capronia , Distoseptispora , Endocalyx , Neocatenulostroma , Neodeightonia , Paraconiothyrium , Peroneutypa , Phaeoacremonium and Vanakripa . We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.

Fungi are an essential component of any ecosystem, but they can also cause mild and severe plant diseases. Plant diseases are caused by a wide array of fungal groups that affect a diverse range of hosts with different tissue specificities. Fungi were previously named based only on morphology and, in many cases, host association, which has led to superfluous species names and synonyms. Morphology-based identification represents an important method for genus level identification and molecular data are important to accurately identify species. Accurate identification of fungal pathogens is vital as the scientific name links the knowledge concerning a species including the biology, host range, distribution, and potential risk of the pathogen, which are vital for effective control measures. Thus, in the modern era, a polyphasic approach is recommended when identifying fungal pathogens. It is also important to determine if the organism is capable of causing host damage, which usually relies on the application of Koch’s postulates for fungal plant pathogens. The importance and the challenges of applying Koch’s postulates are discussed. Bradford Hill criteria, which are generally used in establishing the cause of human disease, are briefly introduced. We provide guidelines for pathogenicity testing based on the implementation of modified Koch’s postulates incorporating biological gradient, consistency, and plausibility criteria from Bradford Hill. We provide a set of protocols for fungal pathogenicity testing along with a severity score guide, which takes into consideration the depth of lesions. The application of a standard protocol for fungal pathogenicity testing and disease assessment in plants will enable inter-studies comparison, thus improving accuracy. When introducing novel plant pathogenic fungal species without proving the taxon is the causal agent using Koch’s postulates, we advise the use of the term associated with the “disease symptoms” of “the host plant”. Where possible, details of disease symptoms should be clearly articulated.