Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions. A large number of such taxa are among the most notorious plant and animal pathogens. In addition, they have a key role in food production, biotechnology and medicine. Taxa without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based taxonomy. The number, variation and diversity of asexually reproducing taxa are insufficiently known, even though fungi capable of asexual reproduction may provide an untapped, rich biological resource for future exploitation. Currently, ca. 30,000 asexual species belonging to ca. 3800 genera have been reported (including 1388 coelomycetous and 2265 hyphomycetous genera). Recent reports (2017–2020) reiterate that the number of asexually producing fungi is higher than the number of frequently sexually-reproducing fungi. With the advent of molecular tools and the abandonment of the dual nomenclature system for pleomorphic fungi, priority criteria were established and revisited in the latest outline of fungi and fungus-like taxa. However, species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be addressed. The number of species of speciose genera (e.g. Alternaria, Aspergillus, Cercospora, Fusarium, Phoma and Pseudocercospora), cryptic species, species of pleomorphic genera, less studied life modes (such as lichenicolous taxa, taxa from extreme environments) and species from biodiversity-rich areas still need evaluation to achieve more reliable estimates of their diversity. This paper discusses the current knowledge on the matter, with diversity estimates, and potential obstacles in several chapters on (1) speciose genera; (2) pleomorphic genera; (3) cryptic species; (4) well-studied but insufficiently resolved taxa, e.g. leaf inhabiting species, marine fungi, (5) less studied life modes, e.g. lichenicolous, rock-inhabiting fungi, insect-associated and yeast-forming taxa and (6) species from biodiversity-rich areas.

Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes’ (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.

Over the past three decades, a wealth of studies has shown that palm trees (Arecaceae) are a diverse habitat with intense fungal colonisation, making them an important substratum to explore fungal diversity. Palm trees are perennial, monocotyledonous plants mainly restricted to the tropics that include economically important crops and highly valued ornamental plants worldwide. The extensive research conducted in Southeast Asia and Australasia indicates that palm fungi are undoubtedly a taxonomically diverse assemblage from which a remarkable number of new species is continuously being reported. Despite this wealth of data, no recent comprehensive review on palm fungi exists to date. In this regard, we present here a historical account and discussion of the research on the palm fungi to reflect on their importance as a diverse and understudied assemblage. The taxonomic structure of palm fungi is also outlined, along with comments on the need for further studies to place them within modern DNA sequence-based classifications. Palm trees can be considered model plants for studying fungal biodiversity and, therefore, the key role of palm fungi in biodiversity surveys is discussed. The close association and intrinsic relationship between palm hosts and palm fungi, coupled with a high fungal diversity, suggest that the diversity of palm fungi is still far from being fully understood. The figures suggested in the literature for the diversity of palm fungi have been revisited and updated here. As a result, it is estimated that there are about 76,000 species of palm fungi worldwide, of which more than 2500 are currently known. This review emphasises that research on palm fungi may provide answers to a number of current fungal biodiversity challenges.

