Diaporthe species on palms

<b>Abstract: </b>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 <i>Diaporthe</i>, and species identifications in this genus remains an ongoing challenge. However, the accurate delimitation of <i>Diaporthe</i> 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, <i>Diaporthe</i> species occurring on <i>Arecaceae</i> 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 <i>Diaporthe </i>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 <i>Diaporthe</i> species are discussed. These results demonstrate that intraspecific variability has often been used as an indicator to introduce new species in <i>Diaporthe</i>, 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 <i>Diaporthe </i>species, and a new species, <i>D. pygmaeae</i>, is introduced. Thirteen new plant host-fungus associations are reported, all of which represent new host family records for <i>Arecaceae</i>. This study has recognised and resolved a total of 14 valid <i>Diaporthe</i> species associated with <i>Arecaceae</i> hosts worldwide, some of which are associated with disease symptoms. This illustrates the need for more systematic research to examine the complex of <i>Diaporthe</i> taxa associated with palms and determine their potential pathogenicity. By implementing a more rational framework for future studies on species delimitation in <i>Diaporthe</i>, this study provides a solid foundation to stabilise the taxonomy of species in the genus. Guidelines for species recognition, definition and identification in <i>Diaporthe</i> are included.