The application of traditional morphological and ecological species concepts to closely related, asexual fungal taxa is challenging due to the lack of distinctive morphological characters and frequent cosmopolitan and plurivorous behaviour. As a result, multilocus sequence analysis (MLSA) has become a powerful and widely used tool to recognise and delimit independent evolutionary lineages (IEL) in fungi. However, MLSA can mask discordances in individual gene trees and lead to misinterpretation of speciation events. This phenomenon has been extensively documented in Diaporthe , and species identifications in this genus remains an ongoing challenge. However, the accurate delimitation of Diaporthe species is critical as the genus encompasses several cosmopolitan pathogens that cause serious diseases on many economically important plant hosts. In this regard, following a survey of palm leaf spotting fungi in Lisbon, Portugal, Diaporthe species occurring on Arecaceae hosts were used as a case study to implement an integrative taxonomic approach for a reliable species identification in the genus. Molecular analyses based on the genealogical concordance phylogenetic species recognition (GCPSR) and DNA-based species delimitation methods revealed that speciation events in the genus have been highly overestimated. Most IEL identified by the GCPSR were also recognised by Poisson tree processes (PTP) coalescent-based methods, which indicated that phylogenetic lineages in Diaporthe are likely influenced by incomplete lineage sorting (ILS) and reticulation events. Furthermore, the recognition of genetic recombination signals and the evaluation of genetic variability based on sequence polymorphisms reinforced these hypotheses. New clues towards the intraspecific variation in the common loci used for phylogenetic inference of Diaporthe species are discussed. These results demonstrate that intraspecific variability has often been used as an indicator to introduce new species in Diaporthe , which has led to a proliferation of species names in the genus. Based on these data, 53 species are reduced to synonymy with 18 existing Diaporthe species, and a new species, D. pygmaeae , is introduced. Thirteen new plant host-fungus associations are reported, all of which represent new host family records for Arecaceae . This study has recognised and resolved a total of 14 valid Diaporthe species associated with Arecaceae hosts worldwide, some of which are associated with disease symptoms. This illustrates the need for more systematic research to examine the complex of Diaporthe taxa associated with palms and determine their potential pathogenicity. By implementing a more rational framework for future studies on species delimitation in Diaporthe , this study provides a solid foundation to stabilise the taxonomy of species in the genus. Guidelines for species recognition, definition and identification in Diaporthe are included.

Palm fungi are a diverse and unique group mostly found on Arecaceae hosts. They have been studied for approximately 200 years resulting in a large number of known fungal species representing over 700 genera. The timeline of palm fungal studies could be roughly divided into three phases, based on the methods and frequency of reports. They are the “Historical palm fungi era”, “Classical palm fungi era” and “Molecular palm fungi era”. In the first two periods, the identification of palm fungi was based on morphology, which resulted in a considerable number of morphological species scattered across the data in books, monographs and papers. With the advancement of molecular techniques, studies on palm fungi accelerated. A large number of new species were introduced in the molecular era, especially from Asia, including China and Thailand. However, there is a necessity to link these three generations of studies into a single platform combining data related to host factors, geography and utilisation. Herein, we introduce the palm fungi website: https://palmfungi.org, an integrated data platform for interactive retrieval, based on palm and fungal species. This website is not only a portal for the latest, comprehensive species information on palm fungi, but also provides a new platform for fungal researchers to explore the host-specificity of palm fungi. Additionally, this study uses palmfungi.org and related data to briefly discuss the current status of research on the distribution of palm fungi populations, showing how palmfungi.org links fungi with their palm hosts. Furthermore, the website will act as a platform for collaboration amongst taxonomists, plant pathologists, botanists, ecologists and those who are interested in palms and their relationship with ecological sustainability.

The Botryosphaeriaceae is the largest family in Botryosphaeriales and currently comprises 22 genera of important endophytes, saprobes and plant pathogens. Most botryosphaeriaceous species have a cosmopolitan distribution, occurring on a wide range of woody hosts. Nonetheless, in many hosts, including palms (Arecaceae), the complex of associated Botryosphaeriaceae taxa is as yet unknown. The present study aimed to identify the botryosphaeriaceous species associated with foliar lesions of ornamental palms in Lisbon, Portugal. Twenty-nine Botryosphaeriaceae taxa were isolated from seven different palm species and identified based on both morphological and phylogenetic analyses. Six genera were detected: Botryosphaeria, Diplodia, Dothiorella, Neodeightonia, Neofusicoccum and Sardiniella. A new species of Neodeightonia, N. chamaeropicola, is introduced. Three botryosphaeriaceous species are reduced to synonymy. Thirteen new plant host-fungus associations are reported, while four new geographical records are noted for Portugal. A synopsis of accepted and phylogenetically validated Botryosphaeriaceae taxa reported from palms worldwide is presented. A total of 31 botryosphaeriaceous species have been currently reported from Arecaceae hosts, and many of them are associated with disease symptoms. This illustrates that more systematic studies are needed to examine the complex of Botryosphaeriaceae taxa associated with palms and determine their potential pathogenicity.